Tag Archives: evolution

Curious Platypus Genome is No Surprise

Platypus Genome Found Fittingly Strange by Rick Weiss

a team of scientists has determined the platypus’s entire genetic code. And right down to its DNA, it turns out, the animal continues to strain credulity, bearing genetic modules that are in turn mammalian, reptilian and avian.

There are genes for egg laying — evidence of its reptilian roots. Genes for making milk, which the platypus does in mammalian style despite not having nipples. Genes for making snake venom, which the animal stores in its legs. And there are five times as many sex-determining chromosomes as scientists know what to do with.

“It’s such a wacky organism,” said Richard Wilson, director of the Genome Sequencing Center at Washington University in St. Louis, who with colleague Wesley Warren led the two-year effort, described today in the journal Nature.

Yet in its wackiness, Wilson said, the platypus genome offers an unprecedented glimpse of how evolution made its first stabs at producing mammals. It tells the tale of how early mammals learned to nurse their young; how they matched poisonous snakes at their venomous game; and how they struggled to build a system of fertilization and gestation that would eventually, through relatives that took a different tack, give rise to the first humans.

“As we learn more about things like platypuses,” Wilson said, “we also learn more about ourselves and where we came from and how we work.”

Very cool stuff. Related: Platypus genome explains animal’s peculiar features; holds clues to evolution of mammals – Platypus genome mapping boon for human and livestock researchers – Platypus genetic code unravelled – Weird Creatures – Evolution is Fundamental to Science – Long-Eared Jerboa – Cat Joins Exclusive Genome Club – Your Inner Fish

Amazing Designs of Life

The More We Know About Genes, the Less We Understand by Carl Zimmer

All living things, ourselves included, turn genes on and off in a similar way, by making switch-like proteins called transcription factors. And as scientists have identified more of these, they’ve discovered something remarkable: They form a chain of command. The job of some transcription factors is to switch others on and off, and they in turn are controlled by other transcription factors. Even a seemingly simple microbe like E. coli has an impressive hierarchy. Just nine genes rule over about half of the 4,000-odd genes in E. coli.

E. coli’s network allows it to respond quickly to the challenges it meets, from starvation to heat to the loss of oxygen. It can rapidly reorganize itself, switching on hundreds of genes and switching off hundreds of others. What makes this network all the more impressive are the feedback loops that keep it from spinning out of control. When one gene switches on, for example, it may make a protein that shuts down the gene that switched it on in the first place.

Yet even as scientists uncover this network, they discover yet another mystery. In the latest issue of Nature, scientists reported an experiment in which they wreaked havoc with E. coli’s network. They randomly added new links between the transcription factors at the top of the microbe’s hierarchy. Now a transcription factor could turn on another one that it never had before. The scientists randomly rewired the network in 598 different ways and then stepped back to see what happened to the bacteria.

You might expect that they all died. After all, if you were to pop open the back of an iPod and start linking its components together in random ways, you’d expect it to crash. But that’s not what happened.

About 95 percent of the rewired bacteria did just fine with their new networks. They went on with their lives, feeding, growing and dividing. Some even performed better than microbes with the original wiring, under some conditions.

First Lungless Frog Found

The first recorded species of frog that breathes without lungs has been found in a clear, cold-water stream on the island of Borneo in Indonesia. The frog, named Barbourula kalimantanensis, gets all its oxygen through its skin.
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Previously the only four-limbed creatures known to lack lungs were salamanders. A species of earthwormlike, limbless amphibian called a caecilian is also lungless. Tetrapods, or four-limbed creatures, that develop without lungs are rare evolutionary events, Bickford and colleagues write.

The trait in amphibians is likely an adaptation to life between water and land and their ability to respire through the skin. The researchers suggest lunglessness in B. kalimantanensis may be an adaptation to the higher oxygen content in fast-flowing, cold water.
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Wake added that for most amphibians, the majority of gas exchange happens through the skin. A low but significant amount of respiration occurs via simple, sac-like lungs. Most species, he noted, have mating calls that require lungs. So biologists are unsure why a few species have entirely gotten rid of the organs, Wake said.

Androgenesis

All Dad by Carl Zimmer

This week’s revelation is androgenesis. Androgenesis is what happens when kids get all their genes from their father.
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Androgenesis, it turns out, transforms fatherhood into a parasitic invasion. It begins like normal fertilization, with a sperm fusing to an egg. But then the egg’s DNA gets hurled out of its nucleus, so that the sperm’s genes are the only ones left in the egg. The egg begins to develop into an embryo, but only after it has lost the mother’s DNA.

Mutation Rate and Evolution

Stop the Mutants! by Olivia Judson

I’m going to wave a magic wand and reduce the mutation rate to zero, instantly, in all species, and forever. Then I’m going to watch to see how long it takes for evolution to stop.
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Actually stopping mutations is a physical impossibility – hence the need for a magic wand. But if they were to stop, so would raw invention. But evolution would not. Not for a long time.
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And sometimes natural selection actively promotes the persistence of genetic variation. This can happen when there’s an advantage to having genes that are rare. Among guppies, for example, males with rare color patterns are much more likely to survive than those with common color patterns, presumably because predators get good at spotting the patterns they encounter often. In such situations, the rare type does well, begins to become common – and then becomes the victim of its own success and starts to do badly. In situations like this, the frequencies of different genes can rise and fall, cycling indefinitely.
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Among lifestyles that promote genetic diversity, far and away the most important is sex. Sex shuffles up genes, continually producing new gene combinations. (An important difference between sex and mutation is that sex can only create genetic novelty if it already exists in the population. If everyone is genetically identical, sex will have no effect.) Sex also – and this is important – decouples the fates of genes from one another.

Baby Sand Dollars Clone Themselves When They Sense Danger

Baby sand dollars clone themselves when they sense danger

The odds of growing up aren’t good for baby sand dollars. Smaller than the head of a pin, the larvae drift in the ocean — easy prey for anything with a mouth.

But a University of Washington graduate student has discovered the tiny animal has a surprising survival strategy: Faced with the threat of being gobbled up, it makes like Dr. Evil from the Austin Powers movies and clones itself. The resulting “mini-me” may escape hungry fish because it is even teenier than the original — and harder to see.

“If you are eaten, but the smaller version of you survives, you’re still a winner from an evolutionary standpoint,” said Dawn Vaughn.
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Familiar inhabitants of Washington’s subtidal zone, sand dollars start life though the chance encounter of sperm and egg, simultaneously released into the water by mature adults. The larvae free-float for about six weeks before metamorphosing into miniature sand dollars that settle in colonies and eventually grow to full size.
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The white shells that wash up on the beach are the creatures’ external skeletons. Living sand dollars are covered with velvety, purple spines used to grab food particles. Vaughn knew many other marine invertebrates shift their shape to avoid being eaten. Colonial animals called bryozoans grow spikes when voracious sea slugs crawl across them. Barnacles take on a bent posture to repel snails. Vaughn’s own previous research showed periwinkle larvae narrow their shell openings to keep out marauding crab larvae.

Dino-Era Feathers Found Encased in Amber

Seven dino-era feathers found perfectly preserved in amber in western France highlight a crucial stage in feather evolution, scientists report. The hundred-million-year-old plumage has features of both feather-like fibers found with some two-legged dinosaurs known as theropods and of modern bird feathers, the researchers said.
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The find provides a clear example “of the passage between primitive filamentous down and a modern feather,” said team member Didier NÃ©raudeau of the University of Rennes in France. The study team isn’t sure yet whether the feathers belonged to a dino or a bird. But fossil teeth from two dino families thought to have been feathered were excavated from rocks just above the layer that contained the amber, Perrichot said. “It is entirely plausible that the feathers come from a dinosaur rather than from a bird,” he said.

Your Inner Fish

photo of Neil Shubin

Your Inner Fish: A Journey into the 3.5-Billion-Year History of the Human Body by Neil Shubin. A great piece from the University of Chicago, Fish out of Water, provides a good preview to the book:

What are the leading causes of death in humans? Four of the top ten causes—heart disease, diabetes, obesity, and stroke – have some sort of genetic basis and, likely, a historical one. Much of the difficulty is almost certainly due to our having a body built for an active animal but the lifestyle of a spud.
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The problem is that the brain stem originally controlled breathing in fish; it has been jerry-rigged to work in mammals… This works well in fish, but it is a lousy arrangement for mammals.
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The example from microbes is not unique. Judging by the Nobel Prizes awarded in medicine and physiology in the past 13 years, I should have called this book Your Inner Fly, Your Inner Worm, or Your Inner Yeast. Pioneering research on flies won the 1995 Nobel Prize in medicine for uncovering a set of genes that builds bodies in humans and other animals. Nobels in medicine in 2002 and 2006 went to people who made significant advances in human genetics and health by studying an insignificant-looking little worm (C. elegans). Similarly, in 2001, elegant analyses of yeast (including baker’s yeast) and sea urchins won the Nobel in medicine for increasing our understanding of some of the basic biology of all cells. These are not esoteric discoveries made on obscure and unimportant creatures. These discoveries on yeast, flies, worms, and, yes, fish tell us about how our own bodies work, the causes of many of the diseases we suffer, and ways we can develop tools to make our lives longer and healthier.

Two of my more controversial posts have been: Evolution is Fundamental to Science and Understanding the Evolution of Human Beings by Country. Evolution is not controversial scientifically. Just as gravity is not. Obviously this understanding is far from universal however.

But it is just a matter of time: similar to Galileo Galilei and heliocentric cosmology. See: Galileo’s Battle for the Heavens – Copernican System – Galileo). We now sit maybe 100 years after Galileo’s death (based on the evidence available in support of each scientific theory). At some point the evidence is accepted and life continues. Though I must admit it, I find it a bit disappointing how long it is taking for some people to accept the evidence of evolution. But I probably need to learn to be more patient – I have been told that more than once. All I can do is try to help present some small amount of the great work so many scientists have done to advance our knowledge. And here I am talking about evolution – for the 28% of those in the USA that couldn’t provide the answer that earth revolves around the sun, in 1998, well, they need much more help than I can provide.

Bacteria Can Transfer Genes to Other Bacteria

From page 115 of Good Gems, Bad Germs:

Microbiologists of the 1950’s did not appreciate the stunning extent to which bacteria swap genes… In 1959 Japanese hospitals experience outbreaks of multidrug-resistant bacterial dysentery. The shigella bacteria, which caused the outbreaks, were shrugging off four different classes of previously effective antibiotics: sulfonamides, streptomycins, chloramphenicols, and tetracyclines… In fact, the Japanese researches found it quite easy to transfer multidrug resistance from E. coli to shingella and back again simply by mixing resistant and susceptible strains together in a test tube.

Parasite Rex

Parasite Rex is a great book by Carl Zimmer (one of the bloggers listed in the Curious Cat directory of science blogs). This is the first book read as part of my specific plan to read more about bacteria, cells, virus, genes and the like.

One of the most enjoyable aspects of writing this blog is that I have focused much more on cool things I read. And over time the amazing things I posted about related to these topics made me realize I should put some focused effort to reading more on these topics. Some of the posts that sparked that idea: Tracking the Ecosystem Within Us – Inner Life of a Cell: Full Version – Where Bacteria Get Their Genes, People Have More Bacterial Cells than Human Cells, Biological Molecular Motors – Energy Efficiency of Digestion – Old Viruses Resurrected Through DNA – Midichloria mitochondrii – Microbes – Using Bacteria to Carry Nanoparticles Into Cells – How Bacteria Nearly Destroyed All Life – New Understanding of Human DNA – Soil Could Shed Light on Antibiotic Resistance – Symbiotic relationship between ants and bacteria

Parasite Rex was a great place to start. Carl Zimmer is a great writer, and the details on how many parasites there are and how interconnected those parasites are to living systems and how that has affected, and is affecting, us is amazing. And the next book I am reading is also fantastic: Good Germs, Bad Germs. Here is one small example from Parasite Rex, page 196-7:

A person who dies of sickle cell anemia is less likely to pass on the defective gene, and that means the disease should be exceedingly rare. But it’s not – one in four hundred American blacks has sickle sell anemia, and one in ten carries a single copy of the defective gene. The only reason the gene stays in such high circulation is that is also happens to be a defense against malaria.

Malaria is a parasite. One of the amazing things with repeated examples in the book were parasites that seemed to have extremely complicated life cycles (that don’t seem like a great strategy to prosper but obviously work). Where they grow in one life form (an insect or mammal or whatever) but must leave that life form for some other specific life form for the next stage in life (they cannot have descendants without doing so…). Seems like a crazy way to evolve but it happens over and over again.
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