The Peppered Moth: The Proof of Darwinian Evolution

The case reached a prominence as one of the most cited examples of Darwinian evolution in action because of the visual impact of the case, the ease with which it can be understood by non-specialists, and because empirical evidence was collected, in the 1950s, to show the selective agent responsible for the changes that had been observed.

Scientists Retrace Evolution With First Atomic Structure Of An Ancient Protein

The structures allowed the scientists to identify exactly how the new function evolved. They found that just seven historical mutations, when introduced into the ancestral receptor gene in the lab, recapitulated the evolution of GR's present-day response to cortisol. They were even able to deduce the order in which these changes occurred, because some mutations caused the protein to lose its function entirely if other "permissive" changes, which otherwise had a negligible effect on the protein, were not in place first.

"These permissive mutations are chance events. If they hadn't happened first, then the path to the new function could have become an evolutionary road not taken," Thornton said. "Imagine if evolution could be rewound and set in motion again: a very different set of genes, functions and processes might be the outcome."The atomic structure revealed exactly how these mutations allowed the new function to evolve. The most radical one remodeled a whole section of the protein, bringing a group of atoms close to the hormone. A second mutation in this repositioned region then created a tight new interaction with cortisol. Other earlier mutations buttressed particular parts of the protein so they could tolerate this eventual remodeling.

"We were able to walk through the evolutionary process from the distant past to the present day," said Ortlund, who is now at Emory University in Atlanta. "Until now, we've always had to look at modern proteins and just guess how they evolved."

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Science & Technology at Scientific American.com: Tiny Genome May Reflect Organelle in the Making

Science & Technology at Scientific American.com: Tiny Genome May Reflect Organelle in the Making:

"The bacterial species having the smallest genomes are typically those that spend their entire lives inside a host, exchanging nutrients that the host cannot synthesize in return for free room and board. Because the host supplies nourishment for these so-called endosymbionts, they are able to get by with fewer genes of their own. This reduction seemed to have limits, though. By randomly damaging bacteria, researchers had found about 300 genes essential for their growth. Accordingly, endosymbionts had never really dipped below a genomic sequence length of 500,000 to 600,000 base pairs."

Enter Carsonella rudii, which lives inside a special collection of cells in the abdomen of a certain psyllid, a flying insect that feeds on amino acid-deficient plant sap. Carsonella's genome is a mere 160,000 base pairs long, report Nancy Moran of the University of Arizona and her colleagues in the October 13 Science. The streamlined microbe contains at most 182 genes, which are smaller and overlap more with one another than is usual for bacteria. C. rudii is rich in genes for protein synthesis but lacks many genes for membrane synthesis, energy metabolism and DNA replication. Some of these genes may have been transferred to the host, which could be supplying its symbiont with essential enzymes, Moran notes. "If so, it would be very much like an organelle," she says. The mitochondrion and chloroplast are presumed endosymbionts that were assimilated into nascent plant and animal cells long ago. "This has never been shown to happen in an animal cell, because it's more difficult, but it's possible that Carsonella has basically done the same thing,"

Scientists recover T. rex soft tissue - Science - MSNBC.com

Scientists recover T. rex soft tissue - Science - MSNBC.com:

If we can isolate certain proteins, then perhaps we can address the issue of the physiology of the dinosaur," Schweitzer said.

Of course, the big question is whether it will be possible to see dinosaur DNA. "We don't know yet. We are doing a lot in the lab now that looks promising," Schweitzer said.

"To make sure she was seeing what she thought she was seeing, Schweitzer, a biologist by training, compared the Tyrannosaur samples with bone taken from a dead ostrich. She chose an ostrich because birds are thought to be the closest living relatives of dinosaurs and ostriches are big birds.

Both the dinosaur and ostrich blood vessels contained small, reddish brown dots that could be the nuclei of the endothelial cells that line blood vessels."

Science Now

Can this be true?

Science Now:

"When paleontologists find fossilized dinosaur bones during a dig, they usually do everything in their power to protect them, using tools like toothbrushes to carefully unearth the bones without inflicting any damage. However, when scientists found a massive Tyrannosaurus rex thigh bone in a remote region of Montana a few months ago, they were forced to break the bone in two in order to fit it into the transport helicopter. This act of necessity revealed a startling surprise: soft tissue that had seemingly resisted fossilization still existed inside the bone. This tissue, including blood vessels, bone cells, and perhaps even blood cells, was so well preserved that it was still stretchy and flexible.

A scanning electron microscope revealed that the dinosaur blood vessels, which are 70 million years old, are virtually identical to those recovered from modern ostrich bones. The ostrich is today’s largest bird, and many paleontologists believe that birds are the living descendants of dinosaurs. Scientists may be able to confirm this evolutionary relationship if they can isolate certain proteins from the recently discovered T. rex tissue. These proteins could also help solve another puzzle: whether dinosaurs were cold-blooded like other reptiles or warm-blooded like mammals.

Does this discovery of soft dinosaur tissue mean that scientists will soon be able to clone a Tyrannosaurus rex? Probably not – most scientists believe that DNA cannot survive for 70 million years. Then again, before this discovery, most scientists believed that soft tissue could not survive for 70 million years either."

Fastest-evolving human gene linked to brain boost - being-human - 16 August 2006 - New Scientist

Fastest-evolving human gene linked to brain boost - being-human - 16 August 2006 - New Scientist:

"There are only two changes in the 118 letters of DNA code that make up HAR1 between the genomes of chimps and chickens. But chimps and humans are 18 letter-changes apart. And those mutations occurred in just five million years, as we evolved from our shared ancestor.

“That is an incredible amount of change to have happened in a few million years,” Pollard notes."

John Hawks Anthropology Weblog : Vindija nuclear DNA report

John Hawks Anthropology Weblog : Vindija nuclear DNA report

home :: reviews :: neandertals :: neandertal_dna :: paabo_cold_spring_harbor_report_2006

Nature News is reporting that a million base pairs of a Neandertal specimen from Vindija cave have been sequenced. There's no paper; it's just a press report from a conference talk. So few details to examine.

Grandma Manimal. The Loom: A blog about life, past and future

Grandma Manimal. The Loom: A blog about life, past and future

Before this study, the rough consensus among scientists was that our ancestors diverged from the ancestors of our closest relatives--chimpanzees and bonobos--at some point between five to seven million years ago. That evidence came from studies on DNA, as well as from fossils, such as the oldest hominid fossil, Sahelanthropus, which is estimated to have lived 6.5 to 7.5 million years old. Most scientists argued that the hominids made a relatively clean break from other apes, without any significant hybridizing.

But that's not what has emerged from the new study. The Broad Institute scientists lined up millions of bases of DNA in humans and chimps and measured their differences. Humans and chimpanzees both inherited each segment of DNA from a common ancestor. Over time, the copies of that ancestral segment picked up mutations. The differences between them can offer clues to how long they've been evolving along separate paths. It turns out that the ancestors for some of those segments are much older than others. The only way to make sense of these results, according to the scientists, is to conclude that hominids and the ancestors of chimpanzees were interbreeding--to some extent at least--for four million years.

IBM Research | Press Resources | IBM Discovery Could Shed New Light on Workings of the Human Genome

IBM Research | Press Resources | IBM Discovery Could Shed New Light on Workings of the Human Genome:

"Yorktown Heights, NY, April 25, 2006 – IBM today announced its researchers have discovered numerous DNA patterns shared by areas of the human genome that were thought to have little or no influence on its function and those areas that do.

As reported today in the Proceedings of the National Academy of Sciences (PNAS), regions of the human genome that were assumed to largely contain evolutionary leftovers (called “junk DNA”) may actually hold significant clues that can add to scientists’ understanding of cellular processes. IBM researchers have discovered that these regions contain numerous, short DNA “motifs,” or repeating sequence fragments, which also are present in the parts of the genome that give rise to proteins.
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DNA's Dark Side :: Astrobiology Magazine ::

DNA's Dark Side :: Astrobiology Magazine ::

DNA's Dark Side
Summary (Apr 11, 2006): Chemists at Oregon State University have pioneered a controversial theory about how supposedly-stable DNA bases can be pushed into a "dark state" in which they are highly vulnerable to damage from ultraviolet radiation -- an idea that has challenged some of the most basic concepts of modern biochemistry.

based on an Oregon State University release

"But just since last summer this has been a key point of discussion at several conferences and caused quite an excitement, as people see the data," Kong said. "Among other things, it helps to explain how water, or something else serving the same role, could have helped lead to the evolution of life."

The core of the debate, Kong said, relates to the behavior of the nucleic acid bases -- adenine, thymine, guanine and cytosine -- that as A-T and G-C base pairs form DNA and ultimately become the blueprint for all living things. One of the most basic premises of biochemistry is that these nucleic acid bases are very stable, as they would have to be to prevent rampant mutations and make an organized genetic structure possible.

But studies at OSU, which were done with highly sophisticated electron spectroscopy, showed that the alleged stability of the nucleic acid bases in DNA is largely a myth.

This graph shows how quickly ultraviolet (UV) energy deposited in the electrons of a nucleoside is converted to heat, which is then absorbed by water surrounding the nucleoside. Here, time is measured in femtoseconds, or quadrillions of a second. The diagram to the upper right of the image depicts a particular nucleoside -- adenosine. This molecule consists of a UV-absorbing base (shown in red) and a simple sugar (shown in gray) that binds it to the RNA backbone. This base is also found in DNA. Credit: Ohio State University

"In their biological form, surrounded by other hydrogen-bonded bases, it's true that the nucleic acids which make up DNA are stable," Kong said. "But we found that living things, in their totality, provide an environment which creates that stability, through attachments within base pairs and/or with neighboring bases. These attachments allow damaging photonic energy to be released as heat. But a DNA base as an isolated molecule, just by itself, does not have that stability."

Aetiology

Aetiology :Discussing causes, origins, evolution, and implications of disease and other phenomena.

One historical event that has been the subject of much speculation over the decades has been the Plague of Athens, a mysterious outbreak that is thought to have changed the direction of the Peloponnesian War, and for which the cause still remains uncertain.

This plague has been attributed to bubonic plague, toxic shock syndrome and/or necrotizing fasciitis due to Streptococcus pyogenes or Staphylococcus aureus, Salmonella, yellow fever, malaria, Ebola, influenza, and smallpox, to name just a few. Typhus seems to fit the description best, but it's likely that a cause will never be known with certainty.

So, what good does this do us? The bodies are almost 2500 years old; surely they can't provide a testable sample. Right? Luckily, people cleverer than I have figured out a way to search for microbial DNA in ancient samples: via dental pulp. This is used because it's well-protected, and generally considered to be free of contamination (until you break open the tooth, that is). That's what they did in this study as well, using the polymerase chain reaction (PCR) to search for DNA from Yersinia pestis, typhus, anthrax, tuberculosis, cowpox, and cat-scratch disease (Bartonella henselae) in addition to S. enterica. But, there are a number of problems with the study.

Wellcome Trust Sanger Institute Press Releases

Wellcome Trust Sanger Institute Press Releases:

"On Tuesday 17 January 2006 the Wellcome Trust Sanger Institute's World Trace Archive database of DNA sequences hit one billion entries. The Trace Archive is a store of all the sequence data produced and published by the world scientific community, including the Sanger Institute's own prodigious output as a world-leading genomics institution.

The Archive is 22 Terabytes in size and doubling every ten months - perhaps the largest single scientific database in Europe, if not the world.

All the data are freely available to the world scientific community (http://trace.ensembl.org/), as a resource to geneticists all over the globe. When a researcher is studying a disease or gene, they can download the genetic information known about the area they are studying."

New Scientist Breaking News - Oldest DNA exposes ancient ecosystems

New Scientist Breaking News - Oldest DNA exposes ancient ecosystems:

"The permafrost contained DNA from eight species of mammals including woolly mammoth, steppe bison and musk ox, dating back 30,000 years, as well as 28 families of trees, shrubs, mosses and herbs, some of which lived 300,000 to 400,000 years ago.

By drilling at widely spaced locations, and at different depths, the team could recreate ancient landscapes and watch them evolve. 'From just two grams of soil, you can obtain a meaningful sample of the ecosystem,' says Willerslev."

New Scientist News - Anonymous sperm donor traced on internet

New Scientist News - Anonymous sperm donor traced on internet: "LATE last year, a 15-year-old boy rubbed a swab along the inside of his cheek, popped it into a vial and sent it off to an online genealogy DNA-testing service. But unlike most people who contact the service, he was not interested in sketching the far reaches of his family tree. His mother had conceived using donor sperm and he wanted to track down his genetic father.

That the boy succeeded using only the DNA test, genealogical records and some internet searches has huge implications for the hundreds of thousands of people who were conceived using donor sperm. "

New Scientist Breaking News - Crystal clumps preserve fossilised DNA

New Scientist Breaking News - Crystal clumps preserve fossilised DNA: "Clumps of mineral crystals in fossil bones preserve DNA better than other parts of the bones, a new study shows. The results promise new hope for research on both ancient humans and extinct animals.

Extraction of DNA from fossil bones promises to be a powerful tool for analysing relationships among vanished populations, tracing their migrations, and finding their closest living relatives. "

Scientists crack DNA puzzle, point to 'hot soup' at origin of life | Science Blog

Scientists crack DNA puzzle, point to 'hot soup' at origin of life | Science Blog

Evolution on trial again : Page 1

Evolution on trial again : Page 1: "Conceived as a PR stunt to put the town of Dayton, TN on the map, it succeeded in making a laughingstock of the state, which found Scopes guilty in a trial that garnered enormous publicity. 80 years later, scientists have identified DNA as the medium in which heredity is passed on, constructed a map of the entire human genome and can routinely manipulate genetic information in the laboratory. Yet despite the advances we have made in the field, there remains a certain intransigence towards accepting as unquestioned scientific fact the theory of evolution as it pertains to the development of humankind. Although the Roman Catholic Church and other Christian churches defer to the scientific community on this, a highly vocal and well-funded group of fundamentalists in the United States are still bent on the suppression of evolution in schools."

News

News Teams of researchers from around the world have shown that tiny strands of RNA possess incredible powers of control over genes by shutting them off like a light switch, effectively rendering them impotent by interference. Small strands of RNA can even chop into the DNA of the genes directly to rearrange large pieces of the chromosomes. "Remarkably, in some species, truncated RNA molecules literally shape genomes, carving out chunks to keep and discarding others," Science says. "There are even hints that certain small RNAs might help chart a cell's destiny by directing genes to turn on or off during development, which could have profound implications for coaxing cells to form one type of tissue or another."

Ars Technica: The PC enthusiast's resource

Ars Technica: The PC enthusiast's resource Posted 12/4/2002 - 10:30PM, by zAmboni
In news that rivals the completion of the Human Genome Project, researchers have revealed the first high quality public sequence of the mouse genome. Some researchers believe the mouse genome is more exciting than the human genome. Why? Mainly because libraries full of research have been conducted with mice, and mice are currently being used to study human diseases and basic biology. Needless to say, it is a bit tougher to do the same experimentation on humans.

Early analyses confirm preliminary estimates on the similarity between the mouse and human genomes. Ninety-nine percent of human DNA matches that of mice, and the two genomes both contain an estimated 30,000 genes. Only 300 of the mice genes have no counterpart in the human genome and vice versa.

Probably the most interesting finding, to me at least, is that many non-coding regions of DNA (what many news outlets like to erroneously call "junk DNA"), are conserved between humans and mice. I personally think the non-coding regions are very important in gene regulation, and contain the information on what makes mice, mice and men, men. The journal Nature has put together information on the arrival of the mouse genome here.