Archive for the 'Evolution' Category

Oct 26 2018

Laser Scanning Archaeopteryx

Published by under Evolution

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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Oct 04 2018

Evolution Under Attack

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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Sep 24 2018

Oldest Animal Identified

Published by under Evolution

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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Aug 24 2018

Transitional Turtles

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.

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May 11 2018

The Evolution of Baleen Whales

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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Apr 17 2018

The Rise of the Dinosaurs

Published by under Evolution

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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Apr 05 2018

Humans Are Still Evolving

Published by under Evolution

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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Nov 27 2017

Renewed Antiscience Legislation

The fight over science in public education continues, and if anything picked up considerably in 2017. Earlier in the year Nature reported on various state laws designed to water down science education or allow for equal time to be given to unscientific views. They report:

Florida’s legislature approved a bill on 5 May that would enable residents to challenge what educators teach students. And two other states have already approved non-binding legislation this year urging teachers to embrace ‘academic freedom’ and present the full spectrum of views on evolution and climate change. This would give educators license to treat evolution and intelligent design as equally valid theories, or to present climate change as scientifically contentious.

New Mexico took a more direct approach – simply scrubbing “controversial” ideas from the state’s science standards. The standards no longer mention “evolution”, human contributions to climate change, or even mentioning the age of the Earth. This is not a back door approach – this is straight-up censorship of accepted scientific facts.

A new Florida bill also includes this problematic language:

Controversial theories and concepts must be taught in a factual, objective, and balanced manner.

This is part of the latest strategy. First, don’t mention any one theory (like evolution) by name. That is likely to trigger a constitutional challenge. Second, make the bill sound like it is promoting something positive, like academic freedom, democracy, or just being fair and balanced.

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Nov 09 2017

Evolution Caught in the Act

Published by under Evolution

The hypothesis that life on Earth as it is currently found is the result of biological evolution from a common ancestor over billions of years is supported by such a mountain of evidence that it can be treated as an established scientific fact. Further, it is now a fundamental organizing theory of biology.

This, of course, does not stop ideologically motivated denial. There are those who have been systematically misinformed about the evidence, and the nature of science itself. What they think they know about evolutionary theory they learned from secondary hostile sources. One of the common lies they are repeatedly told is that there are no transitional fossils.

This claim amazes me still, because the evidence is so easily accessible. Lists of transitional fossils are easy to find. One of my favorite examples is the evolution of birds, because the morphological transition from theropod dinosaurs to modern birds was so dramatic.

I also have to point out that this evidence represents a successful prediction of evolutionary theory. When Darwin first published his theory the fossil record was scant. Enough fossils had been discovered for scientists to see that life was dramatically changing over geological time, but the puzzle was mostly empty. There were not enough specimens to see connections between major groups. Evolutionary theory predicts that such connections would be found – and they were, and they continue to be.

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Jul 18 2017

More on Junk DNA

Published by under Evolution

Junk-VennJunk DNA, put simply, is those parts of the genome (human or otherwise) that have no known function. The human genome has about 19,000 genes. A gene is essentially a sequence of base pairs that code for a protein – there are four difference bases with each triplet being a “word” that either codes for an amino acid or tells the process of transcribing the protein to stop.

Even within genes there are noncoding regions, called introns, which have to be removed from the RNA so that the coding regions can be joined together. Between the genes there are also vast non-coding regions. Some of this non-coding DNA is regulatory and structural – it helps regulate when and how much specific genes are transcribed into proteins.

The burning question is, how much of the non-coding regions between the genes serves any function and how much is completely unnecessary, or “junk”? This is an important question for understanding genetics, but also has implication for creationists. Creationists don’t like the concept of junk DNA because it strongly implies an evolutionary history. Why would a designer sloppily insert so much unneeded junk into our pristine genome? Why are genes clogged with non-coding regions that need to be removed? So they claim that all DNA has function, we just don’t know what it is.

ID proponent Stephen Meyer, for example, said:

“For example, we predicted very early on that the junk DNA was not junk. We did that on the basis of an ID perspective. “

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