Evolution

Venter Institute Scientists Create First Synthetic Bacterial Genome

A team of researchers has created the largest man-made DNA structure by synthesizing and assembling the 582,970 base pair genome of a bacterium. This work is the second of three key steps toward the team’s goal of creating a fully synthetic organism. In the next step, the team will attempt to create a living bacterial cell based entirely on the synthetically made genome. The team achieved this technical feat by chemically making DNA fragments in the lab and developing new methods for the assembly and reproduction of the DNA segments.

The evolution of morality

Which of the following people would you say is the most admirable: Mother Teresa, Bill Gates or Norman Borlaug? For most, it's an easy question. Mother Teresa, famous for ministering to the poor in Calcutta, has been beatified by the Vatican, awarded the Nobel peace prize and ranked in a US poll as the most admired person of the 20th century. Bill Gates, infamous for giving us the Microsoft dancing paper clip, has been decapitated in effigy on "I Hate Gates" websites. As for Norman Borlaug … who the heck is Norman Borlaug? Yet a deeper look might lead you to rethink your answers. Borlaug, father of the "Green Revolution" that used agricultural science to reduce world hunger, has been credited with saving a billion lives, more than anyone else in history. Gates, in deciding what to do with his fortune, determined that he could alleviate the most misery by fighting everyday scourges in the developing world such as malaria, diarrhoea and parasites.

Blue-eyed humans have a single, common ancestor

New research shows that people with blue eyes have a single, common ancestor. A team at the University of Copenhagen have tracked down a genetic mutation which took place 6-10,000 years ago and is the cause of the eye colour of all blue-eyed humans alive on the planet today. "Originally, we all had brown eyes. But a genetic mutation affecting the OCA2 gene in our chromosomes resulted in the creation of a 'switch', which literally 'turned off' the ability to produce brown eyes". The OCA2 gene codes for the so-called P protein, which is involved in the production of melanin, the pigment that gives colour to our hair, eyes and skin. The "switch", which is located in the gene adjacent to OCA2 does not, however, turn off the gene entirely, but rather limits its action to reducing the production of melanin in the iris – effectively "diluting" brown eyes to blue.

The Planet

"The Planet" is a Swedish campaign to enhance public awareness of the planet Earth; to show its limits, wonders, possibilities. It is produced by Swedish public service television. This is a Flash app -- when you use it, make sure you hit the back arrow inside the app, otherwise if you use the browser's back arrow, you will get popped outside of the app completely. To get started, I suggest you click on "The Big Picture", then "The Current State", then "Great Acceleration". You can see many of the trends we talk about at the future salon there.

Evolution: Random or Directed?

Evolution is a random process -- or is it? I ask this because we all can name examples of convergent evolution where very different organisms arrived at similar solutions to the challenges they are faced with. One such example is the striking morphological similarities between sharks (marine fishes) and dolphins (marine mammals). Thus, based on observations of convergent evolution, one is tempted to hypothesize that, even if the mutations that underlie evolution itself are random, the "end result" of evolution is not. In fact, this is the central premise of an interesting book by Simon Conway Morris, Life's Solution, where he postulates that "the evolutionary routes are many, but the destinations are limited". This is in direct conflict with the late Stephen Jay Gould's hypothesis that a far different evolutionary outcome would occur if we could only replay the "tape of life". So which is it? Of course, replaying this tape of life is impossible, except when the organisms being studied have a fast enough generation time that we can watch their evolution during our own lifetimes.

Beyond the evolutionary theory of ageing, from functional genomics to evo-gero

By the mid 1970's, the mechanisms by which ageing can evolve had a secure theoretical basis in population genetics. Here, we discuss how subsequent evolutionary work has focussed on testing and extending this theory, and on attempting to integrate it with other emerging facets of the biology of ageing, such as genetic studies of long-lived mutants and of phenotypic plasticity in ageing, such as in response to nutritional status. We also describe how functional genomic studies are providing new insights into the evolutionary forces shaping genome evolution and lifespan control. Future challenges include understanding the biochemistry of longevity and how its failure generates ageing and associated diseases, and the determination of the genetic basis of lifespan evolution and the great plasticity that it displays.

PDF, 7 pages

Blame Our Evolutionary Risk Of Cancer On Body Mass

A key enzyme that cuts short our cellular lifespan in an effort to thwart cancer has now been linked to body mass. Until now, scientists believed that our relatively long lifespans controlled the expression of telomerase--an enzyme that can lengthen the lives of cells, but can also increase the rate of cancer. "Mice express telomerase in all their cells, which helps them heal dramatically fast. Skin lesions heal much faster in mice, and after surgery a mouse's recovery time is far shorter than a human's. It would be nice to have that healing power, but the flip side of it is runaway cell reproduction--cancer."

Estimate of the Mutation Rate per Nucleotide in Humans

The average mutation rate was estimated to be ~2.5 x 10-8 mutations per nucleotide site or 175 mutations per diploid genome per generation. This is a detailed research paper.

Marine bacteria can create environmentally friendly energy source

Bacteria in the world’s oceans can efficiently exploit solar energy to grow, thanks to a unique light-capturing pigment. "It was long thought that algae were the only organisms in the seas that could use sunlight to grow." Many marine bacteria have a gene in their DNA that codes for a new type of light-capturing pigment: proteorhodopsin. Oesearchers collected 20 marine bacteria from different ocean areas and mapped their genomes. Several of them proved to contain the pigment proteorhodopsin. This made it possible to run a series of experiments that clearly show that the pigment converts solar energy to energy for growth.

Modern brains have an ancient core

Multifunctional neurons that sense the environment and release hormones are the evolutionary basis of our brains. Hormones control growth, metabolism, reproduction and many other important biological processes. In humans, and all other vertebrates, the chemical signals are produced by specialised brain centres such as the hypothalamus and secreted into the blood stream that distributes them around the body. Researchers now reveal that the hypothalamus and its hormones are not purely vertebrate inventions, but have their evolutionary roots in marine, worm-like ancestors. Hormone-secreting brain centres are much older than expected and likely evolved from multifunctional cells of the last common ancestor of vertebrates, flies and worms. "Vertebrate-type hormones were found in annelid worms and molluscs, indicating that these centres might be much older than expected." "So far we have always understood the brain as a processing unit, a bit like a computer that integrates and interprets incoming sensory information. Now we know that the brain is itself a sensory organ and has been so since very ancient times."

Female Hyenas Prefer Foreign Mates: Study

When it comes to picking a mate, female hyenas prefer the mysterious stranger to the boy next door, researchers said on Wednesday, in a finding that explains why male hyenas who leave the home clan are luckiest in love. The preference for the outsider helps female spotted hyenas avoid inbreeding.

Mathematicians discover a simple way to formulate complex scientific results

A new analysis of behaviour in a structured population illuminates Darwin’s theories of co-operation and competition between kin, and provides an abstract model that could simplify scientists’ quest to map behaviour among disease-causing organisms within a cell. The study presents a simple formula for balancing the benefit and cost in altruistic acts, allowing researchers to predict behaviour and summarize disparate results in a simple framework.

Menstrual mood swings may have a use after all

The monthly mood swings experienced by many women may serve an evolutionary purpose. "The increased availability, receptivity and desire that may occur during the ovulatory period has been thought to facilitate procreation."

Mastodon DNA sequenced

The mastodon, an extinct relative of modern elephants, has become the latest prehistoric animal to have its DNA sequenced. Using a fossilized tooth, they sequenced all the DNA of the mastodon's mitochondrion, an energy-generating structure in the cell with its own small genome. The tooth is believed to be 50,000-130,000 years old, making the mastodon's the oldest complete mitochondrial genome decoded so far.

Bee fossil, DNA generate a buzz

Scientists have identified the oldest known bee, a 100 million-year-old specimen preserved in amber. The discovery coincides with the publication of the genetic blueprint of the honeybee, which reveals surprising links with mammals, including humans.

Evolutionary genetics, speciation, adaptive radiation and biogeography of bacteria.

Microbial population biologists have recently determined that the character of genetic exchange in bacteria is very different from that in eukaryotes: bacteria do not exchange genes often, but when they do, they are not fussy about their partners. We have modeled the effects of rare but promiscuous genetic exchange on the population structure of bacteria. Recombination is too rare to hinder adaptive divergence between bacterial populations. Therefore, speciation in bacteria does not require evolution of barriers to genetic exchange.

Nobel Laureate Finds 'Elegant' Explanation For DNA Transcribing Enzyme's High Fidelity

Roger Kornberg won the Nobel Prize in Chemistry for his efforts to unravel the molecular basis of eukaryotic transcription, in which enzymes give 'voice' to DNA by copying it into the RNA molecules that serve as templates for protein in organisms from yeast to humans. Now, Kornberg and his colleagues report new structures that reveal another critical piece of the puzzle: how the so-called polymerase II enzyme discriminates among potential RNA building blocks to ensure the characteristic accuracy of the process. The researchers found that a portion of the enzyme known as the trigger loop acts like a 'trap door,' swinging beneath a matching nucleoside triphosphate (NTP) building block, to close off the active center and form an extensive network of interactions with the NTP and other parts of the enzyme.

New findings challenge established views about human genome

The ENCyclopedia Of DNA Elements [ENCODE] today published the results of its exhaustive, four-year effort to build a "parts list" of all biologically functional elements in 1 percent of the human genome. The project served as a pilot to test the feasibility of a full-scale initiative to produce a comprehensive catalog of all components of the human genome crucial for biological function. The findings challenge the traditional view of our genetic blueprint as a tidy collection of independent genes, pointing instead to a network in which genes, regulatory elements and other types of DNA sequences interact in complex, overlapping ways. "Our results provide new perspectives on everything from DNA transcription to mammalian evolution. In particular, we gained significant insight into DNA sequences that do not encode proteins, which we knew very little about before." The ENCODE consortium's major findings include the discovery that the majority of human DNA is transcribed into RNA and that these transcripts extensively overlap one another. This broad pattern of transcription challenges the long-standing view that the human genome consists of a small set of discrete genes, along with a vast amount of "junk" DNA that is not biologically active. The new data indicate that the genome contains little unused sequences; genes are just one of many types of DNA sequences that have a functional impact. They identified many previously unrecognized start sites for transcription and regulatory sequences that contrary to traditional views are located not only upstream but also downstream of transcription start sites. Other surprises have major implications for our understanding of the evolution of genomes. Until recently, researchers had thought that most DNA sequences with important biological function would be constrained by evolution making them likely to be conserved as species evolve. But about half of the functional elements in the human genome do not appear to have been constrained during evolution, suggesting that many species' genomes contain a pool of functional elements that provide no specific benefits in terms of survival or reproduction.

New Clues to How Sex Evolves

Researchers have identified a key family of genes and proteins that help bring C. elegans chromosomes together during meiosis. This specialized cell division produces gametes, or sex cells, each of which has only one copy of each chromosome instead of the two copies most cells carry. During meiosis a cell replicates and then divides twice, resulting in sperm or eggs with just one set of chromosomes each. For meiosis to work properly, corresponding chromosomes must first identify each other, then line up accurately and stay together during the recombination process. Different organisms use different methods for these critical steps; in C. elegans, the job is initiated by regions called Pairing Centers, which are found near one end of each of the worm's six chromosome. Dernburg's lab has been studying the role of these special regions.

The origin of the brain lies in a worm

Researchers discover that the centralised nervous system of vertebrates is much older than expected. The rise of the central nervous system [CNS] in animal evolution has puzzled scientists for centuries. Vertebrates, insects and worms evolved from the same ancestor, but their CNSs are different and were thought to have evolved only after their lineages had split during evolution. Researchers now reveal that the vertebrate nervous system is probably much older than expected. The study suggests that the last common ancestor of vertebrates, insects and worms already had a centralised nervous system resembling that of vertebrates today. Many animals have evolved complex nervous systems throughout the course of evolution, but their architectures can differ substantially between species. While vertebrates have a CNS in the shape of a spinal cord running along their backs, insects and annelid worms like the earthworm have a rope-ladder-like chain of nerve cell clusters on their belly side. Other invertebrates on the other hand have their nerve cells distributed diffusely over their body. Yet, all these species descend from a common ancestor called Urbilateria. The findings provide strong evidence for a theory that was first put forward by zoologist Anton Dohrn in 1875. It states that vertebrate and annelid CNS are of common descent and vertebrates have turned themselves upside down throughout the course of evolution.

Extinct cave bear DNA sequenced

Scientists have extracted and decoded the DNA of a cave bear that died 40,000 years ago. They plan to unravel the DNA of other extinct species, including our closest ancient relatives, the Neanderthals, and they hope to be able to sequence the DNA of ancient humans.

Greenland really was green, world's oldest DNA reveals

The oldest DNA found on earth has been collected from under a kilometre of ice in Greenland, revealing that the frozen island really was once green. A Danish-led team, including the Australian researcher Michael Bunce, extracted the ancient DNA from the muddy bottoms of cores drilled deep into the ice cap in southern Greenland. The researchers identified genetic traces of a surprising variety of tree species, including spruce, pine and yew. The team believes the DNA is between 450,000 and 800,000 years old, based on their analysis of insect genetic material.

Investigating the invisible life in our environment

Microorganisms make up more than a third of the Earth's biomass. They are found in water, on land and even in our bodies, recycling nutrients, influencing the planet's climate or causing diseases. Still, we know surprisingly little about the smallest beings that colonise Earth. A new computational method to analyse environmental DNA samples now sheds light on the microbial composition of different habitats, from soil to water. The study reveals that microbes evolve faster in some environments than in others and that they rather rarely change their habitat preferences over time. Studying microorganisms has proven very difficult because most naturally occurring types do not grow in the lab. The rapidly growing field of environmental DNA sequencing now helps to overcome this problem. Instead of analysing the genome of a specific organism, scientists sequence all the DNA they find in environmental samples, ranging from seawater to soil. They collect vast amounts of sequence fragments, which contain genetic information of thousands of species forming communities that colonise a certain habitat.

Fast-Reproducing Microbes Provide a Window on Natural Selection

In the corner of a laboratory, one of the longest-running experiments in evolution is quietly unfolding. A dozen flasks of sugary broth swirl on a gently rocking table. Each is home to hundreds of millions of E. coli, the common gut microbe. These 12 lines of bacteria have been reproducing since 1989, when Richard Lenski bred them from a single E. coli. "I originally thought it might go a couple thousand generations, but it's kept going and stayed interesting." In that time, the bacteria have changed significantly. And thanks to the falling price of genome-sequencing technology, scientists can now zero in on the precise genetic changes that unfold during evolution, a power previous generations of researchers only dreamed of.

Dan Dennett: Ants, terrorism, and the awesome power of memes

People resist the idea of applying evolutionary thinking to -- thinking. Here's one of those talks that can change your view of the world forever. Starting with the deceptively simple story of an ant, Dan Dennett unleashes a dazzling sequence of ideas, making a powerful case for the existence of "memes" -- a term coined by Richard Dawkins for mental concepts that are literally alive and capable of spreading from brain to brain. On the way, look out for: a powerful one-sentence secret of happiness, a compelling insight into terrorists' motivation, a chilling view of Islam, And just when you think you know where the talk's heading, it dramatically shifts direction and questions some of western culture's fundamental assumptions.

Video, 15 min 39 sec

Researchers shed light on shrinking of chromosomes

Late shortening of chromosomes helps cells to organise and protect their DNA during cell division. A human cell contains an enormous 1.8 metres of DNA partitioned into 46 chromosomes. These have to be copied and distributed equally into two daughter cells at every division. Condensation, the shortening of chromosomes, allows the cell to handle such huge amounts of genetic material during cell division and helps preventing fatal defects in chromosome separation. Researchers tracked chromosome condensation in mammalian cells over the entire course of cell division. They report crucial new insights into timing, function and molecular basis of chromosome condensation. What happens when chromosomes are not correctly separated and distributed during cell division we know very well; two daughter cells with either broken chromosomes or different numbers of chromosomes result and severe diseases including cancer can arise. Using powerful microscopes, researchers looked at living mammalian cells to find out how and when chromosomes shorten during cell division. When the cell starts preparing for division, the chromosomes become shorter and shorter until they are about to separate and migrate towards the poles of the cell. "Shortly after they finish separating, chromosomes actually condense even further. In this way they are shortest when the physical division of one cell body into two takes place. No long chromosome arms extend over the plane of division, because that could expose the DNA to serious mechanical damage."

When hunted becomes more valuable than hunter

In any kind of acquisition, the hunted see their valuations move up and that is not good news for people who like to apply Darwinism as a concept to understand price behaviour in the financial markets. The theory of natural selection by Charles Darwin has been considered the fundamental theory of evolution where species with favourable traits are more likely to survive and reproduce than those with unfavourable traits. If Darwin’s theory is to explain price behaviour in financial markets, then the acquirer should show a higher rise in its market capitalisation compared to the one that is being acquired. Is something wrong with the way we apply Darwinism to financial markets? Ask Vernor Vinge, a science fiction author and a mathematician/computer scientist who is better known for his theory of Singularity where he has made a mathematical prediction that technology will acquire human-like smartness by 2025.

Study Shows Bacteria Are Common in Snow

Those beautiful snowflakes drifting out of the sky may have a surprise inside — bacteria. Most snow and rain forms in chilly conditions high in the sky and atmospheric scientists have long known that, under most conditions, the moisture needs something to cling to in order to condense. Now, a new study shows a surprisingly large share of those so-called nucleators turn out to be bacteria that can affect plants.

Sociable, and Smart

For the past two decades, Kay E. Holekamp has been chronicling the lives of spotted hyenas on the savannas of southern Kenya. She has watched cubs emerge from their dens and take their place in the hyena hierarchy; she has seen alliances form and collapse. She has observed clan wars, in which dozens of hyenas have joined together to defend their hunting grounds against invaders.

The state of the art in the RNA world

As an employee of the National Center for Science Education, Nick Matzke was involved with everything from situations that never made the press to coaching the lawyers in the Dover trial, which gained international attention. One thing that apparently became clear is that, due to the highly technical material and a flood of misinformation on the topic, the public (and even many scientists) simply don't know what the current state of knowledge is when it comes from evolution. As part of an effort to rectify that, the NCSE and the AAAS's Dialog on Science, Ethics, and Religion organized a session on the state of the art in our understanding of evolution, which Matzke moderated. Four speakers took on topics that appear to be the frequently misunderstood by the public.

The Gay Animal Kingdom

Joan Roughgarden thinks Charles Darwin made a terrible mistake. Not about natural selection—she's no bible-toting creationist—but about his other great theory of evolution: sexual selection. According to Roughgarden, sexual selection can't explain the homosexuality that's been documented in over 450 different vertebrate species. This means that same-sex sexuality—long disparaged as a quirk of human culture—is a normal, and probably necessary, fact of life. By neglecting all those gay animals, she says, Darwin misunderstood the basic nature of heterosexuality.

The Encyclopedia of Life, No Bookshelf Required

Imagine the Book of All Species: a single volume made up of one-page descriptions of every species known to science. On one page is the blue-footed booby. On another, the Douglas fir. Another, the oyster mushroom. If you owned the Book of All Species, you would need quite a bookshelf to hold it. Just to cover the 1.8 million known species, the book would have to be more than 300 feet long. And you’d have to be ready to expand the bookshelf strikingly, because scientists estimate there are 10 times more species waiting to be discovered. It sounds surreal, and yet scientists are writing the Book of All Species. Or to be more precise, they are building a Web site called the Encyclopedia of Life (www.eol.org).

Building brains: mammalian-like neurogenesis in fruit flies

Scientists at the Biozentrum have uncovered a new way of generating nerve cells in the developing brain of the fruitfly Drosophila. Their findings reveal that this novel mode of neurogenesis is very similar to that seen in mammalian brains. This newly discovered similarity in brain development in flies and mammals provides further evidence for a surprising evolutionary conservation of the mechanisms for building the brains of all animals.