The notion that ontogeny (development from a fertilized egg to adult) recapitulates phylogeny (evolutionary history) is an outdated notion that has been scientifically rejected. That does not mean, however, that evolutionary history is not reflected in developmental pathways. Creationists often conflate the two in order to create a strawman of the current scientific position.

The difference is interesting and makes sense. What does not happen (and why should it) is stages of embryonic development passing through adult forms of ancestral species. What does happen is stages of embryonic development passing through embyronic forms of ancestral species. This about evolution and development this way – evolution often occurs through altering developmental pathways. But this alteration can occur anywhere along the developmental timeline.

What evolution cannot do is rewrite the genetic code from the ground up. It can only alter the existing code. As evolutionary history gets longer and longer, therefore, the developmental pathway of living creatures gets more and more convoluted and tortuous. At no point can evolution “clean up” the code. So contemporary animals do not develop in a straight line to their mature form. They take a twisting and winding course that reflects their past history. But of course this path does not pass through the adult form of their ancestors, because development doesn’t follow those old pathways all the way to their conclusion. They are diverted along the way.

As the technology to perform high definition 3D scans of embryonic anatomy improve, we are finding more and more examples of this phenomenon. A recent paper gives a dramatic example –  Development of human limb muscles based on whole-mount immunostaining and the links between ontogeny and evolution.

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Old ideas die hard. The first extinct hominids found were Neanderthals, and our cultural conception of them was formed in the 19th century, a time rife with parochial attitudes toward “primitive” peoples. The first Neanderthal skeleton also happened to suffer from crippling arthritis, giving it a hunched over posture.

The cultural notion that our closest relatives were brutish and primitive became deeply embedded. Certainly, this idea has been moderated significantly in the last century, but not completely expunged. Meanwhile, paleontologists have discovered more and more evidence that Neanderthals were just a different breed of human. They were fully bipedal, so their gait was modern. They were more robust than Homo sapiens, because they were adapted to Europe’s Ice Age. But robustness should not be confused with brutishness.

Prof Clive Finlayson, director of the Gibraltar Museum, has a recent commentary on BBC’s website in which he punctures this outdated view of our closest cousins. He points out that this biased view of Neanderthals affects not just public perception, but scientific thinking. There have been many assumptions of Homo sapiens superiority, and that Neanderthals were essentially replaced by us through direct competition.

So this also reflects a common misconception about evolution itself, that “survival of the fittest” is always what determines which species endure, and is all about being more advanced and superior. Finlayson points out that we cannot neglect the factor of luck, which may, in fact, often be dominant. Homo sapiens may not have been objectively superior to Neanderthals in any specific way, but were simply better adapted to a changing environment. Neanderthal robustness, an advantage during glacial periods, may have been a hindrance during a warming climate. Sapiens may simply have inherited a better trade-off of features for that period in time.

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Scientists report in Nature the indentification of two new species of Hemimastigophora, a predatory protist. What makes the paper newsworthy is that the authors are arguing that their genetic analysis suggests Hemimastigophora, currently categorized as a phylum, should instead be its own suprakingdom.

To make sense of this let’s review the basic structure of taxonomy, the system we use to categorize all life. All known life is divided first into three domains, the bacteria, archaea, and eukaryotes. Bacteria and archaea do not have a nucleus, while eukaryotes are larger and have a nucleus which contains most of their DNA.

Eukaryotes are divided into kingdoms, including plants, animals, fungus, protozoa, and chromista (algae with a certain kind of chlorophyll). Kingdoms are then divided into phyla, which are essentially major body plans within that group.

This is a simplified overview, because there is a lot of complexity here, with suprakingdoms, subkingdoms, and further breakdowns. Further, there is a lack of consensus on how to exactly divide up these major groups. Even in the cited paper, the authors say there are 5-8 “suprakingdom level groups” within the domain eukaryotes. The number of kingdoms depends on which scheme you use, and how you interpret the existing evidence.

The reason for uncertainty is that we have not yet done a full genetic analysis on every known group. Further, when we discover new species that lie outside of the existing scheme, we have to rethink how different groups are actually related.

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My favorite fossil is the Berlin specimen of Archaeopteryx lithographica, for several reasons. First, it is straight-up a beautiful fossil, well-preserved, and just a natural work of art. But this is no object of human creativity – it is also a wonderful transitional fossil, catching evolution in the act of transforming theropod dinosaurs into birds. There is a cast of the Berlin specimen at the Peabody museum in New Haven, and it is capable of capturing my attention even in the middle of the hall of dinosaurs.

Recently I was able to visit the Natural History Museum (NHM) in London – where they have the original fossils of the first Archaeopteryx specimen found in 1861 (before the Berlin specimen), making it the type specimen. It too is beautiful, showing both the plate and the counterplate – the limestone that contains the fossil was cracked open, revealing impressions and fossils on both sides.

You can clearly see the feather impressions surrounding what at first looks like a small theropod dinosaur. On closer inspection, however, there are bird-like features as well, but retaining things like teeth and a long bony tail not seen in birds. Again – a dramatic transitional fossil, clearly connecting birds to what are now called non-avian dinosaurs (because birds are dinosaurs).

Creationists have long tried to argue that Archaeopteryx is not transitional, just a weird bird, but the evidence is undeniable. It has as close to halfway features between walking theropods and modern birds as you can get. But to be clear, Archaeopteryx is not on the direct line to birds. It is a side branch from a period in time when small feathered dinosaurs were undergoing adaptive radiation, only one branch of which would lead to modern birds. This is always going to be the case, however, and does not diminish the transitional significance of this species. Also, in recent decades a number of feathered dinosaurs have been discovered, fleshing out much of the evolutionary pathways between theropods and birds.

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As an American it’s very easy to look at issues from a narrow American-centric view (we have a well-earned reputation for this). I am often reminded of this by my many international SGU listeners, and I have had to discipline myself to keep this in mind.

For example, when it comes to teaching science in public schools, I do, of course, feel the most responsibility for my own backyard, but this is an important issue everywhere. But this is an issue in many countries, not just the US. Recent reports indicate that the teaching of evolution is under attack in Israel and Turkey. The Guardian also reports:

This news follows the astonishing statements made by India’s minister for higher education earlier this year. Satyapal Singh claimed Darwin was “scientifically wrong”, and is demanding that the theory of evolution be removed from school curriculums because no one “ever saw an ape turning into a human being”.

India has 1.35 billion people, which is 17.7% of the world population. (China is 1.4 billion, 18.5% – so India and China combined have 36.2% of the world population). I think it’s reasonable to say that it matters what happens in these countries, especially with our increasingly globalized world. Our efforts to curb climate change depend on cooperation from China and India, and having a scientifically literate population will help these efforts.

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Beginning 542 million years ago there was what scientists call the Cambrian Explosion. The name may be a bit misleading, because it is only an explosion in geological terms, taking tens of millions of years. This event refers to the geologically rapid appearance of many different phyla of multi-cellular creatures. All modern phyla (the taxonomic level just below kingdom) are represented in the Cambrian, along with many that did not survive to modern times.

The idea is that once multicellular life appeared, this new strategy was wildly evolutionarily successful, undergoing extreme adaptive radiation. Further, multicellular life evolved hard parts, like shells and bones, that fossilize well. The fossil record essentially turns on at this point, creating the impression of a rapid appearance of many species. However, there are fossils of older living organisms without hard parts, but they are more rare, requiring special conditions for their preservation.

One such pre-Cambrian group is called the Ediacaran fauna, from 571 to 541 million years ago. These are mostly large flat creatures, as if multicellular life had not yet worked out the trick of three-dimensionality. Getting oxygen to deep tissues requires specialized structures, not necessary for a flat organism. Scientists, however, did not know what the Ediacaran fauna were. Were they mats of fungi, or a failed dead-end branch of life wiped out the the more advanced three-dimensional Cambrian fauna? And if either of these two possibilities were true, then were are the precursors to the Ediacaran fauna? Their absence is not shocking, given that they would have been entirely soft creatures, but still, it would be nice to find some evidence of the lead up to the Cambrian.

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Facts matter. While that should be obvious, and skeptics have been pushing that world view for decades, it seems that the central importance of objective facts to both democracy and any intellectual pursuit might be more apparent recently. You tend to notice the importance of something more when you lose it, and the recently popular political tactics of “fake news,” “alternative facts,” and “truth isn’t truth,” have certainly focused attention.

But attacking objective reality in order to promote an ideology or preferred belief system is nothing new, even if it has become more obvious and odorous. Sure, everyone has their narrative and philosophy by which they organize their understanding of reality. This narrative influences how we perceive reality, which facts we accept and remember, and which ones we find reasons to dismiss. The question is a matter of degree – how much do we allow facts to influence our beliefs vs our beliefs to influence the perception of facts?

The main virtue of science is that it systematically puts facts above beliefs, and constantly hits beliefs over the head with facts. Other contexts, not so much. And there are times when ideology becomes so dominant that facts become irrelevant. Belief in creationism is one of those contexts – the creationist culture traffics almost entirely in “alternative facts.” People consuming the creationist literature and culture are effectively being gaslighted – presented with an alternate reality as if it is true. There are countless examples of this, but one of my favorites is the creationist claim that there are no transitional fossils. For example:

Contrary to the impression given by evolutionary books and magazines, evidence of transition is rare and limited to variation within kinds. Sensationalistic claims of ‘evolutionary ancestors’ make it into the newspapers; retractions and more sober evaluations of new fossils do not.

Add some outdated or out-of-context quotes, and a complete misinterpretation of evolutionary theory and the fossil record, and you create an alternate reality. The real reality, as I have discussed many times before, is that there are tons of transitional fossils, supporting the fact that life on earth has changed over time through a pattern of common descent. Here is one more to throw onto the pile – the evolution of the turtle.

Turtles are reptiles, but they have some unique features as a group. They have a beaky mouth with no teeth, a top shell made from fused ribs and vertebra, and a bottom shell. They also lack holes above their eyes used for the insertion of jaw muscles. So – common descent predicts that turtles must be related to other reptiles, which means we should find fossils of turtle ancestors that have some turtle features but not all – a transitional turtle.

But keep in mind, evolution is not a ladder but a bush. There will not be a straight line from the last common ancestor between turtles and other reptiles and modern turtles. There will be a bush of diversity, with different features appearing at different times, and even disappearing, and individual groups with relatively primitive features surviving late in the fossil record. As scientists discover a puzzle piece here and there, a confusing picture will emerge in terms of the specific details of evolutionary history. But the big picture will be clear – a transition over evolutionary time from the common ancestor to modern turtles.

So – in 2008 scientists discovered several turtle fossils 220 million years old that only have a shell on the bottom, not the top, and a beaky mouth. They had some but not all of the turtle unique features. Then, in 2015, they discovered a 240 million year old turtle (Pappochelys rosinae) with just the beginnings of a bottom shell. And now, in 2018, scientists report the finding of an older turtle ancestor, 230 million years old (Eorhynchochelys sinensis), that has no shell but still has the beaky mouth. The ribs are starting to expand into the upper shell or carapace, but only partly. These latter two specimens also still have the skull holes of other reptiles, showing their relationship to other modern reptiles.

The presence of the beaky jaw is early for the turtle line, showing that some later turtle species may have lost the beak. We are looking at a diverse group, only one line of which lead to modern turtles.

These fossils do not represent a straight line, as I said, but they show the existence of turtle relatives over evolutionary time progressively acquiring the classic turtle features. These are stunning transitional fossils that absolutely confirm the predictions of the common descent part of evolutionary theory. The fiction that there are few or no transitional fossils is demonstrable nonsense, but that will not stop creationists in their alternative universe from continuing to make this false claim.

A recent survey finds that knowledge of evolution correlates with acceptance of evolution. This was widely reported as suggesting that educating the public about evolution could lead to higher rates of acceptance. Sure, but to be clear the survey does not actually show this. We can also interpret the same data to suggest that acceptance of evolution leads to greater knowledge of it.

This latter interpretation makes sense in light of the fact that there is a tremendous amount of misinformation about evolution from creationist sources. If you are anti-evolution for ideological reasons, you are likely to be highly misinformed about the science because your rely on secondary hostile creationist sources for your information. If you accept the scientific consensus on evolution, you may be more likely to avail yourself of legitimate scientific sources of information.

But probably both factors are at play, and we certainly should strive to improve public education about evolutionary science. It is a complex and subtle science that is poorly understood by the public. The survey also found that 68% of those surveyed failed to demonstrate a basic knowledge of evolutionary theory. And it is certainly easier to spread misinformation about a science the public generally does not understand. In this case knowledge would be a good defense against propaganda.

It is also true that the evidence for the basic fact that life on Earth is the result of evolutionary processes is a scientific home run. It is a phenomenally well-established fact, with no viable competing theory. This often creates the naive belief among those with a solid understanding of evolution and the evidence for it that if they could only explain that evidence to a typical creationist, they will win them over with the massive force of that evidence. That does sometimes happen, but more often evidence is no match for motivated reasoning.

With all that said, I am still going to write about the evidence for evolution in the hopes of nudging public acceptance even a little.

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It’s clear from the fossil record that at times in the history of Earth there have been massive and geologically rapid changes in the assemblage of life. For each such change, however, there is the question of what caused the change. Perhaps the most famous is the K-Pg extinction (Cretacious-Paleogene extinction) about 66 million years ago, known for the near extinction (except for birds) of perhaps the most iconic prehistoric clades, the dinosaurs.

Although there is still some legitimate debate about the relative contribution of various factors, the coup de grace for the non-avian dinosaurs appears to have been a large impact.

Mass extinctions, however, are not the only type of rapid change that needs explaining. There is also the rapid proliferation of new evolutionary groups. The two types of events may, mass extinctions and proliferation of new groups to dominance, may often be linked. It makes sense that a mass extinction will leave many unfilled niches to fill. They leave an evolutionary vacuum, and surviving species get sucked in, rapidly adapting to fill all the voids.

That does not mean, however, that all instances of new groups coming to dominance are in response to a recent mass extinction. There could be other causes, such as climate changes that do not result in mass extinction, or a tipping point in the ecosystem in which previously stable relationship are disrupted. Perhaps a group just hits upon a new ability or strategy that give it a significant advantage over competitors.

That is arguably what happened with humans. When our ancestors discovered fire and cooking, it enabled them to more efficiently extract nutrients from their food. This turned out to be a huge innovation, supporting larger brains and larger populations. With hunting and cooking, humans spread throughout the world, causing probably the greatest ecological disruption by one species in the history of the Earth.

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We tend to think of evolution as something that occurs over very long timescales – thousands and millions of years. While it is true that big changes require a long time, smaller changes must be occurring on shorter timescales. It is those small changes that accumulate into the bigger changes.

However, it’s difficult to perceive and measure the smaller changes that occur over short periods of time. Those small evolutionary changes can also be lost in the background noise of natural variations in a population.

What we need are techniques for observing populations in greater detail, so we can track evolutionary shifts. A 2016 study demonstrates a technique for doing just that. The researchers are taking advantage of the age of big data, in this case genetic data. There are now large genomic data sets available, and researchers can plow through that data to look for the telltale signs of evolutionary change, even over as little as a generation.

The authors of the current study developed a technique in which they count single base pair mutations near alleles (an allele is one copy of a gene – we have two copies or alleles of each gene, one from each parent). When genes are spliced together during recombination (the process by which alleles from each parent are randomly assembled into the genome of an egg or sperm) DNA near each allele will tend to go along for the ride. So that nearby DNA can be used to track the history of the allele itself.

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