Thursday, 25 January 2018

Evolution is not crocodiles evolving into ducks. Debunking a common special creationist error

In my experience, it's a rare special creationist who knows anything about evolutionary biology, which of course makes their criticisms immaterial. After all, if you want your criticisms of something to be taken seriously, you first need to demonstrate that you know that subject intimately. Otherwise, no one will take anything you say seriously.

One of the most common special creationist errors is to assert that they will only accept evolution if they see one animal evolving into another. This error betrays a profound lack of understanding of the rudiments of evolutionary biology which states that it is populations that evolve, rather than individuals. Pokémon evolution is not the same thing as biological evolution.

It is no exaggeration to say that anyone who refers to individuals evolving has failed to grasp the rudiments of evolution given that by definition it has meaning only with populations:
In the narrow sense, evolution acts only upon these inherited (genetic) changes. If some individuals reproduce more than others, the relative abundances of the genes of these individuals will be different in the next generation (see natural selection). This can happen only in populations. [1] Emphasis mine
Put simply, evolution occurs whenever there is a change in allele frequency in the gene pool of a population. [2] The common creationist argument that evolution involve one modern species turning into another modern species therefore shows a complete failure to understand evolution at its most basic level. Comments such as:

are unfortunately rife among special creationists, and indicate that they simply do not understand evolutionary biology at its most fundamental level.

Evolution and the analogy of language

Most people who have studied English at high school will have encountered Chaucer's Canterbury Tales, both in the modern English translation, and the Middle English original. Six centuries separate the English of Chaucer from the English of the modern world, and as the following excerpt shows, it is barely understandable:
'Wepyng and waylyng, care and oother sorwe
I knowe ynogh, on even and a-morwe,'
Quod the Marchant, 'and so doon oother mo
That wedded been.'
Going back a few more centuries, we arrive at Old English which as the following image comparing the first lines of Psalm 23 in Modern, early Modern, Middle, and Old English shows is all but unintelligible to the contemporary layperson:

Clearly, English has evolved gradually over time. 

While the difference between Old English and Modern English is huge to the point of lack of mutual intelligibility if speakers of Old and Modern English were ever to meet, there was no point in history at which parents were not able to understand the language of their children. More to the point, no one would take anyone seriously who argued that one day everyone during the reign of Richard I suddenly switched from Old English to Middle English. This is exactly the sort of error special creationists make when they claim that evolution involves crocodiles turning into ducks, or dogs into cats.

Change in populations is an observable fact

Moving from language to biology, examples of change in populations over time are easy to demonstrate, with the classic example of industrial melanism in peppered moth populations being one of the most memorable, as well as sadly one about which there is an avalanche of special creationist dishonesty.  I have referred to this elsewhere, but it is worth noting how Michael Majerus, who was easily one of the leading  experts on this subject – who in his review paper pointed out:

Here, the main elements of the case are outlined and the reasons that the peppered moth case became the most cited example of Darwinian evolution in action are described. Four categories of criticism of the case are then evaluated. Criticisms of experimental work in the 1950s that centered on lack of knowledge of the behavior and ecology of the moth, poor experimental procedure, or artificiality in experiments have been addressed in subsequent work. Some criticisms of the work are shown to be the result of lack of understanding of evolutionary genetics and ecological entomology on the part of the critics. Accusations of data fudging and scientific fraud in the case are found to be vacuous. The conclusion from this analysis of criticisms of the case is that industrial melanism in the peppered moth is still one of the clearest and most easily understood examples of Darwinian evolution in action and that it should be taught as such in biology classes. [3] (Emphasis mine)
Nonmelanic (left) and industrial melanic (right) forms of some British moths. From top to bottom: peppered moth—Biston betularia, lobster moth—Stauropus fagi, figure of eighty—Tethea octogesima, scalloped hazel—Gonodontis bidentata, brindled beauty—Lycia hirtaria, pale brindled beauty—Apocheima pilosaria, green brindled crescent—Allophyes oxyacanthae, dark arches—Apamea monoglypha [Source]

Majerus died before he could publish the results of his research into peppered moth colour variation, designed to address weaknesses in earlier studies. In 2012, his data was published in Biology Letters, showing not just the evidence for selection pressure against coloured moths, but that its status as an icon of evolution is well justified:
The lifespan of wild moths is several days, so the approximately 9 per cent reduction in daily survival of melanics is sufficient in magnitude and direction to explain their long-term local decline; the decline rate suggests a selection pressure against melanics of s ≈ 0.1–0.2 per generation. Majerus was able to see predation events from his window, involving nine species of local insectivorous birds. Clearly melanics disappeared faster than non-melanics in this experiment, and Majerus was able to confirm by direct observation that about one-quarter of the disappearances were owing to bird predation.

Factors other than predation have often been argued to play a substantial role in the rise and subsequent post-industrial fall of melanism in Biston. Nonetheless, with this new evidence added to the existing data, it is virtually impossible to escape the previously accepted conclusion that visual predation by birds is the major cause of rapid changes in frequency of melanic peppered moths. These new data answer criticisms of earlier work and validate the methodology employed in many previous predation experiments that used tree trunks as resting sites. The new data, coupled with the weight of previously existing data convincingly show that ‘industrial melanism in the peppered moth is still one of the clearest and most easily understood examples of Darwinian evolution in action’.[4] (Emphasis mine)
Invariably, special creationists will resort to the claim that they are 'still moths', but this completely ignores the fact that this is evolution, namely a change in allele frequency in a gene pool caused by selection acting on mutation. Furthermore, it ignores the fact that special creationists have consistently failed to show that there is a ‘limit to evolution’, or selection acting on mutation is incapable of creating significant morphological change.

Genetic mechanisms for morphological change

The discovery that animals share a group of 'tool kit genes' involved in the development of organs and body parts during embryogenesis not only has been one of the major breakthrough in developmental biology in recent years, but has shown us how mutations in that 'relatively short period' can result in developmental repatterning and large-scale evolutionary change. Developmental biologists and geneticist Sean Carroll gives a splendid example of how this happens:

The three-spine stickleback fish occurs in two forms in many lakes in North America—a shallow-water, bottom-dwelling, reduced-spined form and an open-water, full-spines form...The pelvic spines are actually part of the fishes’ pelvic fin skeleton, and the pelvic and pectoral fins are repeated structures. Pelvic spine length is under selection pressure from predators. In the open water, longer spines help protect the fish from being swallowed by larger predators. But, on the lake bottom, long pelvic spines are a liability. Dragonfly larvae seize and feed on young sticklebacks by grabbing them by their spines.

The evolution of these stickleback populations is very recent. The lakes they inhabit were formed by receding glaciers in the last ice age, approximately 10,000 years ago and each lake was colonized by oceanic sticklebacks that then rapidly and repeatedly diverged into the short-and long-spined populations. Exceptional fossil records of stickleback evolution have been uncovered that document their rapid evolution.

Because the two populations are so recently evolved, they can still mate together and produce offspring. This allows geneticists to trace the genetic changes that underlie the divergence of body forms. Recently, David Kingsley, Dolph Schluter, and their collaborators at Stanford University and the University of British Columbia have been able to pinpoint genes responsible for the evolution of different traits in sticklebacks. The evolution of one trait, the pelvic spines, reveals how the formation of a repeated structure evolves through changes in the way a tool-kit gene is used.

The reduction of pelvic spines in bottom-dwelling populations is due to a reduction in the development of the pelvic fin bud. The major gene responsible for the reduction of the pelvic skeleton was recently identified as a tool-kit gene called Pitx1. This is a typical tool-kit gene—it has several jobs in the development of the fish, it acts by controlling other genes, and has counterparts in other animals, such as the mouse. In the mouse, Pitx1 helps make the hindlimb different from the forelimb (limbs are another repeated structure).

We know from the fossil record that the pelvic fin was the evolutionary forerunner of the hindlimb of four-legged animals. The use of Pitx1 in the development of the pelvic fins in fish and in mammal hindlimbs is a very nice, independent piece of evidence supporting that history. But the main point I want to make here is how the fishes’ pelvic skeleton gets reduced by changes at the Pitx1 gene without affecting other body parts where Pitx1 also functions.

The big clue comes from comparing the Pitx1 proteins of the pelvic-reduced and full pelvic forms. There is not a single difference in the protein sequence.

But, wait, didn’t I say that changes at Pitx1 made the pelvic skeleton different? Yes, I did. The apparent paradox is resolved by understanding that, in addition to the coding part of a gene, every gene also contains noncoding DNA sequences that are regulatory. Embedded in this regulatory DNA are switchlike devices that determine where and when each gene is or is not used. Tool-kit genes can have many separate switches, with each switch controlling the way a gene is used in a different body part. The function of switches depends on their DNA sequence, and changes in their sequence can alter how they work. A critical property of these switches is that changes in one switch will not affect the function of the other switches. And therein lies a huge insight into how form evolves. That is, the use of a tool-kit gene can be fine-tuned in one structure without affecting any other structures.

In the pelvic-reduced stickleback, the Pitx1 gene is, in fact, not used in pelvic fin development. Changes in the switch that govern its use in the hindlimb have enabled the selective reduction of this part of the fishes’ skeleton...The power of this example lies in its demonstration of how, at the fundamental level of DNA, a major change in body anatomy can rapidly evolve. [5] (Emphasis mine)
Two forms of stickleback fish occur in many lakes, the bottom-dwelling form has a reduced pelvic skeleton. The reduction of the skeleton is due to a change in the function of a genetic switch controlling the use of the Pitx1 gene in the developing pelvic fin (X). Drawing by Leanne Olds.

Evolution? Why, the fossils say YES!

Despite its incomplete nature, the fossil record overwhelmingly attests to the reality of large scale evolutionary change over time, with transitional fossils, contrary to special creationist assertions, abounding in the record. [6] Transitions at the species level are however usually not present in the record. Partly, this is due to the incomplete nature of the fossil record, but mainly due to the fact that what we see in the fossil record is what we'd expect to see with allopatric speciation. [7]

I did say usually; vertebrate palaeontologist Donald Prothero provides an example of fine-grained evolutionary change preserved in the fossil record which shows observed extreme morphological change:

 Let us look at just one more classic example, probably the most extreme change in morphology ever documented in the fossil record. If you look at samples of microfossils from the middle Eocene (50 million years ago), you will find distinctive spongy ball-shaped radiolarians known as Lithocyclia ocellus (fig. 8.7). As you trace the spongy balls up through the sediments spanning millions of years, you see them gradually lose their spongy outer layers and develop into a small nucleus with four spongy arms (Lithocyclia aristotelis), then three arms (Lithocyclia angusta), and finally reduced to two arms forming a spindle-like shape (Cannartus tubarius). The Cannartus lineage then gradually develops a “waist” on the central sphere, then the arms get shorter and thicker, and finally, they split into two lineages: Cannartus peterssoni-Ommatartus hughesi, which evolves into a form with two arms with multiple spongy layers, and Ommatartus, which develops shorter arms and a fatter central sphere. If you look at the two extremes (a spongy sphere turning into a spindle-shaped shell with multiple caps), you could never imagine that they are closely related—yet I have looked at the slides from those cores and seen the gradual transition from one extreme to the other with my own eyes. [8]

Figure 8.7. Evolutionary transformation in the cannartid-ommatartid lineage of radiolaria over the past 50 million years, from spongy balls to four- and then three-armed and finally two-armed bipolar structures, with further variations in the spongy caps later in their evolution. Taxa are as follows: 26, Lithocyclia ocellus; 27, Lithocyclia aristotelis; 28, Lithocyclia angusta; 30, Cannartus tubarius; 31, Cannartus violina; 32, Cannartus mammiferus; 33, Cannartus laticonus; 34, Cannartus petterssoni; 35, Ommatartus hughesi; 36, Ommatartus antepenultimus; 37, Ommatartus penultimus; 38, Ommatartus avitus; 39, Ommatartus tetrathalamus. (Modified from Haq and Boersma 1978)

Conclusion - and a comment on monsters in the laboratory

One of the most frequently-committed special creationist errors is their assertion that evolution involves one modern species turning into another modern species. This is incorrect. Individuals do not evolve. Populations evolve. This is of course implicit in the definition of evolution as the change in allele frequency in the gene pool of a population. We have plenty of examples of populations changing in response to selective pressure [9] such as that seen in the peppered moth. Genetic mechanisms for large-scale morphological change have been elucidated over the years, and the fossil record itself bears historical witness to the reality of large-scale evolutionary change. While details about the mechanism of evolutionary change and the precise details of major events in evolutionary history are still subjects of active and lively scientific research, the fact of evolution has not been in serious doubt for well over a century. It reflects poorly on Christianity that people are still trying to deny one of the best-attested facts in science.

Careful readers would have noted that I referred to the special creationist misunderstanding of evolution as one modern species turning into another. The reference to modern was deliberate, and highlighted yet another major special creationist misunderstanding of evolution, namely a failure to grasp that evolution is not a ladder, but a tree. The idea of a cat evolving into a dog reflects this erroneous thinking of evolution as progress up a ladder. As evolutionary biologist Louise Mead points out:
The concept of a “missing link” is an “archaic expression”… tracing back to the Great Chain of Being, a view of the physical and metaphysical world as an unbroken chain. It was later temporalized by the evolutionary thought of the eighteenth and nineteenth century to the idea of evolution as a progressive climb up a ladder… These views of evolution create the false expectation that there should be fossil evidence showing “a complete chain of life from simple to complex”. [10]
While the 'cat evolving into a dog' assertion may for some special creationists be a throwaway line, it does reflect the erroneous thinking of evolution as a ladder, with life arranged in a hierarchy from primitive single celled organisms at the bottom to humans at the top. Of course, given that all existing forms of life share a common ancestor, and have been evolving for the same length of time since their ancestral lineages diverged from the common ancestor, there is no such thing as 'primitive' and 'advanced' forms of life. Related to this is the 'platypus fallacy' which argues that early branching equals primitive. Genomics expert T. R. Gregory neatly skewers this error, made in the context of those using traits of modern species to infer details about the evolution of others, such as humans:
The fallacy here is to assume that the non-human species is “primitive”, such that it can be used as a proxy for a distant human ancestor. This is a fallacy because “primitive” and “derived” refer to individual traits, not entire species, and because the comparison being made is between two modern species, not an ancestor and a descendant. Both lineages have, by definition, been evolving for exactly the same amount of time since diverging from a common ancestor. 
I am going to call this the “Platypus Fallacy”, based on an example that I have used in my lectures. Consider the following quote, by one of the authors of the platypus genome sequence paper:
“The platypus is a very ancient offshoot of the mammal tree, so it was 166 million years ago that we last shared a common ancestor with platypuses, and that puts them somewhere between mammals and reptiles, because they still maintain quite a lot of reptilian characteristics that we’ve lost; for instance, they still lay eggs. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having live-born young.”
Now, if a platypus were asked to summarize the situation, he could just as well say this:
“The lineage of which humans are a part is a very ancient offshoot of our mammalian family tree, so it was 166 million years ago that we last shared a common ancestor with humans, and that puts them somewhere between mammals and reptiles, because they lack a lot of specialized characters that we have gained but the ancestral amniote also lacked; for instance, they have no electroreception, no bills, no webbed feet, and no venom. So we can use them to trace the changes that have occurred as we went from being a reptile, to having fur to making milk to having our specialized features.”
Of course, if a platypus did say such a thing, I hope his colleagues would encourage him to avoid committing the “Human Fallacy”. [11]
Apart from disabusing the reader of any conceit about humans being the pinnacle of creation, this reminds us of the possibility that it is entirely reasonable to expect us to have at the genetic level the legacy of our evolutionary past. Genomic science has confirmed this. Examples include toothless animals having the broken genes for enamel proteins [12] and placental mammals having broken genes for egg yolk protein. [13] Inexplicable from a special creationist viewpoint, but exactly what evolution would predict. Given that birds evolved from dinosaurs (and are in fact dinosaurs), it is possible that they still have the ability to grow teeth like their theropd ancestors?

Why yes:
Working late in the developmental biology lab one night, Matthew Harris of the University of Wisconsin noticed that the beak of a mutant chicken embryo he was examining had fallen off. Upon closer examination of the snubbed beak, he found tiny bumps and protuberances along its edge that looked like teeth--alligator teeth to be specific. The accidental discovery revealed that chickens retain the ability to grow teeth, even though birds lost this feature long ago. [14]
No scientist would ever expect a cat to turn into a dog in the lab. This is not evolution. However, being able to activate latent traits that demonstrate evolutionary history very much is consistent with evolution, and the sort of lab experiment that to a fair-minded person would reinforce the reality of descent with modification.

Note: parts of this article have appeared in an earlier post of mine.

1. Rice Stanley A., Encyclopedia of Evolution (2007: Infobase Publishing) p 151
2. It is after all why population genetics is an integral part of evolutionary theory.
3. Majerus M.E.N. “Industrial Melanism in the Peppered Moth, Biston betularia: An Excellent Teaching Example of Darwinian Evolution in ActionEvo Edu Outreach (2008) 2:63-74
4. Cook L.M. et al “Selective bird predation on the peppered moth: the last experiment of Michael MajerusBiol. Lett. (2012) 8:609-612
5. Carrol S.B. The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution (2006: W. W. Norton & Company) p 205-207
6. Hunt K. Transitional Vertebrate Fossil FAQ TalkOrigins Archive
7. Theobald D All you need to know about Punctuated Equlibrium (almost)
8. Donald Prothero, Evolution: What the Fossils Say and Why It Matters, (2007: Columbia University Press) 182–183.
9. This is not to say that selection is the only mechanism of change. Certainly, at the molecular level,  evolution can occur due to neutral drift.
10. Mead L.S. "Transforming Our Thinking about Transitional Forms" Evo Edu Outreach (2009) 2:310-314
11.  Gregory T.R. "The Platypus Fallacy" Genomicron June 3 2012
12. Meredith RW, Gatesy J, Murphy WJ, Ryder OA, Springer MS (2009) Molecular Decay of the Tooth Gene Enamelin (ENAM) Mirrors the Loss of Enamel in the Fossil Record of Placental Mammals. PLoS Genet 5(9): e1000634. doi:10.1371/journal.pgen.1000634
13. D. Brawand,W. Wali, and H. Kaessmann, “Loss of Egg Yolk Genes in Mammals and the Origin of Lactation and Placentation,” PLoS Biology 6 (2006): 0507–17.
14. Biello D "Mutant Chicken Grows Alligatorlike Teeth" Scientific American Feb 22 2006