Archive for the 'Evolution' Category

Mar 21 2022

Origins of Life From RNA

Published by under Evolution

It is common to observe that one of the greatest unsolved questions of science is how life began. This is a distinct question from how the diversity of the species of living things emerged. It is well established that once life had established a self-replicating system capable of generating some variation, that evolutionary forces would kick in and could, and in fact did, create all life on Earth. But we are a long way from reverse-engineering in any detail how those first organic molecules transitioned from chemistry to life.

This is not a scientific question that will be meaningfully resolved with a single experiment or discovery. Answers will slowly yield over time, as they already are, and it will take decades and perhaps centuries for something approaching a complete picture to emerge. But this progress will be built one study at a time, and Japanese scientists have recently contributing a significant piece to the puzzle.

Researchers at the University of Tokyo published a study in Nature Communications in which they establish that an RNA system can spontaneously evolve complexity. RNA molecules are one of the primary candidates for the first prebiotic molecules that lead to life. RNA is a single-stranded version of DNA, a self-replicating molecule built from four bases forming two pairs. The idea is that life started with the formation of a “replicator” – a molecule that could make copies of itself. RNA is a leading candidate for being the first replicator, but DNA and proteins are also candidates. So far we have not yet been able to connect an “RNA world” with a later world comprised of DNA and proteins. It is this gap that the new research helps fill in.

Continue Reading »

No responses yet

Mar 15 2022

Why Is Life Symmetrical

Published by under Evolution

There is an inordinance of symmetry in living structures. Perhaps this is why humans have an aesthetic predilection for symmetry – but why does life have a probabilistic predilection for symmetry? Of all the possible forms that exist, symmetrical ones are a minority, and yet evolution seems to prefer them. We might hypothesize that there is a functional advantage to symmetry, but this is not obvious, at least not as a general principle. Specific forms likely function better when symmetrical. For example, forces need to balance, when walking or flying, and symmetry achieves that. Imagine a bird with one wing much bigger than the other, or with the wings placed at different positions along the body.

There appears, however, to be symmetry in excess of function, and this symmetry exists as all levels of biology, down to the molecular level. There are exceptions, of course, but symmetry is the rule. Further, some symmetry is baked into evolutionary designs long before any adaptive use. Therefore we need another, non-adaptive, hypothesis to fully explain symmetry. I have long felt that there is probably a mathematical reason, although could not state it in rigorous terms.  The DNA genetic code for a living organism is not a detailed blueprint. Rather it is a set of instructions to be followed. Think of it like a honeycomb beehive. There is no blueprint for the beehive, and no bee knows what it is supposed to look like. The bees follow simple rules over and over again, and the complex honeycomb pattern emerges. That is where the answer must lie.

Researchers have already put a lot of flesh on this skeleton of an idea, and a recent paper adds some further mathematical rigor. The key does lie in the use of simple algorithms to produce the complexity of life. Imagine having to describe to someone else how to create a pattern, such as with tiling a floor. You are not going to tell them where each tile exactly goes. Rather you will explain a technique or pattern that then gets repeated over and over until the space is filled. That, of course, only works if there is a simple pattern. If the ties are laid out in a mosaic creating a complex landscape, then yeah, you may need to describe where each tile goes.

Continue Reading »

No responses yet

Feb 03 2022

Chromosomal Elements Conserved for 600 Million Years

Published by under Evolution

In evolutionary parlance, “conserved” means that some feature has remained relatively unchanged through some period or within a specific clade. Generally features will change over evolutionary time, either through direct selective pressures or genetic drift through random mutations. Therefore, in order for a biological feature to be conserved there must be selective pressure that keeps it from changing. The longer and more tightly that feature is conserved, the more fundamental it must be to biological function. Histones, for example, are proteins that help manage the long strings of DNA in cells – an extremely basic function for all life. Histones are also one of the most conserved proteins in all of biology.

It is therefore highly interesting that researchers recently found that chromosomal elements are highly conserved in virtually all animal groups over 600 million years – which is basically as long as animals have existed. Chromosomes are the organizing units of DNA. Humans, for example, have 23 pairs of chromosomes. Each chromosome contains a number of genes, and humans have about 20,000 functional genes.

Biologists have long known that sequences of genes tend to sort together – they always occur next to each other on the same chromosome, even across species. However, different clades have different numbers of chromosomes and different gene clusters on different chromosomes. Genes, it seems, get shuffled around during evolutionary history. Scientists and the University of Vienna and the University of California were working together to see if they could make more sense out of this chaos, and that’s what they did.

Continue Reading »

No responses yet

Aug 30 2021

Four-Legged Whale Described

In 1985 Michael Denton, arguing against the fact of evolution, made the following observation:

“…to postulate a large number of entirely extinct hypothetical species starting from a small, relatively unspecialized land mammal and leading successively through an otter-like state, seal-like stage, sirenian-like stage and finally to a putative organism which could serve as the ancestor of the modern whales. Even from the hypothetical whale ancestor stage we need to postulate many hypothetical primitive whales to bridge the not inconsiderable gaps which separate the modern filter feeders (baleen whales) and the toothed whales.”
Denton (1985) Evolution: A Theory in Crisis, Adler & Adler Publishers:Chevy Chase, MD. p. 174

In 1992 creationist Duane Gish made an even more bold statement:

“The marine mammals abruptly appear in the fossil record as whales, dolphins, sea-cows, etc. There simply are no transitional forms in the fossil record between the marine mammals and their supposed land mammal ancestors.”
Duane Gish (1992), Evolution: The Challenge of the Fossil Record. Creation-Life Publishers: El Cajon, CA. p. 79

This remains a common strategy for creationists – point to current gaps in the fossil record and then pretend this is a problem for evolutionary theory. The unstated major premise here is that if evolution were true, we would by necessity already possess a fairly complete fossil record for the evolution of every single extant species, or at least (arbitrarily defined) major group. This premise is simply false. We have fossil windows into a process that occurred over 600 million years (if we talk only about multicellular creatures), all over the world, involving an estimated 5 billion species. There are gaps and always will be gaps.

Continue Reading »

No responses yet

Aug 26 2021

Evolution Denial Survey

The idea that all life on Earth is related through a nested hierarchy of branching evolution, occurring over billions of years through entirely natural processes, is one of the biggest ideas ever to emerge from human science. It did not just emerge whole cloth from the brain of Charles Darwin, it had been percolating in the scientific community for decades. Darwin, however, put it all together in one long compelling argument. Alfred Wallace independently came up with essentially the same conclusion, although did not develop it as far as Darwin.

On the Origin of Species was published in 1859, and it quickly won over the scientific community, with natural selection acting on variation becoming the dominant working hypothesis. But that, of course, was not the end of the story, only the beginning. If Darwin’s ideas were wrong, they would have slowly withered from lack of confirming evidence. But they were largely correct, even insightful. The last 162 years of research and observation have confirmed to an extraordinary degree the core ideas that life is related through branching connections, and that natural selection is a primary driving force of evolution. The theory has also evolved quite a bit, and is now a mature and complex scientific discipline sitting on top of mountains of evidence, including fossils, genetics, comparative anatomy, developmental biology, and direct observation. The basic fact of evolution could have been falsified thousands of times over, but it has survived every time – because it is essentially true.

Acceptance of the basic tenets of evolutionary theory, therefore, is a good litmus test for any modern society. Of what, exactly, is another question, but certainly something is going wrong if the population does not accept this overwhelming scientific consensus. The US ranks second from the bottom (only Turkey is worse) in terms of accepting evolutionary theory. Researchers have been tracking the statistics for decades, and now some of the lead researchers in this field have published data from 1985 to 2020 (sorry it’s behind a paywall). There are some interesting details to pull from the numbers.

Continue Reading »

No responses yet

Jul 13 2021

Dogs Understand Humans

Published by under Evolution

Regardless of whether or not you are a cat person or a dog person (I have both as pets, as well as a reptile, and have had birds and fish), there is no denying that dogs are excellent human companions. No other animal known is capable of the same relationship with people. Researchers have been trying to understand the origin of this special relationship, with some interesting results.

First let me review the results of a new study, and then add in some background. The question the researchers are trying to address is this – how much of dog behavior is shared with their wolf ancestors? Specifically, dogs and wolves share a common ancestor between 12,000 and 40,000 years ago. There was likely a lot of interbreeding during this time (as there still is) so it’s probably not possible to declare a clean break. But they are now distinct subpopulations. Dogs show an incredible ability to understand their human companions, even without extensive training. The question is – how much of this ability is innate vs trained and how much is shared with wolves?

The study compared 44 dog pups with 37 wolf pups right after birth. The wolf pups were raised by humans, with maximal human contact after just a few days from birth. The dog pups were kept with their litters with minimal human contact. They were assessed at 5-18 weeks old. The authors found that the dog pups were able to follow human direction (such as pointing and other cues) toward a food reward. The wolf pups did no better than chance, indicating no benefit from the human cues. Dog pups were also able to respond to novel cues, like playing a block next to the target bowl. Further, when a stranger was introduced the dog pups came up and interacted with them (wagging their tail and licking their face) while the wolf pups when into a corner and hid.

None of this is surprising, and it is all consistent with prior research. But it does help confirm that these stark differences are innate, and not learned. So what’s going on?

Continue Reading »

No responses yet

Jun 08 2021

Evolutionary Compromises

Published by under Evolution,Skepticism

Evolution if one of the most fascinating scientific phenomena because it is so complex and operates over such varying and long timescales. It’s a real challenge to wrap one’s head around. There is therefore a tendency to settle on overly  simplistic evolutionary narratives. This is not a criticism, we all do this in an attempt to grapple with evolutionary thinking. The challenge is to recognize this fact, and be open to a deeper, more complex and nuanced understanding of evolutionary processes. It’s a great example of what should be a general intellectual posture – recognize the limits of our current understanding (wherever that may be on the spectrum) and not only be open to, but seek out new information and concepts to keep incrementally pushing our understanding forward.

In that spirit, here is a study on the evolution of broad-horned flour-beetles that illustrates some of evolution’s complexity. The male broad-horned has exaggeratedly large mandibles, which is uses to compete with other males for mating access to females. This is an example of sexual selection, when a feature specifically increases mating success but is not necessarily broadly adaptable. The go-to example of this is the peacock’s tail feathers – a garish display meant to attract females, but an evolutionary burden in many other aspects. This sets up an evolutionary tug-of-war, where a feature may be advantageous in one respect but disadvantageous in another. Evolutionary processes are fairly efficient at balancing such conflicting forces.

As an aside, the balances tend to be only metastable. They can alter with changes in the environment or behavior. Even different individuals within a species can adopt different survival strategies that result in a different balance of traits. If a population within a species does this it may even eventually lead to a speciation event. For example, it has been documented that within some primate species dominant males will have access to females due to their alpha status, while others gain access by currying favor with the alpha, and still others gain access by gaining favor with the females and sneaking behind the alpha’s back. Still others may act as a “wing man” to a close kin, promoting their genes into the next generation by proxy. The lesson here is – no one strategy captures the wide diversity of behavior even within a single species.

Continue Reading »

No responses yet

Apr 29 2021

Evolution of Multicellularity

Published by under Evolution

When studying the history of life evolutionary biologists and paleontologists have no choice but to look where the light is good. There are fossil windows into specific times and places in the past, and through these we glimpse a moment in biological history. We string these moments together to map out the past, but we know there are a lot of missing pieces.

One relatively dark passage in the history of life is the evolution of multicellularity. Beginning about 541 million years ago (mya) we can see the beginning of the Cambrian explosion – the appearance of a vast diversity of multicellular life. But this “explosion” was only partly due to rapid adaptive radiation, it is also an artifact of the evolution of hard parts that can fossilize. That development turned on the lights. The earliest known single-celled organisms are 3.77 billion years old, so we have a 3 billion year time span during which a lot must have happened. We know from changes in the atmosphere that cells evolved that could use sunlight to produce oxygen, and other critters evolved to eat them.

Continue Reading »

No responses yet

Apr 05 2021

The Great Oxygenation Events

Published by under Evolution

The deep history of the Earth is fascinating, and while we have learned much about the distant past there are still many puzzle pieces missing. A new study tweaks our understanding of one of the biggest events in Earth’s history – the Great Oxygenation Event, and also helps better align the other big events in the past.

The Earth as we know it formed about 4.5 billion years ago. Earth is actually Earth 2.0 – the proto-Earth was hit by a Mars-sized object, forming both the current Earth and the Moon. The Earth was fairly molten at this time, still hot from all the impacts, but over the next millions of years the surface cooled, stable pools of liquid water formed on the surface, and it had a stable atmosphere of mostly nitrogen. In this environment life evolved. We are not exactly sure when, but probably by 3.5 billion years ago. There is good evidence for cyanobacteria by 2.9 billion years ago. These critters are important, because they make food from sunlight and produce oxygen as a waste byproduct. For millions of years oceans full of cyanobacteria cranked out oxygen, which built up in the atmosphere.

This is where the new study comes in –  it explores exactly when oxygen built up to high levels. The current atmosphere is about 78% nitrogen, 21% oxygen, 0.04% carbon dioxide, and trace amounts of methane and other gases.  Prior to about 2.45 billion years ago there was essentially zero oxygen in the atmosphere. Between 2.45 and 1.85 billion years ago oxygen built up slowly in the atmosphere, up to 3-5%, but was also mostly absorbed by the oceans and seabed rock. This is the Great Oxygenation Event, still little oxygen by today’s standard, but enough to usher in a major change in the chemistry of earth. From 1.85 to 0.85 billion years ago oxygen had saturated the ocean and so now spread to the land where it was further absorbed into rocks and minerals. During this time atmospheric O2 levels were pretty stable at 3-5%. But then, starting 0.85 billion years ago the surface of the Earth had absorbed all the oxygen it could (the oxygen sinks were full) and so O2 started building up in the atmosphere significantly, peaking about 400 million years ago at over 30% and then settling down to the current 21%. Oxygen levels are now slowly and steadily decreasing.

Continue Reading »

No responses yet

Mar 04 2021

Cuttlefish Pass Marshmallow Test

Cuttlefish are amazing little critters. They are cephalopods (along with octopus, quid, and nautilus), they see polarized light and can use that to change their skin color to match their surroundings. They have eight arms and two tentacles, all with suckers, that they use to capture prey. They, like other cephalopods, are also pretty smart. And now, apparently, they are also in the very elite club of animals who can pass the marshmallow test.

The “marshmallow test” is a psychological experiment of the ability to delay gratification. The basic study involves putting a treat (like a marshmallow, but it can be anything) in front of a young child and telling them they can have it now, or they can wait until the adult returns at which time they will be given two treats. The question is – how long can children hold out in order to double their treats? The interesting part of this research paradigm are all the associated factors. Older children can hold out longer than younger children. The greater the reward, the more children can wait for it. Children who find ways to distract themselves can hold out longer.

For decades the test and all its variations was interpreted as a measure of executive function, and correlated with all sorts of things like later academic and economic success. However, more recent studies have found (unsurprisingly) that there can be confounding factors not previously recognized. For example, children from insecure environments have not reason to trust that adults will return with more treats and therefore take what is in front of them. This could be seen as an adaptive response to their environment.

Continue Reading »

No responses yet

Next »