Last week I wrote about the de-extinction of the dire wolf by a company, Colossal Biosciences. What they did was pretty amazing – sequence ancient dire wolf DNA and use that as a template to make 20 changes to 14 genes in the gray wolf genome via CRISPR. They focused on the genetic changes they thought would have the biggest morphological effect, so that the resulting pups would look as much as possible like the dire wolves of old.

This achievement, however, is somewhat tainted by overhyping what was actually achieved, by the company and many media outlets. Although the pushback began immediately, and there is plenty of reporting about the fact that these are not exactly dire wolves (as I pointed out myself). I do think we should not fall into the pattern of focusing on the controversy and the negative and missing the fact that this is a genuinely amazing scientific accomplishment. It is easy to become blase about such things. Sometimes it’s hard to know in reporting what the optimal balance is between the positive and the negative, and as skeptics we definitely can tend toward the negative.

I feel the same way, for example, about artificial intelligence. Some of my skeptical colleagues have taken the approach that AI is mostly hype, and focusing on what the recent crop of AI apps are not (they are not sentient, they are not AGI), rather than what they are. In both cases I think it’s important to remember that science and pseudoscience are a continuum, and just because something is being overhyped does not mean it gets tossed in the pseudoscience bucket. That is just another form of bias. Sometimes that amounts to substituting cynicism for more nuanced skepticism.

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The evolution of the human brain is a fascinating subject. The brain is arguably the most complex structure in the known (to us) universe, and is the feature that makes humanity unique and has allowed us to dominate (for good or ill) the fate of this planet. But of course we are but a twig on a vast evolutionary tree, replete with complex brains. From a human-centric perspective, the closer groups are to humans evolutionarily, the more complex their brains (generally speaking). Apes are the most “encephalized” among primates, as are the primates among mammals, and the mammals among vertebrates. This makes evolutionary sense – that the biggest and most complex brains would evolve from the group with the biggest and most complex brains.

But this evolutionary perspective can be tricky. We can’t confuse looking back through evolutionary time with looking across the landscape of extant species. Any species alive today has just as much evolutionary history behind them as humans. Their brains did not stop evolving once their branch split off from the one that lead to humans. There are therefore some groups which have complex brains because they are evolutionarily close to humans, and their brains have a lot of homology with humans. But there are also other groups that have complex brains because they evolved them completely independently, after their group split from ours. Cetaceans such as whales and dolphins come to mind. They have big brains, but their brains are organized somewhat differently from primates.

Another group that is often considered to be highly intelligent, independent from primates, is birds. Birds are still vertebrates, and in fact they are amniotes, the group that contains reptiles, birds, and mammals. It is still an open question as to exactly how much of the human brain architecture was present at the last common ancestor of all amniotes (and is therefore homologous) and how much evolved later independently. To explore this question we need to look at not only the anatomy of brains and the networks within them, but brain cell types and their genetic origins. For example, even structures that currently look very different can retain evidence of common ancestry if they are built with the same genes. Or – structures that look similar may be built with different genes, and are therefore evolutionarily independent, or analogous.

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Humans identify and call each other by specific names. So far this advanced cognitive behavior has only been identified in a few other species, dolphins, elephants, and some parrots. Interestingly, it has never been documented in our closest relatives, non-human primates – that is, until now. A recent study finds that marmoset monkeys have unique calls, “phee-calls”, that they use to identify specific individual members of their group. The study also found that within a group of marmosets, all members use the same name to refer to the same individual, so they are learning the names from each other. Also interesting, different families of marmosets use different kinds of sounds in their names, as if each family has their own dialect.

In these behaviors we can see the roots of language and culture. It is not surprising that we see these roots in our close relatives. It is perhaps more surprising that we don’t see it more in the very closest relatives, like chimps and gorillas. What this implies is that these sorts of high-level behaviors, learning names for specific individuals in your group, is not merely a consequence of neurological develop. You need something else. There needs to be an evolutionary pressure.

That pressure is likely living in an environment and situation where families members are likely to be out of visual contact of each other. Part of this is the ability to communicate at long enough distance that will put individuals out of visual contact. For example, elephants can communicate over miles. Dolphins often swim in murky water with low visibility. Parrots and marmosets live in dense jungle. Of course, you need to have that evolutionary pressure and the neurological sophistication for the behavior – the potential and the need have to align.

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Surveys are always tricky because how you ask a question can have a dramatic impact on how people answer. But it is useful to ask the exact same question over a long period of time, because that can indicate how public attitudes are changing. This is one of the benefits of Gallup, which was founded in 1935 and is dedicated to high quality and representative polls. They have been asking the following question since 1982:

“Which of the following statements comes closest to your views on the origin and development of human beings — 1) Human beings have developed over millions of years from less advanced forms of life, but God guided this process, 2) Human beings have developed over millions of years from less advanced forms of life, but God had no part in this process, 3) God created human beings pretty much in their present form at one time within the last 10,000 years or so?”

It’s an imperfect way to ask these questions – the “less advanced life forms” is not really accurate, and the questions all assume or imply the existence of God. But by asking “which one comes closest” it does capture the essence of this issue. Option 3 is basically young-Earth creationism, option 2 is pure scientific evolution, and option 1 is everything else. From my view as a skeptic and science communicator, the results of this survey are dismal but also encouraging. At the start of the survey in 1982 the numbers were stark: 1 – 38%, 2 – 9%, and 3 – 44% (the rest undecided). Therefore 82% of Americans endorsed some form of creationism, and only 9% were willing to say that life resulted from evolution acting all by itself.

The most recent poll from this perspective is encouraging: 1 – 34%, 2 – 24%, and 3 – 37%. There is still a plurality endorsing young-Earth creationism, but those endorsing scientific evolution is up to 24%. These numbers also track with surveys on religion in the US. The young-Earth creationism figure is about the same as the number of Americans who identify as some kind of evangelical (something between 30 and 39%). Admittedly, this number can be squirrely depending on how you define “evangelical” and ask the question, but broadly defined, the numbers track. The scientific evolution numbers also track with those who answer on surveys that they are religiously unaffiliated, also now in the 20’s.

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Evolution deniers (I know there is a spectrum, but generally speaking) are terrible scientists and logicians. The obvious reason is because they are committing the primary mortal sin of pseudoscience – working backwards from a desired conclusion rather than following evidence and logic wherever it leads. They therefore clasp onto arguments that are fatally flawed because they feel they can use them to support their position. One could literally write a book using bad creationist arguments to demonstrate every type of poor reasoning and pseudoscience (I should know).

A classic example is an argument mainly promoted as part of so-called “intelligent design”, which is just evolution denial desperately seeking academic respectability (and failing). The argument goes that natural selection cannot increase information, only reduce it. It does not explain the origin of complex information. For example:

A big obstacle for evolutionary belief is this: What mechanism could possibly have added all the extra information required to transform a one-celled creature progressively into pelicans, palm trees, and people? Natural selection alone can’t do it—selection involves getting rid of information. A group of creatures might become more adapted to the cold, for example, by the elimination of those which don’t carry the genetic information to make thick fur. But that doesn’t explain the origin of the information to make thick fur.

I am an educator, so I can forgive asking a naive question. Asking it in a public forum in order to defend a specific position is more dodgy, but if it were done in good faith, that could still propel public understanding forward. But evolution deniers continue to ask the same questions over and over, even after they have been definitively answered by countless experts. That demonstrates bad faith. They know the answer. They cannot respond to the answer. So they pretend it doesn’t exist, or when confronted directly, respond with the equivalent of, “Hey, look over there.”

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In 1931 a fossil lizard was recovered from the Italian Alps, believed to be a 280 million year old specimen. The fossil was also rare in that it appeared to have some preserved soft tissue. It was given the species designation Tridentinosaurus antiquus and was thought to be part of the Protorosauria group.

A recent detailed analysis of the specimen, hoping to learn more about the soft tissue elements of the fossil, revealed something unexpected. The fossil is a fake (at least mostly). What appears to have happened is that a real fossil which was poorly preserved was “enhanced” to make it more valuable. There are real fossilized femur bones and some bony scales on what was the back of the lizard. But the overall specimen was poorly preserved and of not much value. What the forger did was carve out the outline of the lizard around the preserved bones and then paint it black to make it stand out, giving the appearance of carbonized soft tissue.

How did such a fake go undetected for 93 years? Many factors contributed to this delay. First, there were real bones in the specimen and it was taken from an actual fossil deposit. Initial evaluation did reveal some kind of lacquer on the specimen, but this was common practice at the time as a way of preserving the fossils, so did not raise any red flags. Also, characterization of the nature of the black material required UV photography and microscopic examination using technology not available at the time. This doesn’t mean they couldn’t have revealed it as a fake back then, but it is certainly much easier now.

It also helps to understand how fossils are typically handled. Fossils are treated as rare and precious items. They are typically examined with non-destructive techniques. It is also common for casts to be made and photographs taken, with the original fossils then catalogued and stored away for safety. Not every fossil has a detailed examination before being put away in a museum drawer. There simply aren’t the resources for that.

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Have you heard of Cope’s Rule or Foster’s Rule? American paleontologist Edward Drinker Cope first noticed a trend in the fossil record that certain animal lineages tend to get bigger over evolutionary time. Most famously this was noticed in the horse lineage, beginning with small dog-sized species and ending with the modern horse. Bristol Foster noticed a similar phenomenon specific to islands – populations that find their way to islands tend to either increase or decrease in size over time, depending on the availability of resources. This may also be called island dwarfism or gigantism (or insular dwarfism or gigantism).

When both of these things happen in the same place there can be some interesting results. On the island of Flores a human lineage, Homo floresiensis (the Hobbit species) experienced island dwarfism, while the local rats experienced island gigantism. The result were people living with rats the relative size of large dogs.

Based on these observations, two questions emerge. The first (and always important and not to be skipped) is – are these trends actually true or are the initial observations just quirks or hyperactive pattern recognition. For example, with horses, there are many horse lineages and not all of them got bigger over time. Is this just cherry-picking to notice the one lineage that survived today as modern horses? If some lineages are getting bigger and some are getting smaller, is this just random evolutionary change without necessarily any specific trend? I believe this question has been answered and the consensus is that these trends are real, although more complicated than first observed.

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The largest and heaviest animal to ever live on the Earth, as far as we know, is the blue whale, which is extant today. The blue whale is larger than any dinosaur, even the giant sauropods. The average weight of a blue whale is 160 tons, with the largest specimen being 190 tons, and 110′ 17″ (33.58m) long. The largest sauropod, Argentinosaurus, weighed up to 110 tons. The reason the largest whales are bigger than the largest dinosaurs is simple – whales swim in the ocean, so they have buoyancy to help carry their incredible heft. The ancestors of whales were land mammal of modest size. It was only when they adapted to the water that they grew very large, and the age of gigantism among whales started about 4.5 million years ago.

At least that is what we thought from existing evidence. That is one of the interesting things about paleontology – a single specimen can upend our phylogenetic charts, the history of what evolved into what and when. Essentially we have scattered puzzle pieces that we try to fit together into a branching tree of evolutionary relationships. One specimen that fits outside of the branches of this tree forces scientists to redraw some of the lines, or add new ones.

That is what has happened with a new extinct whale species, discovered in Peru in 2010 but only recently described in detail. The species is appropriately named Perucetus colossus, and it is a whopper. Scientists estimate the weight at 85 to 320 tonnes, depending on assumptions about soft tissue like organs and blubber. If we take the middle of that range, 180 tonnes, that puts it at the upper range for blue whales. If we assume this is an average specimen (statistically likely but not a guarantee) then its size range may exceed that of the blue whale. Perucetus is not, however, longer than the blue whale, it’s a little shorter. But it’s bones are a lot heavier, they are denser and overgrown, which is an adaption found in other shallow water mammals. It’s the heavy bones that makes it potentially heavier than the blue whale, and regardless, this species has the heaviest skeleton known.

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Researchers report a 3D scan of the oldest vertebrate fossil brain yet discovered – in the head of a 319 million year old ray-finned fish. The specimen was actually found a hundred years ago in a coal mine in England, and has been sitting in a museum draw after it was initially described. It is a skull bone only, and the only specimen of this species (Coccocephalus wildi). New technology now allows us to scan the fossil, peering inside to see the fossilized soft tissue of the brain and cranial nerves. Of course, such a specimen will change the way we view the evolution of the vertebrate brain.

As a point of interest, it is not uncommon for paleontologists to make discoveries in museum drawers. Often field work yields many more specimens than can be carefully examined. One summer in the field can haul in a cache that would take many years to properly prepare, reconstruct, and examine. Many specimens therefore sit in drawers without being fully examined. Perhaps they were misidentified at the time, or something interesting about them was missed. It’s also common for statistical examination to be done on vast collections of specimens.

There is also the fact that now we have new and better technology for examining specimens, including non-destructive techniques and scans like CT scans (use in this case) that can look inside specimens in a way not possible before. In a way it is good that there are many neglected specimens, preserved for our current technology to examine.

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Our ability to detect, amplify, and sequence tiny amount of DNA has lead to a scientific revolution. We can now take a small sample of water from a lake, and by analyzing the environmental DNA in that water determine all of the things that live in the lake. This is an amazingly powerful tool. My favorite application of this technique was to demonstrate the absence of DNA in Loch Ness from any giant reptile or aquatic dinosaur. So-called eDNA is perhaps the most powerful evidence of a negative, the absence of a creature in an environment – you can’t hide your eDNA.

The ultimate limiting factor on eDNA is how long such DNA will survive. DNA has a half-life, it spontaneously degrades and sheds information, until it is no longer useful for sequencing. Previously scientists extracted DNA from ice cores in Greenland, and were able to sequence DNA up to 800,000 years old. The oldest DNA ever recovered was probably 1.1-1.2 million years old. Based on this  scientists estimated that the ultimate lifespan of usable DNA was about 1 million years. This put the final nail in the coffin of any dreams of a Jurassic park. Non-avian dinosaurs died out 65 million years ago, so none of their DNA should still be left on Earth (the closest we can get is related DNA in birds). But no T. rex DNA in amber.

According to a new assay in the most norther region of Greenland, however, we have to push back the estimate of how long DNA can survive to at least 2 million years. That is a significant increase (but still a long way from T. rex). The site is Kap København Formation located in Peary Land in north Greenland. This is now a barren frozen desert. There are also very few macrofossils here, mostly from a boreal forest and insects, with the only vertebrate being a hare’s tooth. Conditions there are apparently not conducive to fossilization. We do know that 2 million years ago Greenland was much warmer, about 10 degrees C warmer than present. So there is no reason it should not have been teeming with life.

The new analysis of eDNA finds that, in fact, it was. They found DNA from hares, but also other rodents, reindeer, geese, and mastodons. They also found DNA from poplars, birch trees, and thuja trees (a type of coniferous tree), as well as a rich assortment of bushes, herbs, and other flora. Basically this was a mixed forest with a rich ecosystem. In addition they found marine species including horseshoe crab and green algae, confirming the warmer climate.

This ancient eDNA gives us a much more complete picture of the ecosystem than was provided by macrofossils alone. But perhaps more importantly – it demonstrates that eDNA can survive for up to two million years, doubling the previous estimate. The researchers speculate that minerals in the soil bound to the DNA and stabilized it, slowing its degradation. DNA is negatively charged. This property is used to separate out chunks of DNA in a sample by size. You apply a magnetic field which attracts the DNA pieces, which move through a gel at a range proportional to their size. In this case the negatively charged DNA bound to positively charged minerals in the soil. I guess this is the DNA version of fossilization.

The question is – in such environments where DNA is stabilized by binding to minerals, how much is the degradation process slowed down, and therefore how long can DNA survive? DNA breaks down due to “microbial enzymatic activity, mechanical shearing and spontaneous chemical reactions such as hydrolysis and oxidation.” DNA breaks down faster with warmer temperature, so the fact that this DNA remained frozen for so long is crucial. But freezing alone was not enough, which is why scientists think that binding to minerals also played a role.

They measured the “thermal age” of the DNA – if the DNA were at a constant temperature of 10 degrees C how long would it have taken to degrade to its current state – at 2.7 thousand years, 741 times less than its actual age of 2 million years. Therefore it degraded 741 times slower then exposed DNA at 10 degrees C. The average temperature at the site is -17 degrees C. They further found that the DNA was bound mostly to clay minerals, and specifically smectite (and to a lesser degree, quartz).

Perhaps this is the limit of DNA survival – although we thought the previous record of 1.1-1.2 million years was the limit. It is possible there may be environmental conditions elsewhere in the world that could slow DNA degradation even further. Slow DNA degradation by a factor of 30 or so beyond the Kap København Formation and we are getting into the time of dinosaurs. This is probably unlikely. Constant freezing temperatures are required, in addition to geological stability and optimal soil conditions. But I don’t think we can say now that it is impossible, just highly unlikely. I did not see any estimate in the study about the ultimate upper limit of DNA lifespan, but I suspect we will see such analyses based on this latest information.

The best evidence, however, will come from simply looking in new locations for eDNA, especially those that likely have the optimal conditions for maximal DNA longevity. But for now, being able to reconstruct ecosystems from 2 million years ago is still pretty cool.