Tag Archives: theory of evolution

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Evolution in a lab flask: scientists witness virus speciating into two distinct species

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Credit: Pixabay

One of the backbone’s of Charles Darwin’s Theory of Evolution is speciation — the branching of a species into two incipient species. Indirect evidence like genome analysis, fossils or plant and animal population surveys support speciation. However, the process is very slow requiring many breeding cycles, prompting some to question evolution. ‘How can a fish turn into an ape?! Prove it!” is a rhetorical question I often see on facebook and forums across the web. Well, here’s something to show them: a virus speciating in a lab flash, all under the watchful eye of researchers at University of California San Diego.

Justin Meyer, an assistant professor of biology at UC San Diego and lead author of the new study, began his experiments while still a doctoral student at Michigan State University. He and colleagues started breeding  a “bacteriophage lambda”, which is a virus capable of infecting E. coli bacteria using two receptors. These are molecules that line the outside walls of the cell which, like holes for grappling, are used by the virus to attach itself to the infected cell.

What the researchers did was introduce two different types of bacteria to the virus, each with its different kinds of receptors. It didn’t take too long for the virus to branch into two distinct species, each specialized to handle the different cell receptors, as reported in the paper.

Molecular models of the two receptors the virus evolved to specialize on. Credit: Justin Meyer, UC San Diego

Molecular models of the two receptors the virus evolved to specialize on. Credit: Justin Meyer, UC San Diego

“The virus we started the experiment with, the one with the nondiscriminatory appetite, went extinct. During the process of speciation, it was replaced by its more evolved descendants with a more refined palette,” explained Meyer.

Per Darwin’s natural selection, the ‘jack-of-all-trades virus’ went extinct and only those individuals that specialized in attacking the new cell types passed on their genes. “The survival of the fittest led to the emergence of two new specialized viruses,” Meyer explained.

“With these experiments, no one can doubt whether speciation occurs,” Meyer added. “More importantly, we now have an experimental system to test many previously untestable ideas about the process.”

It’s worth mentioning that this isn’t the first time speciation has been observed in real time. For instance, scientists proved speciation occurs in fruit flies, which are far more complex organisms than viruses. If you’d like to learn more about speciation and the various case studies that prove it, check this link.

 

 

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Theory of Evolution might be in for an overhaul. Top biologists discuss much needed update

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Credit: YouTube

The theory of evolution is the best biological framework that explains how all life on the planet got to where it is today. It has not be proven wrong once, but that doesn’t mean it’s perfect. In the past decade alone, accelerated by the immense progress made in genomic sequencing and big data analysis, scientists have come to understand that there’s more depth to evolution. As such, some are suggesting the Theory of Evolution should be updated.

Earlier this month, some of the top biologists in the field met in London for an event hosted by The Royal Society. The main subject of the evening were recent developments in biology that “have produced calls for revision of the standard theory of evolution.”

Wait a minute. Does that mean there’s something wrong with the theory of evolution? Not at all. It’s just that, in light of what we now know about what drives evolution and the biological evolutionary mechanisms, we can come up with a better definition of evolution.

The theory of evolution is the brainchild of Charles Darwin’s Theory of Natural Selection and Gregor Mendel’s Mendelian Inheritance, which underpins classic genetics. Natural Selection leads to evolutionary change when individuals with certain characteristics have a greater survival or reproductive rate than other individuals in a population and pass on these inheritable genetic characteristics to their offspring.

During his time, however, Darwin was not aware of genes and genetic drift. This is where Mendelian Inheritance comes in, which recognizes that characteristics are inherited as discrete entities called genes and that random genetic drift may be as important as natural selection itself.

When the two landmark theories are combined, you get the modern evolutionary synthesis which basically postulates that speciation is (usually) due to the gradual accumulation of small genetic changes. In other words, macroevolution is simply a lot of microevolution.

Since it was first proposed in the 1940s, the modern synthesis has been the go-to model for the theory of evolution. But a lot has happened since, and the modern synthesis might be in for an overhaul.

Post-Darwin world

At the event in London, Eva Jablonka, a biologist at Tel Aviv University, argues that a complete, contemporary theory of evolution needs to take account the notion of heredity absent genes. What Jablonka was referring to was ‘epigenetics’ — heritable changes in gene expression. For instance, while there are thousands of genes coded by our DNA, not all are active. Genes are regularly switched ‘on’ or ‘off’ during our lifetimes through chemical changes called methylation. This can happen for a lot of reasons, and it all depends on the environment. For instance, smoking modifies 7,000 genes.

When the cell divides, the methylation is present in the new cell as well. Moreover, changes in genes that were active early in life, but switched off later in adulthood, can be transmitted to offspring in certain cases.

One textbook example is the case of the Dutch Hunger Winter, which lasted from the start of November 1944 to the late spring of 1945. During this time, West Holland was still under German control. A German blockade resulted in a catastrophic drop in the availability of food to the Dutch population. At one point the population was try­ing to survive on only about 30 percent of the normal daily calorie intake. They ate anything they could get their hands on; grass, tulip bulbs, book covers. By the time Holland was liberated in May 1945, some 20,000 people had died of starvation.

Mothers well fed around the time of conception, but malnourished only for the last few months of pregnancy gave birth to smaller babies, on average. On the other hand, mothers who were malnourished for the first three months of pregnancy, but were then well fed (the blockade was lifted) were likely to birth normal-size babies. The fetus “caught up” in body weight, so to speak. That’s pretty straightforward so far, but in the course of decades, doctors they found those who were born small stayed small all their lives, with lower obesity rates than the general popula­tion, despite having access to as much food as they wanted. That’s not all. The children of the mothers who had been malnourished only early in their pregnancies had higher obesity rates than normal. Then, some of the same effects were observed, to a lesser degree, in the children of those who had been born in those troubled time, that is to say, the grandchildren of the malnourished mothers.

Remarkably, Holocaust survivors also passed down stress to their offspring.

Epigenetics does not contradict Natural Selection. Carl Zimmer quotes Jablonka for Quanta as saying “epigenetic differences could determine which organisms survived long enough to reproduce.”

Another factor that’s not included in modern synthesis but seems to drive evolution is the so-called ‘plasticity’. It’s plasticity that helps explain the weird but startling diversity in Homo fossils. These fossils include the remains of our ancestors who lived 1.5 to 2.2 million years ago. Most can be pinpointed to the same species, but in some cases you get some fragments that look like they come from two separate species. Some were tall, others short. Some have big brains, some have smaller brains, despite being essentially the same species.

At a meeting in London,  Susan Antón, a paleoanthropologist at New York University, argued that Africa’s went through periods of wild and dramatic swings. She says that this plasticity is highly responsive and time sensitive. For instance, the quality of food a pregnant woman eats can influence the size and health of the baby, and this influence can last well into adulthood.

Why farm basically ‘nothing’ when you can hunt or gather? It doesn’t make sense per standard modern synthesis.

Then there’s the case of the advent of farming some 13,000 years ago. When viewed through an evolutionary lens, persistent behaviors have to be explained by means of selection. For instance, we’re still farming because it gave us an evolutionary edge as it increased the available food resources. That’s pretty straightforward but the first human farmers had to go through a lot of pain and, likely, a negative return of investment. The first crops were woefully inadequate since they were not yet adapted. Just look at what fruits and veggies used to look like before we domesticated them.

Melinda Zeder, an archaeologist at the Smithsonian Institution, says there’s no evolutionary advantage per the modern synthesis that can explain this seemingly masochistic resilience to keep experimenting with crops. “You don’t get the immediate gratification of grabbing some food and putting it in your mouth,” Zeder told Zimmer, who was presented at the event in London.

“Zeder argues that there’s a better way of thinking about this transition. Humans are not passive zombies trying to survive in a fixed environment. They are creative thinkers who can change the environment itself. And in the process, they can steer evolution in a new direction. Scientists call this process niche construction, and many species do it. The classic case is a beaver. It cuts down trees and makes a dam, creating a pond. In this new environment, some species of plants and animals will do better than others. And they will adapt to their environment in new ways. That’s true not just for the plants and animals that live around a beaver pond, but for the beaver itself,” Zimmer wrote.

The extended evolutionary synthesis, as described in the Proceedings of the Royal Society Battempts to include these new trains of thought into the theory of evolution. Critics abound so many other such meetings will likely have to be held before the theory of evolution can itself stand by its own definition: adapt, respond, pass on — evolve.

One of the fossils in question - Dickinsonia. Currently, scientists are positive this was a sea-dwelling invertebrate, but recent findings suggest it may actually have been a land-dwelling lichen. (c) Greg Retallack

Controversial study challenges tree of life and claims complex life first originated on land

Professor Gregory Retallack of  University of Oregon has launched a highly controversial claim that stirred the scientific community recently, implying that ancient fossils found in South Australia from Ediacaran period, a geological time that preceded the great Cambrian explosion, were actually living being living on land, not water as “common sense” dictates.

One of the fossils in question - Dickinsonia. Currently, scientists are positive this was a sea-dwelling invertebrate, but recent findings suggest it may actually have been a  land-dwelling lichen. (c) Greg Retallack

One of the fossils in question – Dickinsonia. Currently, scientists are positive this was a sea-dwelling invertebrate, but recent findings suggest it may actually have been a land-dwelling lichen. (c) Greg Retallack

The Ediacaran period ended some 540 million years ago, and during these geological times life on Earth was highly primitive, comprised of individual cells organized in colonies at best.  Ediacaran fossils have been thought of as fossil jellyfish, worms and sea pens, however Retallack argues that he has found evidence that these invertebrates actually originated on land – a claim that has severe implications for our understanding of how life evolved on our planet.

“This discovery has implications for the tree of life, because it removes Ediacaran fossils from the ancestry of animals,” says Retallack, who is originally from Australia.

“These fossils have been a first-class scientific mystery,” he posited. “They are the oldest large multicellular fossils. They lived immediately before the Cambrian evolutionary explosion that gave rise to familiar modern groups of animals.”

Using an assortment of high-tech chemical and microscopic technique, including electron microprobe and scanning electron microscope, Retallack claims he has found soils with fossils that are distinguished by a surface called ‘old elephant skin,’ which is best preserved under covering sandstone beds.

“They show variation in chemistry, variation in grain size, and variation in clay minerals that is quite comparable with a modern desert soil,” he says.

“The key evidence for this new view is that the beds immediately below the cover sandstones in which they are preserved were fossil soils,” Mr. Retallack said. “In other words the fossils were covered by sand in life position at the top of the soils in which they grew. In addition, frost features and chemical composition of the fossil soils are evidence that they grew in cold dry soils, like lichens in tundra today, rather than in tropical marine lagoons.”

Bold claims

Moreover, the geologist claims that many  Ediacaran fossils exhibit features that he believes resemble today’s lichens, than marine invertebrates as the current scientific consensus,  and he also says there is evidence the land they were growing on was sometimes frozen.

This means the Ediacaran fossils represent “an independent evolutionary radiation of life on land that preceded by at least 20 million years the Cambrian evolutionary explosion of animals in the sea.”

Mr. Retallack says that elevated chemical weathering by organisms on land may have been necessary to propel the demand of nutrient elements by Cambrian animals, and based on other fossils from the Cambrian period similar to those studied by him from the Ediacaran, the geologists goes as far to say life on land may have been more complex than life in the sea during the Cambrian explosion. If this is true, then Ediacaran fossils represent an independent branch on the tree of life.

Of course, such a controversial theory was followed by a wave of protest, as scientists called for more substantial evidence to back up the claims.

“I’m sorry, I’m not a creationist. I do not believe that the Cambrian animals popped into existence out of the blue at the beginning of the Cambrian,” Dr Jim Gehling of the South Australian Museum comments on the paper, referring to the fact that if the Ediacaran fossils are  not of marine origin, than the whole boom of life from the Cambrian simply came from “nothing”.

“It’s the right of every scientist to put up controversial hypotheses but you really have to have good evidence if you want to set up a new paradigm,” he says.

Tree of life revamp

Many scientists have no doubts concerning the marine ancestry of the Ediacaran fossils, pointing to wave ripples and other features only formed in marine environments.  Retallack tackles back these comments stating these ripple features could have very well come from subsequent  floods or lakes. Regarding Retallack’s chemical analysis that revealed evidence of fossils soils, Gehling believes these are mere contaminants from more recent weathering events of the ancient rock outcrops that the fossils are found in. Present scientific consensus has that animals only crawled onto land 100 million years after the Ediacaran.

“I find Retallack’s observations dubious, and his arguments poor. That this was published by Nature is beyond my understanding,” wrote Martin Brasier, a paleobiologist at the University of Oxford.

Retallack doesn’t seem bothered at all by the fact that his hypothesis warrants a whole revamp of the current life evolution cycle we call tree of life. On his part, life on land before the Cambrian evolution makes perfect sense as it would have changed the soil chemistry, he says, allowing the release of mineral ions into the soil water.

“Some of this soil water runs off into streams end eventually the ocean,” says Retallack. “That is going to be the engine that drives the Cambrian explosion.”

“What we’re looking at here is the early stages of the ramping up of that process to create the nutrients needed for animal life in the sea.”

Retallack’s findings were published in the journal Nature.

Keep religion out of science class !

In a recent act that just baffles my mind, Tennesee, not one of the US brightest states, has passed a bill that makes it easier for virtually any creationist teacher to include religion in science class. They did this by including mythology in science classes to promote critical thinking. Now I wonder, do you think there’ll be discussions about the Egyptian gods, or about Norse mythology, or about Zeus ?

Might as well do this

Let’s get one think straight; regardless of my beliefs, I do believe anyone is entitled to believe in whatever they want, as long as they don’t try to impose it directly or indirectly upon others. But religion is in religion class, science is in science class, doesn’t that make sense ? We’re talking about centuries of research, tens of thousands of peer reviewed papers against the Bible – I strongly believe that this bill is absurd.

The Tennessee Science Teachers Association had a firm and prompt response, declaring itself disgusted by the bill, and declaring it “unnecessary, anti-scientific, and very likely unconstitutional.”. As a matter of fact, creationism has lost every major U.S. federal court case for decades, and legislators are still trying to find a way to bring God into the biology class. This sort of meddling in the educational system is going out all over the US, and it will not bring anything good to the table, quite the opposite. Critical thinking is encouraged by trusting what is proven, and not what is believed; it’s dissapointing.