Tag Archives: evolution

Evolution in New York City Wildlife

Evolution Right Under Our Noses by Carl Zimmer

White-footed mice, stranded on isolated urban islands, are evolving to adapt to urban stress. Fish in the Hudson have evolved to cope with poisons in the water. Native ants find refuge in the median strips on Broadway. And more familiar urban organisms, like bedbugs, rats and bacteria, also mutate and change in response to the pressures of the metropolis. In short, the process of evolution is responding to New York and other cities the way it has responded to countless environmental changes over the past few billion years. Life adapts.
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Dr. Wirgin and his colleagues were intrigued to discover that the Hudson’s population of tomcod, a bottom-dwelling fish, turned out to be resistant to PCBs. “There was no effect on them at all,” Dr. Wirgin said, “and we wanted to know why.”

In March, he and his colleagues reported that almost all the tomcod in the Hudson share the same mutation in a gene called AHR2. PCBs must first bind to the protein encoded by AHR2 to cause damage. The Hudson River mutation makes it difficult for PCBs to grab onto the receptor, shielding the fish from the chemical’s harm.

The AHR2 mutation is entirely missing from tomcod that live in northern New England and Canada. A small percentage of tomcod in Long Island and Connecticut carry the mutation. Dr. Wirgin and his colleagues concluded that once PCBs entered the Hudson, the mutant gene spread quickly.

Carl Zimmer again does a good job of explaining science in an engaging way. It is interesting to learn about science and evolution in urban environments. Lots of life manages to survive the challenges of urban life and it is interesting to learn what scientists are finding about that life.

Cambrian Explosion Song

via Smithsonian’s Surprising Science:

What does a music teacher do when he ends up teaching science? He teaches about evolution and the geologic timeline with music, of course, and that’s what Canadian elementary school teacher John Palmer did. He originally played “Cambrian Explosion” as a rock/hip hop creation in class but has since recorded an acoustic version. (The trio is called Brighter Lights, Thicker Glasses and consists of Palmer on the guitar/vocals, Michael Dunn on the dobro and Brian Samuels [from UBC civil engineering department] on the cello.)

The video was filmed in the Beaty Biodiversity Museum (Canada) atrium with the blue whale exhibit in the background.

Evolution of Altruism in Robots

The webcast explores robots evolving cooperative behavior. A Quantitative Test of Hamilton’s Rule for the Evolution of Altruism (open access paper)

One of the enduring puzzles in biology and the social sciences is the origin and persistence of altruism, whereby a behavior benefiting another individual incurs a direct cost for the individual performing the altruistic action. This apparent paradox was resolved by Hamilton’s theory, known as kin selection, which states that individuals can transmit copies of their own genes not only directly through their own reproduction but also indirectly by favoring the reproduction of kin, such as siblings or cousins. While many studies have provided qualitative support for kin selection theory, quantitative tests have not yet been possible due to the difficulty of quantifying the costs and benefits of helping acts. In this study, we conduct simulations with the help of a simulated system of foraging robots to manipulate the costs and benefits of altruism and determine the conditions under which altruism evolves.

By conducting experimental evolution over hundreds of generations of selection in populations with different costs and benefits of altruistic behavior, we show that kin selection theory always accurately predicts the minimum relatedness necessary for altruism to evolve. This high accuracy is remarkable given the presence of pleiotropic and epistatic effects, as well as mutations with strong effects on behavior and fitness. In addition to providing a quantitative test of kin selection theory in a system with a complex mapping between genotype and phenotype, this study reveals that a fundamental principle of natural selection also applies to synthetic organisms when these have heritable properties.

Ten Things Everyone Should Know About Science

As the writer of this blog (which is located at engineering.curiouscatblog.net) I am a strong believer in the importance of scientific literacy. Neil Degrasse Tyson stated the importance very well, as I mentioned in a previous post, the scientifically literate see a different world

If you are scientifically literate the world looks very different to you. Its not just a lot of mysterious things happening. There is a lot we understand out there. And that understanding empowers you to, first, not be taken advantage of by others who do understand it. And second there are issues that confront society that have science as their foundation. If you are scientifically illiterate, in a way, you are disenfranchising yourself from the democratic process, and you don’t even know it.

The Financial Times has complied a list of the 10 things everyone should know about science

Evolution – previous posts: Evolution is Fundamental to Science – posts tagged: evolution
Genes and DNA – tags: genes – genetics – DNA – RNA
Big bang – tags: physics, posts mentioning big bang
Relativity – General Relativity Einstein/Essen Anniversary Test – posts mentioning relativity
Quantum mechanics – Quantum Mechanics Made Relatively Simple Podcasts, Quantum mechanics
Radiation
Atoms and nuclear reactions
Molecules and chemical reactions – posts on chemistry
Digital data – I must admit, even reading their comments, I don’t understand what they are thinking here. There certainly is a great deal of digital data and the future certainly going to involve a great deal more, but this just doesn’t fit, in my opinion.
Statistical significance – Seeing Patterns Where None Exists, Statistics Insights for Scientists and Engineers, Correlation is Not Causation post on statistics – experimentation

It is a challenge to create such a list. I agree with most of what they have. I would like to look at changing the last 2 and radiation, though. I would probably include something about the scientific method rather than statistical significance. Another area I would consider is something about bacteria and/or viruses. You can maybe include them under genes, but viruses and bacteria are amazing in the very strange things they do with genes and I think that is worthy of its own item. Another possibility is thinking of separating out a second spot for things related to the scientific method – causation, randomized testing, multivariate experiments… I would also consider one, or more of the following or something related to them biology – chlorophyll, the the life of bacteria in our bodies, something related to human health (how drugs work, medical studies…), etc..

The Ten Things Everyone Should Know About Science

Evolution through natural selection remains as valid today as it was 150 years ago when expressed with great elegance by Charles Darwin in The Origin of Species. The mechanism of evolution depends on the fact that tiny hereditable changes take place the whole time in all organisms, from microbes to people.
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An important feature of Darwinian evolution is that it operates at the level of the individual. There is no mechanism for natural selection to change the species as a whole, other than through the accumulation of changes that lead to the survival of the fittest individuals.

The rate of evolution varies enormously between different types of organism and different environmental circumstances. It can proceed very quickly when the pressure is great, as, for example, with bacteria exposed to antibiotics, when drug-resistant mutations may arise and spread through the bacterial population within months.

Why does it matter? Evolution is coming under renewed assault, particularly in the US, from fundamentalist Christians who want creationism to be taught in schools. Although evolution has had virtually unanimous support from professional scientists for at least a century, polls show that American public opinion still favours creationism.

Lobopodians from China a Few Million Years Ago

image of a lobopodian fosil nicknamed the walking cactus

image of a lobopodian fosil from Nature

Cactus Walking On 20 Legs Found In China

There was a wild period — roughly 520 million years ago — when life, for no obvious reason, burst into a crazy display of weird new fantastic forms — producing creatures in shapes never seen before or since. Consider this animal, the newest fossil discovery from Jianni Liu in China. She calls it “the walking cactus.”

This is not a plant, not a sculpture. It was a live animal, with no eyes, what may or may not be a head, mostly a gaggle of limbs, armor-plated, covered in thorns, attached to a stomach.

What is it? Taxonomically, Jianni Liu thinks it’s a lobopodian, a group of animals described as “worms with legs.” Lobopodians are about the craziest looking critters that ever lived. A whole zoo of them appear in the rocks around Chengjiang, China.
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All we know, says Richard Fortey in his classic history Life, is that a long time ago, the first of these strange animals popped into view and for a short while “there was a chain reaction, unstoppable once it started, a bacchanalia of zoological inventiveness, which has never been matched again.”

Every living thing on earth today is what’s left over from that amazing burst of forms. It’s true we now live on land and in the air, not just in the sea. We have grasses and flowers and beetles in more varieties than you can imagine, and yet, in some deep architectural way, the developmental paths were set way back then, 500 million years ago. The Walking Cactus is just another souvenir of that crazy moment.

Very cool. Actual science is so full of such interesting things. The Cambrian explosion of life, about 540-490 million years ago, marked the beginning of complex life on earth. Before Cambrian, the sea floor was covered by microbial mats. By the end of the period, burrowing animals had destroyed the mats through bioturbation, and gradually turned the seabeds into what they are today. Generally it is accepted that there were no land plants at this time, although it is likely that a microbial “scum” comprising fungi, algae, and possibly lichens covered the land.

Complex organisms gradually became more common in the millions of years immediately preceding the Cambrian, but it was not until this period that mineralized (readily fossilized) organisms became common. Before about 580 million years ago, most organisms were simple, composed of individual cells occasionally organized into colonies. Over the following 70 or 80 million years the rate of evolution accelerated by an order of magnitude (as defined in terms of the extinction and origination rate of species) and the diversity of life began to resemble today’s.

Robots That Start as Babies Master Walking Faster Than Those That Start as Adults

In a first-of-its-kind experiment, Bongard created both simulated and actual robots that, like tadpoles becoming frogs, change their body forms while learning how to walk. And, over generations, his simulated robots also evolved, spending less time in “infant” tadpole-like forms and more time in “adult” four-legged forms.

These evolving populations of robots were able to learn to walk more rapidly than ones with fixed body forms. And, in their final form, the changing robots had developed a more robust gait — better able to deal with, say, being knocked with a stick — than the ones that had learned to walk using upright legs from the beginning.

Bongard’s research, supported by the National Science Foundation, is part of a wider venture called evolutionary robotics. “We have an engineering goal,” he says “to produce robots as quickly and consistently as possible.” In this experimental case: upright four-legged robots that can move themselves to a light source without falling over.

Using a sophisticated computer simulation, Bongard unleashed a series of synthetic beasts that move about in a 3-dimensional space. “It looks like a modern video game,” he says. Each creature — or, rather, generations of the creatures — then run a software routine, called a genetic algorithm, that experiments with various motions until it develops a slither, shuffle, or walking gait — based on its body plan — that can get it to the light source without tipping over.

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Naturally Curious Children

I write this blog because when I was a kid I was curious and had parents who gave me enough interesting answers and interesting resources to build on that curiosity. And I am still curious today. I love learning. And I love to hear about kids learning.

The Big Girl has worked out evolution

She was ecstatic when we ended up with a rooster in our ‘sexed’ chickens even though Mummy and Daddy weren’t too impressed, because she wants more little fluffy chicks. I think that counts as evidence she knows you need boys and girls to get babies.
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“What would happen if there were no boys?” This is the question she came out with the other day.

“Well, there would be no babies.” I didn’t quite get the problem seeing we were feeding the rather prolific guinea pigs at the time and we’ve been talking about separating them.
“But what if there were no boys at all? So no-one could have babies?”
“Eventually, they would all die.”
“But there wouldn’t be any left!”
“No, they would die out.”
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“How did humans start?”… a puzzled little crease in her forehead. “Because if there weren’t any around with the dinosaurs they must have started sometime. How could there be no humans and then they’re there? What was the Mummy?”
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“Well, they weren’t sudden. You know how you are a little bit different to Mummy and Daddy? That’s how it happened. The babies were just a little bit different to their parents and over a really, really long time they became people.”
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“But if there was only one it would die out.”
Well that came out of nowhere, did I miss half of this conversation?
“You know, the first person. It needs to have both a boy and a girl to have more people babies. So if there was only one it would die out.”
“Oh, from yesterday. Yes, you’re right. But people live in groups, so they’re all changing a tiny little bit at the same time.”

It is great to see developing minds at work. Exploring their natural curiosity. And taking in new information puzzling it out over time and then coming back to the ideas. This kind of curiosity is what drives learning and success.

Changing Life as We Know It

Update: Independent researchers find no evidence for arsenic life in Mono Lake

NASA has made a discovery that changes our understanding of the very makeup of life itself on earth. I think my favorite scientific discipline name is astrobiology. NASA pursues a great deal of this research not just out in space but also looking at earth based life. Their astrobiology research has changed the fundamental knowledge about what comprises all known life on Earth.

Felisa Wolfe-Simon processing mud from Mono Lake to inoculate media to grow microbes on arsenic.

Carbon, hydrogen, nitrogen, oxygen, phosphorus and sulfur are the six basic building blocks of all known forms of life on Earth. Phosphorus is part of the chemical backbone of DNA and RNA, the structures that carry genetic instructions for life, and is considered an essential element for all living cells.

Phosphorus is a central component of the energy-carrying molecule in all cells (adenosine triphosphate) and also the phospholipids that form all cell membranes. Arsenic, which is chemically similar to phosphorus, is poisonous for most life on Earth. Arsenic disrupts metabolic pathways because chemically it behaves similarly to phosphate.

Researchers conducting tests in the harsh, but beautiful (see photo), environment of Mono Lake in California have discovered the first known microorganism on Earth able to thrive and reproduce using the toxic chemical arsenic. The microorganism substitutes arsenic for phosphorus in its cell components.

“The definition of life has just expanded,” said Ed Weiler, NASA’s associate administrator for the Science Mission Directorate. “As we pursue our efforts to seek signs of life in the solar system, we have to think more broadly, more diversely and consider life as we do not know it.” This finding of an alternative biochemistry makeup will alter biology textbooks and expand the scope of the search for life beyond Earth.

In science such huge breakthroughs are not just excepted without debate, however, which is wise.

Thriving on Arsenic:

In other words, every experiment Wolfe-Simon performed pointed to the same conclusion: GFAJ-1 can substitute arsenic for phosphorus in its DNA. “I really have no idea what another explanation would be,” Wolfe-Simon says.

But Steven Benner, a distinguished fellow at the Foundation for Applied Molecular Evolution in Gainesville, FL, remains skeptical. If you “replace all the phosphates by arsenates,” in the backbone of DNA, he says, “every bond in that chain is going to hydrolyze [react with water and fall apart] with a half-life on the order of minutes, say 10 minutes.” So “if there is an arsenate equivalent of DNA in that bug, it has to be seriously stabilized” by some as-yet-unknown mechanism.

It is sure a great story if it is true though. Other scientists will examine more data and confirm or disprove the claims.

“We know that some microbes can breathe arsenic, but what we’ve found is a microbe doing something new — building parts of itself out of arsenic,” said Felisa Wolfe-Simon, a NASA Astrobiology Research Fellow in residence at the U.S. Geological Survey in Menlo Park, Calif., and the research team’s lead scientist. “If something here on Earth can do something so unexpected, what else can life do that we haven’t seen yet?”
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Boa Constrictor Gives Birth to Clones

Snake gives ‘virgin birth’ to extraordinary babies

A female boa constrictor snake has given birth to two litters of extraordinary offspring. Evidence suggests the mother snake has had multiple virgin births, producing 22 baby snakes that have no father. More than that, the genetic make-up of the baby snakes is unlike any previously recorded among vertebrates, the group which includes almost all animals with a backbone.
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“All offspring are female. The offspring share only half the mother’s genetic make-up,” he told the BBC.
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Humans for example have X or Y sex chromosomes; females have two X chromosomes and males have a combination of an X and a Y chromosome. In place of X and Y, snakes and many other reptiles have Z and W chromosomes.

In all snakes, ZZ produces males and ZW produces females. Bizarrely, all the snakes in these litters were WW. This was further proof that the snakes inherited all their genetic material from their mother, as only females carry the W chromosome.

“Essentially they are half clones of their mother,” says Dr Booth. That is because the baby snakes have inherited two copies of one half of their mother’s chromosomes, including one W chromosome.
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More astonishing though, is that no vertebrate animal in which the females carry the odd sex chromosome (in this case the W chromosome) has ever been recorded naturally producing viable WW offspring via a virgin birth.

“For decades WW has been considered non-viable” says Dr Booth. In such species, all known examples of babies that are the product of parthenogenesis are male, carrying a ZZ chromosomal arrangement.

Monarch Butterflies Use Medicinal Plants

Monarch butterflies eat toxic plants (that they have evolved to tolerate and make the butterflies themselves toxic to predators). They use medicinal plants to treat their offspring for disease, research by Emory biologists shows. When the butterflies are infected by certain parasites the butterflies have a strong preference to lay their eggs on a plant (tropical milkweed) that will help the caterpillar fight the parasite when it eats those leaves (it serves as a drug for them). Their experiments may be the best evidence to date that animals use medication.