Friday, 20 June 2014

Crows Picking at the Neanderthal Creationist Corpse

A creationists 'explains' two sorts of evolution.
Note the lie that evolutionary biologists claim trilobites were our ancestors
and that foxes are the same species as dogs and wolves.
The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

How carrion and hooded crows defeat Linnaeus's curse

Creationists don't understand what evolution is. Creation pseudo-scientists on the other hand, understand perfectly well what evolution is - which is why the term has to be deliberately misrepresented, and the ignorance maintained by misinformation, misrepresentation and lies. And the most important muddle that must be maintained is what the term 'species' means, how it's understood by biologists and how evolutionary theory explains the mechanism by which it arises.

Unable to argue against the massive amount of observed and observable evidence that change over time can be seen both in the phenotype and in the genotype of a species, they have tried to come up with a compromise position that somehow the mechanism of this change is materially different from the mechanism by which different populations gradually change until they can be classified by taxonomists as distinct species. To this end they misrepresent and misclassify the technical terms 'microevolution' and 'macroevolution' as though evolutionary biologists use these terms themselves to distinguish between different mechanisms, instead of simply the magnitude of the changes the same evolutionary process produce over different timescales and so far as they relate to the human taxonomic classification system.

I believe that microevolution is true, but macroevolution doesn't exist and isn't possible for as it says in Genesis 1;27

"So God created mankind in his own image, in the image of God he created them; male and female he created them."

And yet there is no satisfactory definition of the term 'species' which all scientists can use for every occasion and, for most species, it is impossible to say precisely when and where a 'speciation' occurred because it actually occurred slowly over time and across the population as a whole. It was not an event but a process. (See Why Species? and Evolution - Making a Monkey).

This difficulty with definitions of speciation and especially with trying to fit specimens of a taxon which was diversifying into a neat classification system actually devised to classify existing species, and especially how biologist live with this imprecision was highlighted by a couple of papers published in Science this week, and an article which explained the significance of one of them for our taxonomic systems.

The first deals with a subject that has long fascinated me - the carrion crow/hooded crow complex across Euro-Asia. I previously blogged about this last March in Evolution Has More to Crow About so it's pleasing to see another paper which highlights this phenomenon and the problem it creates for taxonomists:

Abstract
The importance, extent, and mode of interspecific gene flow for the evolution of species has long been debated. Characterization of genomic differentiation in a classic example of hybridization between all-black carrion crows and gray-coated hooded crows identified genome-wide introgression extending far beyond the morphological hybrid zone. Gene expression divergence was concentrated in pigmentation genes expressed in gray versus black feather follicles. Only a small number of narrow genomic islands exhibited resistance to gene flow. One prominent genomic region (<2 megabases) harbored 81 of all 82 fixed differences (of 8.4 million single-nucleotide polymorphisms in total) linking genes involved in pigmentation and in visual perception—a genomic signal reflecting color-mediated prezygotic isolation. Thus, localized genomic selection can cause marked heterogeneity in introgression landscapes while maintaining phenotypic divergence.

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
J. W. Poelstra, N. Vijay, C. M. Bossu, H. Lantz, B. Ryll, I. Müller, V. Baglione, P. Unneberg, M. Wikelski, M. G. Grabherr, and J. B. W. Wolf
Science 20 June 2014: 344 (6190), 1410-1414. [DOI:10.1126/science.1253226]

Commenting on this rather technical paper, Peter de Knijff, pointed out:

Ever since Linnaeus invoked his taxonomic "curse," by requiring all biologists to use a stringent hierarchical species classification, researchers have been unable to define a single all-inclusive species concept. In this context, it is fascinating to read how 100 years later, Charles Darwin dealt with this problem. He simply preferred not to address the issue of species concepts, stating: "But to discuss whether they are rightly called species or varieties, before any definition of these terms has been generally accepted, is vainly to beat the air". Obviously, forcing complex patterns of biological variation into a single hierarchically structured archive is a purely anthropogenic project. No matter how hard we try, there cannot be a robust, all-inclusive, objective species concept.

How carrion and hooded crows defeat Linnaeus's curse; Peter de Knijff
Science 20 June 2014: 344 (6190), 1345-1346. [DOI:10.1126/science.1255744]

What this team took into account was not just the DNA but how it is expressed in the individuals by looking also at the RNA trascriptome, i.e. the DNA which is actually used by being transcribed into RNA. Combining this data from near complete genomes from different crow populations with some powerful statistical tools, they were able to show that, despite considerable gene flow between the two species, phenotypic divergence is maintained by less than 1% of the genome because of the role the same genes play both in plumage colour and in colour perception and so in sex selection for grey plumage. This accounts for hybrids being less frequently selected as mates by hooded females when fully grey hooded males are available, so gene flow tends to be into the carrion crow population.

The extent of this gene flow into the German carrion crows can be seen from the fact that German carrion crows are genetically more similar to Polish hooded crows than they are to Spanish carrion crows, yet they appear to be phenotypically identical to one another and distinct from hooded crows. According to strict Linnaean principles therefore, German and Spanish crows have to be classified as a single species and hooded crows as a different one, though some taxonomists argue, with some justification, that they are really subspecies of the same species.

Although this is a fascinating academic argument for evolutionary biologists, confirming as it does the understood mechanisms for genetic evolution and confirming the wisdom of Darwin's reluctance to get involved in semantic arguments about 'species' or 'varieties', it represents a major problem for creationists. According to their idiotic utility parody version of 'evolution', if hooded crows and carrion crows are different species they couldn't have evolved from a common ancestor because that mechanism is 'impossible'; however, if they are subspecies or colour varieties, that's perfectly okay.

And yet you and I and anyone who bothers to try to understand evolution knows perfectly well, crows don't care about this problem for human classifications systems and nature doesn't feel any need to fit itself neatly into it for us. It also appears to require creationists to believe that the mechanism for how something evolved changes retrospectively when humans change their mind about how to classify them.

Only creationism requires the facts to be ignored so the conclusion meets sacred requirements.

The Institute for Creation Research seems to be trying to ride both horses at once on the subject of micro- vs macro-evolution. Whilst they pay lip-service to the idea that creationists should not argue that micro and macroevolution are different things, and this 2006 blog by one of their pseudo-scientists mentions that they no longer endorse it, the link she gives actually says nothing about it, and she proceeds to argue it by inference, having understandably tried to dissociate herself from it. Perhaps the ICR have again reviewed their list of what lies they should not be using and have reverted to using the more useful ones in disguise.

This is how Dr. Georgia Purdom copes with the problem when discussing an article about Darwin's Finches in the Galapagos Islands which showed how their beaks can respond quite quickly and measurably in response to evolutionary pressures, confirming Darwin's observations and explanation for it:

Defining terms

The tagline to the news article states: "Finches Named for Charles Darwin on Galapagos Islands Confirming His Theory of Evolution" (italics added). Is this really evolution? Certainly not the molecules-to-man evolution Darwin promoted. The author later quotes a geneticist from the Smithsonian saying, "This was certainly a documented case of microevolution." Exactly! Although we don't endorse using the phrases macro/microevolution [my emphasis], we would agree that this is a small-scale change allowing an organism to adapt to its environment (which is what is meant by the author’s use of microevolution). This idea is even further refined by the Grants in the Science article as character displacement, which is adaptation resulting from competition with another species for limited food resources. This very accurately describes what is occurring; however, this small-scale variation within a kind is being misrepresented (as always!) as proof for Darwinian evolution from one kind to another [my emphasis].

Dr. Georgia Purdom; "Evolution" of Finch Beaks—Again, 2006

So, although "we don't endorse using the phrases macro/microevolution", Dr Purdom still argues that "small-scale variation" is "not the molecules-to-man evolution Darwin promoted". How that differs from arguing that microevolution and macroevolution are somehow completely different processes is anyone's guess.

Neandertal roots: Cranial and chronological evidence from Sima de los Huesos

The second paper this week concerns a basically similar problem only this time related to the evolution of a what is probably a sister species to Homo sapiens, H. neanderthalensis. I qualified that sentence with 'probably' because the only question is exactly how we and Neanderthals are related: are we subspecies of the same species; sister species sharing a common ancestor or, conceivably, are they one of our parents?

The problem here is that, frankly, there are too many of what look like transitional fossils from a single site in Spain. The authors examined 17 skulls which have been independently and reliably dated:

Abstract
Seventeen Middle Pleistocene crania from the Sima de los Huesos site (Atapuerca, Spain) are analyzed, including seven new specimens. This sample makes it possible to thoroughly characterize a Middle Pleistocene hominin paleodeme and to address hypotheses about the origin and evolution of the Neandertals. Using a variety of techniques, the hominin-bearing layer could be reassigned to a period around 430,000 years ago. The sample shows a consistent morphological pattern with derived Neandertal features present in the face and anterior vault, many of which are related to the masticatory apparatus. This suggests that facial modification was the first step in the evolution of the Neandertal lineage, pointing to a mosaic pattern of evolution, with different anatomical and functional modules evolving at different rates.

Neandertal roots: Cranial and chronological evidence from Sima de los Huesos; J. L. Arsuaga, et al;
Science 20 June 2014: 344 (6190), 1358-1363. [DOI:10.1126/science.1253958]

The skulls appear to show that the 'masticatory' changes in this population of Neanderthals giving typically Neanderthal facial features while the cranial anatomy remained close to H. heidelbergensis - the assumed ancestor of both H. sapiens and H. neanderthalensis. On the basis of this cranial anatomy, the team propose that the Sima de los Huesos fossils and all the European early and middle Middle Pleistocene specimens should be reclassified as H. heidelbergensis which should be redefined as including "fossils with a generally more primitive morphology than the late Middle Pleistocene and Late Pleistocene Neandertals".

On that classification, the Spanish hominids belong to the stem group of both modern humans and Neanderthals, although that is not to argue that present-day H. sapiens evolved in Spain, or even in Europe. It still looks much more likely that H. heidelbergensis came out of Africa before H. sapiens evolved from the African population and came out later after these earlier migrants had disappeared during the last Ice Age.

Another layer of complication comes from the fact that the mitochondrial DNA recovered from a hominid femur from the Sima de los Huesos site has been found to be closer to the 'Denisovan' mtDNA recovered from a finger bone found in the Denisova cave in Siberia. Whilst Europeans have about 3% Neanderthal DNA, several Southeast Asian and Austronesian peoples have been found to have various amounts of Denisovan DNA in their genomes. And yet again, a site in Georgia has yielded several hominid fossils which appear to be those of H. habilis, the assumed immediate ancestor of H. heidelbergensis, but these have been shown to have as wide a range of features as the several hominids normally regarded as different co-existent African species of Homo.

So, the picture is emerging of a widespread genus with geographical variation existing probably as small bands but with almost certainly a certain amount of interbreeding. In places these may well have diversified enough to be regarded by taxonomists and paleoanthropologists as distinct species whilst in other areas the distinction was not nearly so clear-cut.

What we are seeing is perfectly in line with what we might expect to see with Darwinian evolution playing out in a widespread species, especially one moving out of its ancestral homelands and diversifying into new climates and new habitats in several successive waves at different stages in its evolution. Given that humans and chimpanzees seem to have remained in occasional contact over part of their range and sometimes interbred for approximately 1.2 million years up to final separation some 5.3 million years ago, it would be astonishing if we had split off suddenly from our parent species and had nothing to do with sibling species for a period of only a few hundred thousand years.

And of course, part of the problem for taxonomists is in trying to comply with "Linnaeus's curse" and fit these specimens of a variable and evolving genus into well-defined species, despite this term not being fully defined and having different uses in different situations. Evolutionary biologist, paleoanthropologists and taxonomists all understand that and use slightly different definitions when it is needed.

For scientists who understand the subject, this isn't a problem. For creationists who don't it is presented by their pseudo-scientists as a major obstacle for Darwinian evolution. One of the strongest cards in the creationist hand is the carefully nurtured ignorance of their victims.

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1 comment :

  1. I want to quote some sentences from another article you've written on this same topic, Rosa. See: http://rosarubicondior.blogspot.se/2014/03/your-ancestors-mated-with-chimpanzees.html .

    And of course, in species where sex has a social and recreational role, as well as a reproductive one, this tendency to interbreed would likely have been more marked than where sex depends more on hormones and visual or other sensory stimulation and serves a purely procreational function.

    What you will never get a creationist to acknowledge is that this mode of evolution not only would not produce the 'missing link' they keep demanding science produce but that we should not expect to find any. We would expect the fossil evidence to be exactly what it is - a slightly muddled, fuzzy picture with no strong demarcations and a series showing gradual change over millions of years, just as the DNA evidence is reflecting.

    Unfortunately creationists seem to be unable to understand the mechanisms of evolution. Instead they argue like this (and now I quote from another part of the same article):

    1. 'Whatever the Bible says is so; whatever man says may or may not be so,' is the only [position] a Christian can take..."
    2. If [scientific] conclusions contradict the Word of God, the conclusions are wrong, no matter how many scientific facts may appear to back them.
    3. Christians must disregard [scientific hypotheses or theories] that contradict the Bible.

    Source: W.S. Pinkston, J.A. Graham, G. Kuzmic and C. Vogt; Biology for Christian Schools; Bob Jones University Press

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