Understanding creationism: An insider’s guide by a former young-Earth creationist - 6
Part 6 of former YEC David MacMillan's series on how the YEC mind deceives itself when confronting the evidence for evolution is up at Panda's Thumb. This time, he looks at how the YEC tries to explain away the genetic evidence. As I've explained repeatedly, along with biogeography, this provides some of the most compelling evidence for the reality of common descent, and the special creationist attempts to explain it away are frankly pitiful.
The 'common design' explanation is frequently cited in an attempt to explain away the evidence. Ignoring the fact that the multiple shared identical genomic 'glitches' such as pseudogenes, retrotransposons, and endogenous retroviral elements make the case for common descent unassailable:
[t]he obvious problem is that common design is unfalsifiable. There’s no limit to what it can explain, no level of commonality it cannot be used with. We recognize that an explanation which can fit literally anything is useless; it doesn’t tell us anything. Unfortunately, creationists don’t care whether their explanations are falsifiable. Their presuppositionalist background tells them that it doesn’t matter whether explanations are falsifiable – it’s just necessary to make sure they have the right presupposition at the outset, and everything else flows from that. As long as their denial of mainstream science seems vaguely plausible, they are okay.
So instead of pointing out the unfalsifiability of common design, it’s better to let them use it, but challenge them to take it to its logical conclusion. If their divine common design can really produce the observed levels of genetic similarity, then it should also produce clear and obvious genetic similarities in species that aren’t anywhere close on the evolutionary tree. Not just small sequences in common, but entire gene suites. If God is in the practice of re-using the exact same gene sequences in creatures that happen to show up close together, then we should see the same thing in distant species. Species identified in mainstream science as examples of convergent evolution – the same traits or abilities having evolved separately – should have perfectly matching gene sequences placed there by the creator. For example, bats and birds evolved echolocation separately using different genes, but the “common design” argument would predict the same exact gene sequences.Full article is here.
"birds evolved echolocation". Which birds have echolocation?
ReplyDeleteSwiftlets and oilbirds. From the Map Of Life:
Delete"The best known example of echolocating birds are the South American oilbirds (Steatornis caripensis), so called because their flesh yields abundant oil. Although confined to South America today, where they are known as guacharos, in the geological past they had a much wider distribution with fossils being found in the Green River Formation of the western United States, and also in English deposits. In terms of relationships they appear to be fairly close to the trogons. Trogons inhabit caves and are effectively entirely nocturnal, foraging forth at night to feed on fruit. They have eyes, although they lack the capacity for binocular vision, and in their entire lives they never see the world in anything brighter than moonlight. The eyes, however, have some remarkable features including an extraordinarily large number of photoreceptors, achieved by having the rods banked up to three deep. This density exceeds that of any other bird, including the falcon, but it evidently provides extreme sensitivity and not acuity, and not surprisingly finds some interesting parallels to the eyes of deep-sea fish. Oilbirds can, therefore, see at extremely low levels of light. They can also navigate in total darkness and not surprisingly they employ echolocation, in the form of a series of auditory clicks that have a quite complex wave-form with some pulsatile intervals. The sounds themselves are produced in the syrinx and presumably received by the ears, although these do not have any obvious modifications.
"The other group of birds that have evolved echolocation are the Asian swiftlets, a diverse assemblage that typically occupy the recesses of caves in areas of Asia such as Borneo and Ceylon. Swiftlets such as Collocalia and Aerodramas may not be familiar on account of their echolocation but are well known because of their ability to construct their nests with the aid of saliva, these nests being highly prized in Asia for the delicacy of "bird's nest soup". Like oilbirds they too produce a series of clicks (single and double) via the syrinx, and like them can navigate in complete darkness. Typically they employ the echolocation in the caves, where they roost in darkness, but at least one species (the Papuan swiftlet) may also be active at night. Whilst the clicks are certainly used for navigational purposes, they also appear to have a social role. In general despite the echolocatory capacity there are no obvious modifications to the relevant brain structure, or apparently the middle ear.
"Importantly the ability of Asian swiftlets to echolocate has evidently evolved at least twice, and possibly more. In addition there is some circumstantial evidence for swiftlets in Brazil also employing echolocation which if correct is almost certainly independent of their relatives in Borneo and surrounding areas.
"It is clear that whilst in general the ability to echolocate in olibirds and swiftlets does not rival that of the bats, nevertheless the birds are adept at flying in the pitch-dark, avoiding obstacles and finding the appropriate roost. In neither the case of the oil-bird or swiftlets, of course, are the birds blind and in non-crepuscular settings vision is also employed."
Map of Life - "Echolocation in birds: oilbirds and swiftlets"
http://www.mapoflife.org/topics/topic_436_Echolocation-in-birds-oilbirds-and-swiftlets/
July 06, 2014
Thank you for that. However, I have questions about the logic David MacMillan employs to argue against a common designer. (For one thing, he tries to make some kind of statistical argument about probability of DNA matching between species, using a nominal 22-codon / 66-base-pair sequence in a 3-billion-base-pair genome, but his working and conclusions are both quite wrong.)
ReplyDeleteAs the article you helpfully cited shows, the echolocating oilbird, a fruit-eater, generates (human-audible) clicks, for navigation even in total darkness, and apparently needs no special hearing capabilities to do so. By contrast, several species of echolocating bats have special apparatus (including two mechanisms of sound generation), both to emit and to hear far higher frequency signals; those high frequencies are necessary for the more difficult task of precise detection, tracking and capture of flying insects, in darkness.
Oilbird “echolocation” and bat “echolocation” are far from being the same exact function. Though there may be some overlap (bats may also navigate by sound) they are neither identical in detail, nor are they used for perfectly matching purposes. So why would a designer (i.e. God) be constrained to make them use "perfectly matching" gene sequences? This is not logically required at all.
The irony here is that in fact there do exist extensive detailed genomic alignments, not between certain species of birds and bats, but between echo-locating bats and echo-locating cetaceans. Both are mammals of course, though they could hardly be farther apart in most other respects. Yet nearly 200 genomic loci, taken to be linked to their specialised hearing (and also low-light vision) capabilities, which in both classes of creatures are used for hunting prey, have been found to match between them. Given the vast difference in their general characteristics otherwise, the use of the same genomic elements for these particular rare features makes a much stronger case for a common designer!
(Sorry, I should have given the reference for the bat/dolphin genome match paper. It is:
ReplyDeletehttp://www.nature.com/nature/journal/v502/n7470/full/nature12511.html )
>> I have questions about the logic David MacMillan employs to argue against a common designer.
ReplyDeleteMacMillan made an error in his mathematics which was quickly pointed out by a commenter:
"I’m not sure where you got your numbers, but for five species there are only 105 branching trees (dichotomous, rooted trees, that is; there are more, but not astronomically more, if we count polytomies). Still, the number goes up pretty fast. (It’s [2n-3]!!, where x!! means the product of all odd integers from 1 to x.)
"Also, fossils provide two sorts of data: morphological characters and stratigraphic position. The former should probably not be considered a property of fossil data, and fossils are most often combined in analyses with extant taxa. The latter is an independent source of data to be compared with phylogenetic trees, and the fit of stratigraphy to phylogeny is a fine confirmation of common descent.
"I also think your take on phylogenetic analysis is a bit garbled, perhaps partly because you are using “sequence” in two different ways. We commonly test many trees against some criterion of fit to the data and choose the one that has the best fit. But even if the data have no phylogenetic signal it’s likely that there will be one best-fitting tree, purely by chance. The question to ask is whether this fit is better than could be expected by chance, and there are tests for that. Presumably, a fit indistinguishable from chance is the creationist expectation and creationists would have no explanation for a significant fit.
"Now, one way to examine signal is agreement: if different data sets give us the same or very similar trees, that’s very unlikely to be due to chance. But there are also ways to test agreement within data sets.
"Finally, it should be noted that we expect some disagreement among trees using different DNA sequences because of what’s called incomplete lineage sorting. Alleles bounce around for some time in populations, and a given allele’s true tree may not quite match the true tree of the population." [1]
MacMillan acknowledged and corrected his error: "Yikes…it seems I mistook the double factorial x!! for the iterated factorial (x!)!. Thanks to John Harshman for pointing that out; I’ll have to add an errata." [2]
More to the point, not one of the non-creationist commenters asserted that MacMillan's error completely invalidated his argument. The evidence for common descent from the genomic data is beyond dispute. Evolutionary biologist Eugene Koonin, in a paper criticising a claimed mathematical demonstration of common descent stressed "[n]evertheless, the evidence in support of this hypothesis provided by comparative genomics is overwhelming." [3]
I included MacMillan's argument because it represents an insight into the mind of a YEC, not because he is an expert in evolutionary biology. Obsessing over errors he makes in his argument no more invalidates evolution than pointing out errors in a term paper by a physicist means quantum theory has been invalidated. Personally, I thought hard about including part six as I thought it was the weakest, but having committed myself to the series, I felt obliged to complete it, and trust that my readers would be perceptive enough to differentiate between the big picture and minor errors made by lay defenders of mainstream science. Evidently, that is not the case.
1. http://pandasthumb.org/archives/2014/07/understanding-c-5.html#comment-328521
2. http://pandasthumb.org/archives/2014/07/understanding-c-5.html#comment-328566
3. http://www.biologydirect.com/content/5/1/64
Finally, the Nature article you cited does not provide a "much stronger case for a common designer." Two words: convergent evolution. Tellingly, the authors of the paper did not think their work provided a stronger case for a common designer. The editorial summary should have provided you with an accessible overview of the paper:
ReplyDelete"Convergent evolution, through which similar traits evolve in unrelated lineages, is a familiar demonstration of the power of natural selection. These traits are usually viewed as representing alternate evolutionary solutions involving different sets of genes, but that view is challenged by a study of echolocating mammals. Analysis of the genomic sequences in 22 echolocating species, including four new bat genomes, reveals that convergence is not a rare process restricted to a handful of loci but is widespread, continuously distributed and commonly driven by natural selection acting on a small number of sites per locus. Convergence is particularly strong in genes linked to hearing or deafness, but surprisingly, also to vision."
Evidently, the editor and the authors did not think that special creation is a better explanation of the data. If you want those such as myself who regard the case for common descent as compelling to believe your 'special creation hypothesis' do the research, write a paper, get it published, get it positively cited, show us that the mainstream community regards your argument as a better explanation for the data. When that happens, send me a copy of the paper, and I will be inclined to take your argument seriously.
Finally, as I have pointed out many times, the evidence for common descent from shared genomic 'errors', even more than the consonance between phylogenetic trees constructed from gene sequences and from the standard evolutionary tree (with due allowance for incomplete lineage sorting), provides overwhelming evidence for common descent, one for which special creationists have no compelling answer. Shared identical retrotransposon insertions (mobile parasitic junk DNA elements) at the same place in DNA of species provides powerful evidence in favour of common descent, with the original insertion taking place in the common ancestor of the extant species, and being subsequently inherited. Nikaido et al in a 1999 PNAS paper note:
"Insertion analysis of short and long interspersed elements is a powerful method for phylogenetic inference. In a previous study of short interspersed element data, it was found that cetaceans, hippopotamuses, and ruminants form a monophyletic group. To further resolve the relationships among these taxa, we now have isolated and characterized 10 additional loci. A phylogenetic analysis of these data was able to resolve relationships among the major cetartiodactyl groups, thereby shedding light on the origin of whales. The results indicated (i) that cetaceans are deeply nested within Artiodactyla, (ii) that cetaceans and hippopotamuses form a monophyletic group, (iii) that pigs and peccaries form a monophyletic group to the exclusion of hippopotamuses, (iv) that chevrotains diverged first among ruminants, and (v) that camels diverged first among cetartiodactyls. These findings lead us to conclude that cetaceans evolved from an immediate artiodactyl, not mesonychian, ancestor." [1]
The case for common descent was regarded as compelling decades ago. Genomic data merely confirms this fact.
1.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC17876/