Biosphere

The date when Darwin and Wallace announced the theory of evolution

Good article from Wired.

Darwin’s first draft of his theory of evolution now goes online, now joining the 20,000 archive items in the online archive run by Cambridge University ‘The Complete Work of Charles Darwin Online‘.

This will definitely be a valuable resource for educators and scientists alike.

For more read:
Darwin’s first draft goes online

This might be a milestone in macroevolutionary studies. How does a tetrapod lose its lungs?

Sad thing is that frog faces severe threat of habitat degradation.

For more reads -

The Enigmatic Bornean Lungless Frog – Barbourula kalimantanensis (Anura: Bombinatoridae) - A First Hand Encounter - By Dr Tan Heok Hui

First Lungless Frog Found - By National Geographic

Siva’s writeup

Here’s a good animation and summary of the major evolutionary events on Earth since its formation 4.5 billion years ago.

One big bane of our medical advances and and classic case of evolution action. MRSA has claimed 19 000 lives in the US in 2005.

Read the article from NY Times.

October 16, 2007
Infection Killed 19,000 in 2005, Study Says

By KEVIN SACK
ATLANTA, Oct. 16 — Nearly 19,000 people died in the United States in 2005 after being infected with a virulent drug-resistant bacterium that has spread rampantly through hospitals and nursing homes, according to the most thorough study to be conducted of the disease’s prevalence.

The study, which was published today in The Journal of the American Medical Association, suggests that invasive infections with methicillin-resistant Staphylococcus aureus, or M.R.S.A., may be twice as common as previously thought, according to its lead author, Dr. R. Monina Klevens. If the mortality estimates are correct, the number of deaths associated with M.R.S.A. each year would exceed those attributed to HIV/AIDS, Parkinson’s disease, emphysema or homicide.

By extrapolating data collected in nine locations, the researchers established the first true baseline for M.R.S.A. in the United States, projecting that 94,360 patients developed an invasive infection from the pathogen in 2005 and that nearly one of every five, or 18,650 of them, died.

The authors, who work for the Centers for Disease Control and Prevention, cautioned that their methodology differed significantly from previous studies and that direct comparisons were therefore risky. But they said they were surprised by the prevalence of the serious infections they found, which they calculated as 32 cases per 100,000 people.

In an accompanying editorial in the medical journal, Dr. Elizabeth A. Bancroft, an epidemiologist with the Los Angeles County Department of Public Health, characterized that finding as “astounding.” She wrote that the prevalence of invasive M.R.S.A. — when the bacteria has not merely colonized on the skin, but has attacked a normally sterile part of the body, like the organs or bloodstream — is greater than the combined rates for other conditions caused by invasive bacteria, including bloodstream infections, meningitis and flesh-eating disease.

The study also concluded that 85 percent of invasive M.R.S.A. infections are associated with health-care treatment. Previous research had indicated that many hospitals and long-term care centers have become breeding grounds for M.R.S.A. because bacteria may be transported from patient to patient by doctors, nurses and unsterile equipment.

“This confirms in a very rigorous way that this is a huge health problem,” said Dr. John A. Jernigan, the deputy chief of prevention and response in the C.D.C.’s Division of Healthcare Quality Promotion. “And it drives home that what we do in health care will have a lot to do with how we control it.”

The findings are likely to further stimulate an already active debate about whether hospitals and other medical centers should test all patients for M.R.S.A. upon admission. Some hospitals have had notable success in reducing their infection rates by isolating infected patients and then taking extra precautions, like requiring workers to wear gloves and gowns.

But other research has suggested that such techniques may be excessive, and may have the unintended consequence of diminishing medical care for sequestered patients. The C.D.C., in guidelines released last year, recommended that hospitals attempt to reduce their infection rates by first improving hygiene procedures and that they resort to screening high-risk patients only if other methods fail.

Dr. Lance R. Peterson, an epidemiologist with Evanston Northwestern Healthcare, said the Chicago-area hospital system reduced its rate of invasive M.R.S.A. infections by 60 percent after it began screening all patients in 2005.

“This study puts more onus on organizations that don’t do active surveillance to demonstrate that they’re reducing their M.R.S.A. infections,” he said. “Other things can work, but nothing else has been demonstrated to have this kind of impact. M.R.S.A. is theoretically a totally preventable disease.”

Numerous studies have shown that busy hospital workers disregard basic standards of hand-washing more than half the time. This week, Consumers Union, the nonprofit publisher of Consumer Reports, called for hospitals to begin publishing their hand-washing compliance rates.

“This study just accentuates that the hospital is ground zero, that this is where dangerous infections are occurring that are killing people every day,” said Lisa A. McGiffert, manager of the group’s “Stop Hospital Infections” campaign.

Though the C.D.C. estimates that M.R.S.A. represents only 10 percent to 20 percent of all infections acquired in health-care settings, the bacterium is feared for its opportunism and deadliness.

First isolated in the United States in 1968, it is resistant to a number of antibiotics and can cause infections of surgical sites, the urinary tract, the bloodstream and the lungs, leading to extensive and expensive hospital stays. The bacteria can be brought unknowingly into hospitals and nursing homes by patients who show no symptoms, and then takes advantage of weakened immune systems, incisions and wounds.

Of the infections studied by Dr. Klevens and her colleagues, 27 percent were considered to have originated during a patient’s current hospital stay. Another 58 percent were deemed to be associated with a previous hospitalization, nursing home stay, surgery or dialysis. Only 14 percent were cases without a defined health care risk factor, meaning the infection likely originated in the community.

A major difference with previous analyses is that the new study compiled actual confirmed cases of M.R.S.A. infection, rather than relying on coded patient records that sometimes lack precision. In the new study, higher prevalence rates and death rates were found for the elderly, blacks and men. The figures also varied greatly by geography, with Baltimore’s incidence rates far exceeding those of the eight other locations studied.

Dr. Klevens said further research would be needed to understand the racial and geographic disparities.

The C.D.C.’s latest estimate of all infections associated with health care, also taken from a study by Dr. Klevens, was 1.7 million cases and 99,000 associated deaths in 2002.

View this amazing presentation with a nice cup of coffee and a cosy chair. Sit back and let life unfold before you.

Frans Lanting’s Lyrical View of Life

Resources for understanding and simulating evolution.

All block quotes extracted from wikipedia.

Avida Digital Life Platform:

Download Mac version here

Avida is an artificial life software platform to study the evolutionary biology of self-replicating and evolving computer programs (digital organisms). Avida is under active development by Charles Ofria’s Digital Evolution Lab at Michigan State University and was originally designed by Ofria, Chris Adami and C. Titus Brown at Caltech in 1993. The software was inspired by the Tierra system.

Evolve 4.0

Download here.

Evolve 4.0 is an open source, freeware artificial life simulator, developed by Ken Stauffer. It provides a virtual environment in which a number of digital organisms interact, fight for resources, and eventually reproduce and evolve. This version of the software was released in May of 2006. This simulator runs on Windows and the batch mode utility runs on Linux.
Evolve 4.0 is designed to simulate thousands of organisms for many billions of births and deaths. To achieve this level of performance the universe has been simplified to a 2D grid.

Coming up, possibly the coolest game of all time - SPORE. A game with infinite possibilities.

Spore is a PC game under development by Maxis and designed by Will Wright. The game has drawn wide attention for its promise to simulate the development of a species through open-ended, procedural generation, user-guided evolution.

The July 17 Issue of PNAS has an article citing the energy efficiency of bipedalism. This article proposes that being bipedal helps reduce energy costs associated with moving about. By measuring the energy consumption of chimps and humans on a treadmill, Herman Pontzer’s team, from Washington University in St Louis, found that for a given weight, humans used only one-quarter of the energy as the chimps.

Such energy savings may equate to reduced costs incurred during foraging for food.

For the abstract -

Michael D. Sockol, David A. Raichlen, and Herman Pontzer 2007 “Chimpanzee locomotor energetics and the origin of human bipedalism” Proc. Natl. Acad. Sci. USA, 10.1073

Article in Foxnews
Walking on Two Legs Better Than Four by Ker Than

We all do know that genotype precedes phenotype.
Could it happen the other way?

A lovely article from Pharyngula answers this question.

VARIANT GENES-IN-WAITING

An interesting article on Sexual Reproduction by Liza Gross, PLOS Biology.
PLOS Biology - Liza Gross Gross L (2007) Who Needs Sex (or Males)

If you own a birdbath, chances are you’re hosting one of evolutionary biology’s most puzzling enigmas: bdelloid rotifers. These microscopic invertebrates—widely distributed in mosses, creeks, ponds, and other freshwater repositories—abandoned sex perhaps 100 million years ago, yet have apparently diverged into nearly 400 species. Bdelloids (the “b” is silent) reproduce through parthenogenesis, which generates offspring with essentially the same genome as their mother from unfertilized eggs. Biologists have yet to find males, hermaphrodites, or any trace of meiosis—the process that creates sex cells—challenging the long-held assumption that evolutionary success requires genetic exchange.

The genetic variation created by meiosis and fertilization, theory holds, bolsters a species’s capacity to weather shifting environmental conditions or resist rapidly evolving parasites. (During meiosis, the genome splits in two, and chromosome pairs swap bits of their DNA; during fertilization, the sex cells fuse to restore the complete genome.) Many multicellular eukaryotes pass through a sexual and asexual phase in their life cycle. But eschewing sex altogether, à la bdelloids, is not theoretically consistent with a long-lived evolutionary life span or extensive species diversification.

In a new study, Diego Fontaneto, Timothy Barraclough, and colleagues developed new statistical techniques for combined molecular and morphological analyses of rotifers to test the notion that species diversification requires sex. The researchers show that, despite an ancient aversion for interbreeding, bdelloids display evolutionary patterns similar to those seen in sexually reproducing taxa. How they have avoided the pitfalls of a lifestyle widely regarded as evolutionary suicide remains an open question.

Bdelloids have remained such an enduring enigma in part because biologists are still debating whether species exist as true evolutionary entities. And if they do, what forces determine how they diverge? Traditional taxonomy relies on morphological differences to classify species, but it can’t distinguish whether such differences reflect physical variations among a group of clones or adaptations among independently evolving populations. In the traditional view of species diversification, interbreeding promotes cohesion within a population—maintaining the species—and barriers to interbreeding (called reproduction isolation) promote species divergence. With no interbreeding to maintain cohesion, the thinking goes, asexual taxa might not diversify into distinct species.

Scanning electron micrographs showing morphological variation of bdelloid rotifers and their jaws. Have these asexual animals really diversified into evolutionary species? (Image: Diego Fontaneto)

Fontaneto et al. defined species as independently evolving, distinct populations (or units of diversity) subject to distinct evolutionary mechanisms. They predicted that if factors other than interbreeding—such as niche specialization—controlled species cohesion and divergence, then asexual taxa should diverge along the same lines as sexually reproducing organisms. And if this were the case, they would expect to find genetic and morphological cohesion within independently evolving populations and divergence between them.

To detect independently evolving populations, the researchers analyzed marker genes isolated from clones of bdelloids collected from diverse habitats around the world. They constructed evolutionary trees using both mitochondrial and nuclear DNA sequences (the molecular “barcode” cox1and 28S ribosomal DNA sequences, respectively) to identify species within the samples. For the morphological analysis, they measured the size and shape of the rotifers’ jaws (called trophi).

The morphological results largely fell in line with traditional taxonomic classifications for most bdelloid species. And species identified as related on the DNA trees typically had similar morphology. The correspondence between the molecular and morphological results suggests that the majority of traditionally identified bdelloid species are what’s known as monophyletic—individuals in the same species assort together on the evolutionary tree and share a common ancestor. Only two of these traditional, monophyletic species showed significant variation in trophi size or shape among the populations; both also showed significant divergence in the DNA trees.

Using statistical models to determine the likely origin of the observed DNA tree branching patterns, the researchers show that these distinct monophyletic genetic clusters represent independently evolving entities (rather than variations within a single asexual population). But what caused them to evolve independently? Are they geographically isolated populations that evolved under neutral selection, or did they evolve into ecologically discrete species as a result of divergent selection pressures on trophi morphology?

If bdelloids have experienced divergent selection, the researchers explain, they would expect to see high variation in trophi traits between species, and low intraspecies variation (compared to neutral changes). And that’s what they found—bdelloids have experienced divergent selection on trophi size (and to a lesser degree, on trophi shape) at the species level.

Altogether, these results show that the asexual bdelloids have indeed experienced divergent selection on feeding morphology, most likely as they adapted to different food sources found in different niches. By showing that asexual organisms have diverged into “independently evolving and distinct entities,” the researchers argue, this study “refutes the idea that sex is necessary for diversification into evolutionary species.” They hope others use their approach to study mechanisms underlying species divergence in sexual taxa to clarify the hazy nature of species and biological diversity.