This is a blog detailing the creation/evolution/ID controversy and assorted palaeontological news. I will post news here with running commentary.
Tuesday, September 29, 2015
Debating Homo naledi on Premier Christian Radio
Sunday, October 23, 2011
Fuz Rana on Human Evolution
It is commonly reported that humans and chimps share 99 percent genetic similarity. For many people, this high degree of genetic similarity means humans must have evolved from an ape-like primate, sharing a common ancestor with chimpanzees. However, it should be noted that, when comparing the full genomes of humans and chimps, around one quarter of the two genomes don’t align and the similarity of those portions that do align is between 90 and 95 percent. (Go here and here for comparisons.)He argues that a key portion of evolutionary biology is violated because these genetic trees do not completely agree with each other and don't completely agree with the fossil record. In support of this idea, he cites three articles, the first of which is called “Incomplete Lineage Sorting Patterns among Human, Chimpanzee, and Orangutan Suggest Recent Orangutan Speciation and Widespread Selection.” (http://dx.doi.org/10.1101/gr.114751.110). Ironically, in a section of the article to which Rana does not refer, the authors of this paper write:According to the evolutionary model, humans and chimps share a common ancestor with gorillas. And humans, chimps, and gorillas share a common ancestor with orangutans. These presumed evolutionary relationships should be reflected in genetic comparisons between humans and the great apes, where scientists expect to find gorillas and orangutans displaying less similarity, respectively, to humans than to chimpanzees.
Yet, this is not always the case. Researchers have recently discovered that about one percent of the human genome displays a greater genetic similarity to orangutans than it does to chimpanzees. This result follows on the heels of an earlier study that found that 23 percent of random sequences sampled from the human genome point to a primate other than chimpanzees as our closest evolutionary relative.2 In other words, depending on the region of the genome that is selected, differing “evolutionary trees” result for humans and the great apes.
The exact amount of ILS [interlineage sorting] locally in the genome depends on the recombination rate and factors such as functional constraints (Figs. 4, 5). The observed ~1% of ILS is entirely consistent with the effective population size of 50,000 inferred for the human–chimpanzee ancestor and the speciation time difference of 8 Myr inferred between human–chimpanzee and human–chimpanzee–orangutan, assuming a generation time of 20 yr [emphasis mine].How does this not fit an evolutionary model? These authors of this paper certainly think it does, an expected one, at that. No evolutionary biologist has ever said that there has to be 100% agreement between all different kinds of trees. It has never occurred to them that this would ever be a problem. That is a straw man argument that Rana has put up. In response to the argument of discordant trees, Dennis Venema has posted a great article on this concept of incomplete lineage sorting. He writes:
The fact that gene phylogenies/trees and species phylogenies/trees don’t always match is not something that surprises scientists, since it is a well-known phenomenon and the mechanisms underlying it are understood: species arise from genetically diverse populations and that diversity does not always sort completely down to every descendant species.The second article that Rana cites is “Mapping Human Genetic Ancestry,” by Ebersberger et al. (http://dx.doi.org/10.1093/molbev/msm156). Once again, in a part of the article to which Rana does not refer, they write:
For about 23% of our genome, we share no immediate genetic ancestry with our closest living relative, the chimpanzee. This encompasses genes and exons to the same extent as intergenic regions. We conclude that about 1/3 of our genes started to evolve as human-specific lineages before the differentiation of human, chimps, and gorillas took place. This explains recurrent findings of very old human-specific morphological traits in the fossils record, which predate the recent emergence of the human species about 5-6 MYA. Furthermore, the sorting of such ancestral phenotypic polymorphisms in subsequent speciation events provides a parsimonious explanation why evolutionary derived characteristics are shared among species that are not each other's closest relatives [emphasis mine].Funny, it doesn't look like the authors are proposing a non-evolutionary relationship here. Once again, it fits perfectly with what we think is going on with the fossil record, which indicates a human-chimp separation time at around 6 million years ago. In fact, this kind of scenario fits perfectly with the recent finding about the frame-shift mutation of the sugar molecule Neu5Gc, suggesting that sympatric speciation may have happened in the human fossil line (the G.G. Simpson in me just shuddered). It is, consequently, difficult to see how this article supports Rana’s conclusion.
The third article that Rana has marshaled to his argument is by Morris Goodman, one of the dons of genetic analysis. The Goodman article appears in The Cambridge Encyclopedia of Human Evolution1. He quotes Goodman as writing thus:
If the biblical account of creation were true, then independent features of morphology, proteins, and DNA sequences would not be expected to be congruent with each other. Chaotic patterns, with different proteins and different DNA sequences failing to indicate any consistent set of species relationships, would contradict the theory of evolution.Rana is using this statement by Goodman to indict evolutionary theory, since, given what he thinks he has shown, that is exactly what the evidence of the first two papers is. The problem is that a bit further in the article, Goodman says:
Human serum proteins shown only small antigenic differences from orang-utans and gibbons, and tiny differences from gorillas and chimpanzees. Given the extensive morphological evolution involved, the extent of protein evolution between humans and other hominoids is surprisingly small. Alternatively, if the 'molecular clock' is applied to immunological distances and the divergence between hominoids and old world monkeys arbitrarily set at 30 million years ago, the human-African ape split occurs at 5 million years ago [emphasis mine].Once again, perfectly in keeping with evolutionary theory and perfectly in keeping with the results by Ebersbrerger et al, who also (twenty years later!) see the evidence as pointing to a human/ape split between five and six million years ago.
It is difficult to find anything redeeming in Rana's post. It is further difficult to derive a conclusion that these articles don't support the evolutionary paradigm, since they all clearly do. Did he simply not read them? Did he hope that none of his readers would? For someone who is trained in molecular biology to employ such a standard creationist trick is astounding and deeply, deeply disappointing. It also lends more credence to what Todd Wood recently said about RTB:
I would recommend that no one accept any of RTB's arguments without fact-checking their claims first. I do not know whether these problems are due to lazy scholarship, ignorance, intentional deception, or ideological blinders. What I do know is that you cannot trust Reasons to Believe.I can't add much to that.
1Goodman, Morris (1992) “Reconstructing Human Evolution from Proteins,” in Steve Jones, Robert Martin, and David Pilbeam, eds., The Cambridge Encyclopedia of Human Evolution, New York: Cambridge University Press, pp. 307–13.
----------------
Now playing: Renaissance - The Sisters
via FoxyTunes
Friday, September 16, 2011
Sigmund Comments on the BioLogos/Discovery Institute Rift
The slow descent into irrelevancy of BioLogos continues apace. From its inception by Francis Collins in 1997, the BioLogos Foundation’s original emphasis on increasing the acceptance of science amongst evangelical Christians has been gradually replaced by a more traditional focus on ‘worship’ and an increasing defense of Christianity from the challenges of secular reason.This is a mite peculiar since many of the posts recently that I have seen including my own don't deal with what he describes whatever. My series of posts deals with the evidence for human evolution and three days ago, Dennis Venema started a series of posts on the basics of evolutionary theory. While it is true that Pete Enns expends much energy writing excellent columns on the nature of biblical interpretation, there are quite a few posts about basic science and, ironically, Sigmund writes that BioLogos has gotten away from science yet the whole purpose of his post is to illuminate a rift between the two organizations that is science-based.
He comments on the recent reaction to Dennis Venema's review (which I thought was smack on the money) of Stephen Meyer's Signature in the Cell by the author. Meyer argues that complex specified information such as that found in the cell can only come from intelligent causes, while Venema states that there are natural causes that can create complex specified information without the need to invoke a designer. Meyer responds to this charge (in a way that Sigmund describes as “shifting the goalposts”) by arguing that he was only writing about biopoesis, not established life. Darrel Falk responded to Meyer's article in a way that Sigmund finds baffling. Sigmund and Falk are both fully aware that Meyer moved the goal posts, however Sigmund writes:
It was at this point that the real problems with the new BioLogos strategy become apparent. Falk, needing to see the best in every Christian, comes across as the theological equivalent of Woody Allen in the aftermath of the nymphomaniac scene in ‘Play it again Sam’. Falk spends almost the entire article wondering “How did I misread those signs?” and getting sidetracked into talking about “complex specified information” an imprecise term regarding complexity, only used by ‘Intelligent Design’ supporters.I feel for Darrel here, because, as Christians, we are called to see the best in people, even in a scientific setting. But Darrel has been on the receiving end of questionable Discovery Institute practices before at the Vibrant Dance conference. Commenting on it at the time, Steve Matheson wrote:
While it is clearly a case of the usual dishonest creationist tactics of trying to be vague and then shifting the goalposts when caught out, Falk doesn’t seem to be able to state the obvious.
The question is not whether Christians should point to the things they agree on. It's not about whether affirmations of shared belief are beneficial or appropriate when Christians find themselves in disagreement. For me and, I suspect, most of the critics that Falk was referring to, the question is whether BioLogos should cosponsor a conference on faith and science with organizations that seek to mislead people about science.Here, Steve is referring to both the Discovery Institute and Reasons to Believe, an organization that Todd Wood has dealt with. I have written about them as well.
Those of us who follow Jesus Christ want to believe the best in our fellow Christians but the sad fact is that we have examples in Christendom where scientific evidence is very poorly treated or misrepresented outright. I would never accuse Ken Ham of not being a Christian. But I would also never state that he honestly treats the scientific evidence. It is our duty to point out these errors in the hopes of reaching our fellow Christians and informing them that honest scientific inquiry can go hand in hand with Christianity. If the goal posts get moved, it is our duty to point that out as well. Darrel has done this. We might fault the force of his response, but we should not fault his intentions.
Sunday, August 07, 2011
Hugh Ross on Common Ancestry
One of my readers clued me in to a podcast by Hugh Ross in which he tackles theistic evolution, otherwise known as evolutionary creationism. The title of the series is “I did not know that.” This particular talk can be found here.
The focus of the talk is how there is evidence for a historical Adam and Eve and that they were created between fifty and sixty thousand years ago. He specifically contrasts theistic evolution with what he calls the “Biblical model for human origins,” as if there is no theological basis for TE.
His understanding of TE is that we evolved from early ape forms but that it was controlled by God in a way that we scientists can never discover. This is a peculiar statement because science, left to its own devices, is not in the business of discovering whether or not God controlled events and processes. It is through faith that people believe in God.
Ross is one of the original proponents of the “tweaking” argument—that the universe shows evidence of a divine hand that tweaked the gravitational constants and elemental formation in just such a way as to allow life to occur. One degree off either way and...nothing. This is put forth in his book Fingerprint of God.
As I have mentioned before, the problem with this argument is that it is post hoc. We think that it is tweaked because we are here to observe it. There was always a slight probability that the universe would have developed like this anyway.
First he argues that evolution cannot explain the complexity of life because the second law of thermodynamics will degrade the genome of any species over time.
Wrong.
The second law of thermodynamics only applies to closed systems. Hugh Ross is a physicist and he is not aware that the earth is not a closed system? How can that be? It is part of the earth/sun system. There is also interaction with other bodies such as the moon. Everything on earth receives energy from the sun and this, in itself, is a thermodynamic process. Further, as someone else put it, if the earth really is a closed system, then God cannot operate in it. As soon as you introduce intervention from outside, the system opens. Onward...
He then says that the human genome has gotten more decayed over time since the creation of Adam and Eve also because of the influence of the second law of thermodynamics.
Wrong.
The second law of thermodynamics does not explain this. Genetics does. Our genome is more decayed (if you will) because of the influence of genetic load. With extensive gene flow, bad alleles are masked and can persist in a population in large numbers without expression. As we have been able to address many genetic defects with medical treatments, the number of these alleles has increased in our population. This is especially true in western nations, where our diet and behavior has created even more problems for us.
Ross states that there is evidence that modern humans have not been around very long because in Chromosome 21, there are only three different haplotypes and that, if humanity was older than that, there would be more.
Wrong.
This is a complete misread of a paper by Jin, et al (1999)1 in which the authors study the haplotypes of Chromosome 21 in an effort to shed light on modern human origins. For one thing, there aren't three haplotypes, as Ross asserts. There are ten. There are three haplogroups that suggest that there were three migratory episodes of modern humans out of Africa. Ross focuses on the word “entropy” and, unfortunately, interprets it the way a physicist would. In this case, entropy refers to a function of Wrights Fst, which is a measure of genome variability. For example, North Americans have less entropy because they have greater genetic homogeneity than other groups that were studied. It has nothing to do with thermodynamics.
Ross argues that the chromosomal evidence that humans and the higher apes have a different number of chromosomes is invalid or misunderstood. In the early 1990s, it was discovered that human chromosome two is an end-to-end-fusion of two ape chromosomes. A close examination of chromosome two revealed that, while the other twenty-two chromosomes have one centromere, or central segment, human chromosome two has an extra non-functional centromere. Furthermore, while every chromosome has end segments known as telomeres, human chromosome two has inactive adjacent telomere segments in the middle of the chromosome. It is argued that, sometime in our early past, there was a translocation of two chromosomes to form Chromosome two. Ross argues that such a translocation could not possibly have happened because this would be “catastrophic for the organism” and would result in death.
Wrong.
There are many documented cases of translocation in animal species. There are species of horses that have different numbers of chromosomes and yet can produce fertile offspring. Ross further hampers his argument by saying that the jury is still out on whether or not the evidence is real because they might only appear to be centromeres and telomeres. This is, again, nonsense. It is obvious what they are. Further, how does he explain the duplication of the genes sequences in each chromosome?
Ross then tackles evidence for common ancestry contained in the disovery that the great apes and humans share the inability to manufacture vitamin C. He argues that in place of the inability to produce vitamin C is a new mechanism that recycles vitamin C in apes and humans. This is, he argues, not a loss of genetic function so much as it is a gaining of a new function. What Ross side-steps here and never mentions is that the arising of this mechanism in apes and humans is still evidence of common ancestry. In fact, it is better evidence because it means that exaptation happened in a common ancestor which was then passed on to each line.
And how does the evidence of the creation of a new mechanism in apes and humans figure into his idea of genome degradation?
He then launches into a discussion of the mitochondrial DNA evidence for the origins of modern humans and suggests that it demonstrates that we are descended from one woman (Eve) and then argues that this person likely lived between 50 and 60 thousand years ago. He further argues that Adam lived at the same time, based on Y-Chromosome evidence. This is their “testable creation model.”
There is a distinct problem with the harmonization of this evidence and the Bible. First, you have to really stretch the biblical genealogies to get them as far back as 50 to 60 thousand years. Second, while it is true that there was one original mtDNA variant from which modern humans are said to have arisen, that does not mean that there was only one woman alive at the time. In fact, there is evidence that there were thousands of modern humans alive at the time and that there was no distinct human couple at all.
Worse, the new evidence indicating that modern humans have 9% Neandertal genes calls into serious question the integrity of modern Homo sapiens as a unique species, suggesting that we are much, much older than we thought—perhaps 200 to 300 thousand years old.
He closes out by suggesting that the DNA evidence supports the disembarkation of four women and four men from Noah's ark, like that in Genesis 6-8. Aside from the genetic data indicating that the modern human population bottleneck reported by Venema occurred in sub-Saharan Africa, not the Middle East, there is not a scrap of biological, geological or palaeontological evidence that there was a world-wide flood of any kind.
In one fell swoop, RTB has turned its back on its historical Old-earth, progressive creation model and embraced the heart of young earth creationism, a model that has no serious scientific support of any kind. Is this really what RTB wants to do? If it really is accepting the idea that there were only eight people alive at the time of the flood, it must. It has always carved out a place that is separate from that of the major YEC groups and attempted to use conventional science as support for its apologetics. Now it seems that they are willing to accept a completely concordist model, even if it means the world-wide flood model, warts and all.
Not a fine day for scholarship.
1Jin, L., Underhill, P. A., Doctor, V., et al. (1999). Distribution of haplotypes from a chromosome 21 region distinguishes multiple prehistoric human migrations. Proceedings of the National Academy of Sciences, 96(7), 3796-3800. doi: http://www.pnas.org/content/96/7/3796.abstract
----------------
Now playing: Yes - Into the Storm
via FoxyTunes
Wednesday, August 03, 2011
Chris Mooney Wonders “Why The Scientifically Literate Can Believe Silly Things”
If you understand motivated reasoning, then you understand that high levels of knowledge, education, and sophistication are no defense against wrongheaded views like climate change denial and anti-evolutionism. What I’ll call “sophistication” may even make these phenomena worse, at least among those with deeply ideological or religious views.There is also the considerable problem of “a little knowledge is a dangerous thing. ”For some of the large groups that deal with this issue, such as the Institute for Creation Research, Answers in Genesis and Creation Research Ministries, they get things so obviously wrong that blowing the arguments out of the sky is a comparatively easy task. Other groups, however, such as Reasons to Believe and The Discovery Institute use arguments that are subtle and require a considerable amount of knowledge in a given field to determine where they go off the rails. Just ask Steve Matheson and Todd Wood. Given the Discovery Institute's active role in trying to influence anti-evolution legislation, it becomes increasingly important to alert people to these errors, since your average legislator won't be able to spot them.
The reason is that when we “reason” in areas where we have strong beliefs, our emotions come first and then we rationalize our pre-existing views. And those better at generating self-affirming arguments will be better rationalizers, will fall in love with their own seemingly brilliant arguments, and their minds will become harder to change (but they’ll love to argue).
----------------
Now playing: Rush - New World Man
via FoxyTunes
Tuesday, February 15, 2011
Hugh Ross on Evolution
For one thing, he states that most mutations are harmful. Mutations are only harmful if they disrupt the genome in such a way that reduced fitness is conferred on the organism. Many mutations are fitness neutral. Mutations do not drive a species to extinction, changing environments drive a species to extinction. That is basic evolutionary ecology. This is worse than William Dembski's math.
He talks about the fossil record by asking where you see the evidence for transitional forms and then focuses only on whales and horses. That is ridiculous. There are transitional forms all over the fossil record at every major level. If this is really the biology coming out of RTB then Todd Wood is correct, they absolutely cannot be trusted for anything.
The comments on Sandwalk's page are priceless. One in particular: “So why didn't God make more dinosaurs and unicorns and dodo birds? Or maybe he just doesn't love them as much as he loves horses and whales. He sure seems to love roaches and bedbugs, too.”
Amazing.
Wednesday, January 12, 2011
Reasons to Believe and the Credibility Gap
To be honest, I do not believe that RTB will pay any attention whatsoever to this series of posts. Given Rana's insulting response to Venema's critique, I expect that they'll treat this as yet another "ad hominem attack." I've mostly written this series for third parties that might be confused about the Venema/Rana exchange. As far as I'm concerned, RTB's credibility is completely shot (read my analysis of their handling of the Neandertal genome for more evidence of errors and exaggerations on the part of Ross, Rana, and Samples: parts one, two, three). I would recommend that no one accept any of RTB's arguments without fact-checking their claims first. I do not know whether these problems are due to lazy scholarship, ignorance, intentional deception, or ideological blinders. What I do know is that you cannot trust Reasons to Believe.This is very disappointing but, having read enough of Steve Matheson's writings, not entirely surprising. Once upon a time I had much respect for Hugh Ross and the work he did to try to convince the evangelical community that there could be a fulfilling theological construct that incorporated an old creation. He came to the University of Tennessee in the early 1990s and gave a series of compelling, cogent lectures on the astrophysical evidence. Even then, though, I had misgivings about what his (and his organization's) treatment of the biological data would be like. Now, it seems that my misgivings were well-founded and we have our answer.
Tuesday, January 11, 2011
Todd Wood Continues Taking Apart Fuz Rana
In his latest post, Rana asserts the following about the argument for common ancestry from pseudogenes:As Glenn Reynolds would say: OUCH! I would encourage you to read the whole debate. I am not qualified to comment at more than a superficially cogent level but I might try to say a few things. I haven't seen Steve Matheson wade in yet, but he may yet. If he does, expect fireworks. He has no love for RTB.When evolutionary biologists present this argument, they make a number of assumptions, all of which appear to have questionable validity based on recent research results. For the pseudogene evidence to have potency: (1) pseudogenes must lack function; (2) their origin must be due to rare, random events; and (3) their juxtaposition to other genes must be arbitrary.Everything he wrote there is utterly false. None of those conditions are required to argue for common ancestry from pseudogene similarity. Not one.
----------------
Now playing: Flash - Small Beginnings
via FoxyTunes
Saturday, January 08, 2011
Praise for Todd Wood
Fortunately for us, Todd Wood of the Center for Origins Research at Bryan College in Dayton, Tennessee, USA is on the case. Todd belongs to a young-Earth creation study group [BSG] but don't let that fool you. He's doing a pretty good job of sorting out the facts in the case.This might seem somewhat backhanded but if you read what Wood has to say, he is obviously struggling with the lack of integrity on the part of RTB. It is nice to see a young earth creationist try to deal with the data honestly. Most of the time the lack of integrity exhibited by young earth creationists is maddening, distasteful and disheartening. Hats off to Todd Wood.
Thursday, December 02, 2010
Evolutionary Christianity
This tele-series (telephone & computer, not television) will feature Michael Dowd and 30 other leaders in the nexus of science and religion (a number of whom who are Clergy Letter Project members), including two Nobel laureates, three Templeton Prize-winners, and more than two dozen others who exemplify by word and deed that religious faith can be positively strengthened and enriched by a science-honoring, evolutionary view of the world.I have signed up, although with four small kids and many time commitments, I am not sure I will be able to participate. It was gratifying to hear from Michael that he is doing much better and is cancer-free. Matt also notes that this is being co-sponsored by the Clergy Letter Project. I wonder how many of the people from the DI and RTB will weigh in.
Some of the things that will be discussed include:
• How scientific and historical evidence, interpreted meaningfully, can enhance our lives and faith;
• Compassionate responses to both those who reject science and those who reject religion;
• How an evolutionary view of human nature can validate and deepen our appreciation of scriptural and traditional wisdom;
• And much more . … [ellipsis in original]
Hat tip to Panda's Thumb.
----------------
Now playing: Peter Ilyich Tchaikovsky - Childrens Gallop and Dance of the Parents
via FoxyTunes
Friday, November 12, 2010
Steve Matheson: More on BioLogos and Chrisian Unity
What I'm trying to do here is make it clear that I don't think that Darrel Falk and Dennis Venema and Deb Haarsma were mistaken to participate in the Vibrant Dance or to call for respectful engagement with those there who disagree with them. I'm saying that they must make it clear that the DI and RTB regularly violate standards of intellectual integrity. Both the DI and RTB promulgate falsehoods, and they do it knowingly. It should go without saying that such behavior is unacceptable among self-described scholars; that the scholars in question are Christians, functioning as public Christian apologists who seek to influence the thought and actions of millions of fellow Christians, only amplifies this concern.It is becoming increasingly clear that the Discovery Institute has no intention of treating the data in an honest fashion. The first hints of that came with the Wedge Document and were on startling display at the Dover trial in 2005. Steve has stated in the past that he still holds out hope for RTB, although even here there seem to be problems of integrity.
Perhaps the odd thing about Reasons to Believe is that they treat the astrophysical data in an honest fashion and yet make a complete hash of the biological data and evolutionary theory. It is as if, when it comes to anything involving humans directly, the blinders go on. The Discovery Institute is a one-trick pony. Anything not dealing with evolution is ignored and then the evidence for evolution is twisted and misinterpreted.
It is not clear that there will a change anytime soon regarding any interactions between groups like BioLogos, which seeks to actually honestly interpret the data in a way that is in keeping with the integrity demanded by both science and a Christian walk and groups like RTB and the Discovery Institute, which do not seem to.
----------------
Now playing: Anthony Phillips - Guitar Song (Demo, 1973)
via FoxyTunes