New evidence emerges on the origins of life

Via Phys.org:

In the beginning, there were simple chemicals. And they produced amino acids that eventually became the proteins necessary to create single cells. And the single cells became plants and animals. Recent research is revealing how the primordial soup created the amino acid building blocks, and there is widespread scientific consensus on the evolution from the first cell into plants and animals. But it's still a mystery how the building blocks were first assembled into the proteins that formed the machinery of all cells. Now, two long-time University of North Carolina scientists - Richard Wolfenden, PhD, and Charles Carter, PhD - have shed new light on the transition from building blocks into life some 4 billion years ago...

Related:

• Science News: Peptides May Hold 'Missing Link' to Life
• Science Sunday Bonus: Research on possible origins of primitive cells
• Structure of 450 million year old protein reveals evolution's steps details new research from the August 17th, 2007 journal Science.
• Discover Magazine (Nov. 1995): First Cell

Neural Network Assisted Evolution

Expanded DNA alphabet provides more options for nanotechnology:

Long-time readers of Nanodot may remember the section of Chapter 15 of Nanosystems in which Drexler explores options for producing easier to design proteins for the protein engineering path toward atomically precise manufacturing by incorporating specially chosen amino acids in addition to the 20 genetically encoded amino acids. Back in 1992 the only option for incorporating unnatural amino acids into proteins was Merrifield solid phase peptide synthesis, using the methods of organic chemistry rather than biological systems. However, this becomes problematic and expensive for longer chains. Consequently, finding ways to expand the repertoire of biologically encoded amino acids would be quite useful. One way to accomplish this goal would be to expand the DNA ‘alphabet’ from two to three base pairs (that is, from four to six ‘letters’). We noted progress in this direction back in February of 2008 when Floyd Romesberg, at the Scripps Research Institute, La Jolla, California created two artificial DNA letters that were accurately and efficiently replicated by a natural enzyme. In September of 2011 we noted a different approach taken by a team at the Salk Institute that keeps the current DNA alphabet but alters one three-letter word to mean an unnatural amino acid, increasing the amino acid repertoire by one. We noted in June of 2012 that continued work by Romesberg had revealed how the new base pair was efficiently replicated in the test tube by a natural enzyme. In a major advance, Romesberg and his collaborators have engineered a living organism to stably propagate the expanded genetic alphabet...

Amazing Parasitic Mind Control

Ed Yong: Suicidal wasps, zombie roaches and other parasite tales:



Related: Daniel Dennett's Dangerous Memes:

Devolution

Texting for long periods 'could lower life expectancy': The United Chiropractic Association warns that bad posture due to mobile phone use could shorten your life :

Texting and using mobile devices for long periods of time could lead to lower life expectancy, chiropractors have warned.

The forward-leaning posture that many people adopt when texting, going online, sending emails or playing games on phones and other mobile devices increases the risk of an early death in elderly people, and there are fears that younger people could also be knocking time off their lives...

Organic Chemicals Self Assemble

Intelligent Design need not apply, both figuratively and literally.  More evidence:

Study shows short peptides can self-assemble into catalysts:

A team of researchers with members from Syracuse University and the University of California, has found that naturally forming peptides can self-assemble into catalysts. In their paper published in the journal Nature Chemistry, the team describes how they designed seven peptides, allowed the resulting molecules to self-assemble into amyloids and then noted how many of them could catalyze the hydrolysis of esters...

...To learn more, the team created seven modest peptides, each of which were constructed from just seven amino acids—putting them together in a dish, with a dash of zinc iron to help move things along, allowed the peptides to self-form into different sheet-like fibril amyloids. During testing, four of the amyloids the team created were found to be able to catalyze the hydrolysis of esters.

The results of the team's experiments suggest that enzymes didn't necessarily have to spring forth fully formed from the primordial soup for life to begin, perhaps amyloids came first, serving as an intermediary, or a sort of blueprint—over millions of years the amyloids could have given way to the much more complicated enzymes, leading eventually to living organisms.

Related (Amino Acids occur naturally):

• Life Ingredients Found in Superhot Meteorites—A First: New evidence that space rocks may have seeded life on Earth.
• Origins of life: New model may explain emergence of self-replication on early Earth

ScienceDaily: Life On Earth Shockingly Comes from out of This World

Early Earth was not very hospitable when it came to jump starting life. In fact, new research shows that life on Earth may have come from out of this world...

TED Video: The Evolution of Compassion

Related:

• Game Theory Explained
• Generous players: game theory explores the Golden Rule's place in biology
• Religion: A man-made, two-edged sword
• Response to "If there is no God, then why be moral?"

The Two-Edged Sword of Evolution

Recent developments should remind us that Evolution implements an 'Error-then-Trial' dynamic; mutations followed by adaptive fitness tests in the environment.

The Moffitt Cancer Center made available the following press release: 'Moffitt Cancer Center Researchers: Darwin s Principles Say Cancer Will Always Evolve to Resist Treatment: However, principles of natural selection may also hold key to thwarting emergence of drug resistance'.

Science Magazine reports that 'Chicken Vaccines Combine to Produce Deadly Virus'.  This echoes findings in 2009 that certain types of bacteria integrate the DNA that they have captured from invading enemies into their own genetic makeup to increase their chances of survival.

We must be mindful that the strategy of mutations followed by a test for evolutionary fitness by its very nature has unintended consequences; at least from a human perspective.  Evolution couldn't care less.  Even implying that it could 'care' one-way-or-the-other is an anthropomorphic fallacy.

Research has also revealed that prions, bits of infectious protein devoid of DNA or RNA, evolve.

That fact that cancer cells resist treatment, different virus/bacterial strains share genetic material and even lifeless disease causing proteins undergo Evolution should remind us that it is a two-edged sword.

You Don't Need a Meaning of Life to Have a Meaningful Life

Like fairness, perception of meaning has neural correlates.  It would be a logical fallacy to conclude that there's a 'Meaning of Life' just because we have evolved the capacity to perceive meaning.

Therefore, you don't need a 'Meaning of Life' to have a meaningful life; a life full of meaning.  Reflecting, another skill/dynamic of the mind, on the probability of life in the universe is sufficient to conclude that the life we do have is 'special'; or at least rare.  All the more special with the knowledge that death terminates one's possible, but low probability life.

The same mental dynamics that result in 'meaning' are also making great strides in revealing the origin's of life:

• Scientists Discover New Clue to Chemical Origins of Life 
• Biologists Replicate Key Evolutionary Step
• Scientists Take First Step Towards Creating 'Inorganic Life' 
• Peptides May Hold 'Missing Link' to Life
• Simple membranes could have allowed nutrients to pass into primitive cells
• Structure of 450 million year old protein reveals evolution's steps
• Discover Magazine (Nov. 1995): First Cell
• 'Lifeless' Prions Capable of Evolutionary Change and Adaptation
• Evolution Can Occur In Less Than 10 Years, Guppy Study Finds
• Bacteria make major evolutionary shift in the lab
• Two New Discoveries Answer Big Questions in Evolution Theory
• Evolution in Action
• New Evidence Emerges on the Origin of Life

Prions and Long-term Memories

Making Memories Last: Prion-Like Protein Plays Key Role in Storing Long-Term Memories

ScienceDaily (Jan. 27, 2012) — Memories in our brains are maintained by connections between neurons called "synapses." But how do these synapses stay strong and keep memories alive for decades? Neuroscientists at the Stowers Institute for Medical Research have discovered a major clue from a study in fruit flies: Hardy, self-copying clusters or oligomers of a synapse protein are an essential ingredient for the formation of long-term memory

The finding supports a surprising new theory about memory, and may have a profound impact on explaining other oligomer-linked functions and diseases in the brain, including Alzheimer's disease and prion diseases.

"Self-sustaining populations of oligomers located at synapses may be the key to the long-term synaptic changes that underlie memory; in fact, our finding hints that oligomers play a wider role in the brain than has been thought," says Kausik Si, Ph.D., an associate investigator at the Stowers Institute, and senior author of the new study, which is published in the January 27, 2012 online issue of the journal Cell.

Related: Evolution May be a Process that is Indpendent of Genetic Material: 'Lifeless' Prions Capable of Evolutionary Change and Adaptation

Scientists Discover New Clue to Chemical Origins of Life

ScienceDaily (Jan. 24, 2012) — Organic chemists at the University of York have made a significant advance towards establishing the origin of the carbohydrates (sugars) that form the building blocks of life.

A team led by Dr Paul Clarke in the Department of Chemistry at York has re-created a process which could have occurred in the prebiotic world.

Working with colleagues at the University of Nottingham, they have made the first step towards showing how simple sugars -- threose and erythrose -- developed. The research is published in Organic & Biomolecular Chemistry...

Fascinating Research on the Origins of Multicellular Life

Biologists Replicate Key Evolutionary Step

ScienceDaily (Jan. 17, 2012) — More than 500 million years ago, single-celled organisms on Earth's surface began forming multicellular clusters that ultimately became plants and animals. Just how that happened is a question that has eluded evolutionary biologists.

But scientists in the University of Minnesota's College of Biological Sciences have replicated that key step in the laboratory using natural selection and common brewer's yeast, which are single-celled organisms. The yeast "evolved" into multicellular clusters that work together cooperatively, reproduce and adapt to their environment -- in essence, precursors to life on Earth as it is today.

Their achievement is published in the January 16 issue of Proceedings of the National Academy of Sciences...

...In essence, here's how the experiments worked. The two chose brewer's yeast or Saccharomyces cerevisiae, a species of yeast used since ancient times to make bread and beer, because it is abundant in nature and grows easily. They added it to a nutrient-rich culture media and allowed the cells to grow for a day in test tubes. Then they used a centrifuge to stratify the contents by weight. As the mixture settled, cell clusters landed on the bottom of the tubes faster because they are heavier. They removed the clusters, transferred them to fresh media, and grew them up again. Sixty cycles later, the clusters -- now hundreds of cells -- looked roughly like spherical snowflakes.

Analysis showed that the clusters were not just groups of random cells that adhered to each other, but related cells that remained attached following cell division. That was significant because it meant they were genetically similar, which promotes cooperation. When the clusters reached a critical size, some cells essentially committed suicide (apoptosis) to allow offspring to separate. The offspring reproduced only after they attained the size of their parents.

"A cluster alone isn't multicellular," Ratcliff said. "But when cells in a cluster cooperate, make sacrifices for the common good, and adapt to change, that's an evolutionary transition to multicellularity."

In order for multicellular organisms to form, most cells need to sacrifice their ability to reproduce, an altruistic action that favors the whole but not the individual, Ratcliff said. For example, all cells in the human body are essentially a support system that allows sperm and eggs to pass DNA along to the next generation. Thus, multicellularity is by its nature extremely cooperative. "Some of the best competitors in nature are those that engage in cooperation, and our experiment bears that out," said Travisano...

Scientists Discover 'Hidden' Code in DNA Evolves More Rapidly Than Genetic Code

Just when we thought we had it all figured out:

ScienceDaily (Sep. 16, 2011) — A "hidden" code linked to the DNA of plants allows them to develop and pass down new biological traits far more rapidly than previously thought, according to the findings of a groundbreaking study by researchers at the Salk Institute for Biological Studies...

Scientists Take First Step Towards Creating 'Inorganic Life'

ScienceDaily (Sep. 15, 2011) — Scientists at the University of Glasgow say they have taken their first tentative steps towards creating 'life' from inorganic chemicals potentially defining the new area of 'inorganic biology'...

Science News: Peptides May Hold 'Missing Link' to Life

ScienceDaily (May 7, 2010) — Emory scientists have discovered that simple peptides can organize into bi-layer membranes. The finding suggests a "missing link" between the pre-biotic Earth's chemical inventory and the organizational scaffolding essential to life.

"We've shown that peptides can form the kind of membranes needed to create long-range order," says chemistry graduate student Seth Childers, lead author of the paper recently published by the German Chemical Society's Angewandte Chemie. "What's also interesting is that these peptide membranes may have the potential to function in a complex way, like a protein."...

Related:

• Science Sunday Bonus: Research on possible origins of primitive cells
• Structure of 450 million year old protein reveals evolution's steps details new research from the August 17th, 2007 journal Science.
• Discover Magazine (Nov. 1995): First Cell:

Evolution May be a Process that is Indpendent of Genetic Material

'Lifeless' Prions Capable of Evolutionary Change and Adaptation:

ScienceDaily (Jan. 3, 2010) — Scientists from The Scripps Research Institute have determined for the first time that prions, bits of infectious protein devoid of DNA or RNA that can cause fatal neurodegenerative disease, are capable of Darwinian evolution.

The study from Scripps Florida in Jupiter shows that prions can develop large numbers of mutations at the protein level and, through natural selection, these mutations can eventually bring about such evolutionary adaptations as drug resistance, a phenomenon previously known to occur only in bacteria and viruses. These breakthrough findings also suggest that the normal prion protein -- which occurs naturally in human cells -- may prove to be a more effective therapeutic target than its abnormal toxic relation.

The study was published in the December 31, 2009 issue of the journal Science Express, an advance, online edition of the journal Science.

"On the face of it, you have exactly the same process of mutation and adaptive change in prions as you see in viruses," said Charles Weissmann, M.D., Ph.D., the head of Scripps Florida's Department of Infectology, who led the study. "This means that this pattern of Darwinian evolution appears to be universally active. In viruses, mutation is linked to changes in nucleic acid sequence that leads to resistance. Now, this adaptability has moved one level down -- to prions and protein folding -- and it's clear that you do not need nucleic acid for the process of evolution."

Infectious prions (short for proteinaceous infectious particles) are associated with some 20 different diseases in humans and animals, including mad cow disease and a rare human form, Creutzfeldt-Jakob disease. All these diseases are untreatable and eventually fatal. Prions, which are composed solely of protein, are classified by distinct strains, originally characterized by their incubation time and the disease they cause. Prions have the ability to reproduce, despite the fact that they contain no nucleic acid genome.

Mammalian cells normally produce cellular prion protein or PrPC. During infection, abnormal or misfolded protein -- known as PrPSc -- converts the normal host prion protein into its toxic form by changing its conformation or shape. The end-stage consists of large assemblies (polymers) of these misfolded proteins, which cause massive tissue and cell damage.

"It was generally thought that once cellular prion protein was converted into the abnormal form, there was no further change," Weissmann said. "But there have been hints that something was happening. When you transmit prions from sheep to mice, they become more virulent over time. Now we know that the abnormal prions replicate, and create variants, perhaps at a low level initially. But once they are transferred to a new host, natural selection will eventually choose the more virulent and aggressive variants."...

Evolution in the Blink of an Eye

Science News: Evolution Can Occur In Less Than 10 Years, Guppy Study Finds:

How fast can evolution take place? In just a few years, according to a new study on guppies led by UC Riverside's Swanne Gordon, a graduate student in biology.

Gordon and her colleagues studied guppies — small fresh-water fish biologists have studied for long — from the Yarra River, Trinidad. They introduced the guppies into the nearby Damier River, in a section above a barrier waterfall that excluded all predators. The guppies and their descendents also colonized the lower portion of the stream, below the barrier waterfall, that contained natural predators.

Eight years later (less than 30 guppy generations), the researchers found that the guppies in the low-predation environment above the barrier waterfall had adapted to their new environment by producing larger and fewer offspring with each reproductive cycle. No such adaptation was seen in the guppies that colonized the high-predation environment below the barrier waterfall.

"High-predation females invest more resources into current reproduction because a high rate of mortality, driven by predators, means these females may not get another chance to reproduce," explained Gordon, who works in the lab of David Reznick, a professor of biology. "Low-predation females, on the other hand, produce larger embryos because the larger babies are more competitive in the resource-limited environments typical of low-predation sites. Moreover, low-predation females produce fewer embryos not only because they have larger embryos but also because they invest fewer resources in current reproduction."

Natural guppy populations can be divided into two basic types. High-predation populations are usually found in the downstream reaches of rivers, where they coexist with predatory fishes that have strong effects on guppy demographics. Low-predation populations are typically found in upstream tributaries above barrier waterfalls, where strong predatory fishes are absent. Researchers have found that this broad contrast in predation regime has driven the evolution of many adaptive differences between the two guppy types in color, morphology, behavior, and life history.

Gordon's research team performed a second experiment to measure how well adapted to survival the new population of guppies were. To this end, they introduced two new sets of guppies, one from a portion of the Yarra River that contained predators and one from a predator-free tributary to the Yarra River into the high-and low-predation environments in the Damier River.

They found that the resident, locally adapted guppies were significantly more likely to survive a four-week time period than the guppies from the two sites on the Yarra River. This was especially true for juveniles. The adapted population of juveniles showed a 54-59 percent increase in survival rate compared to their counterparts from the newly introduced group.

"This shows that adaptive change can improve survival rates after fewer than ten years in a new environment," Gordon said. "It shows, too, that evolution might sometimes influence population dynamics in the face of environmental change."...

Federal Judge says University of California can deny religious course credit

Judge says UC can deny religious course credit (empahsis added):

A federal judge says the University of California can deny course credit to applicants from Christian high schools whose textbooks declare the Bible infallible and reject evolution.

Rejecting claims of religious discrimination and stifling of free expression, U.S. District Judge James Otero of Los Angeles said UC's review committees cited legitimate reasons for rejecting the texts - not because they contained religious viewpoints, but because they omitted important topics in science and history and failed to teach critical thinking.

Otero's ruling Friday, which focused on specific courses and texts, followed his decision in March that found no anti-religious bias in the university's system of reviewing high school classes. Now that the lawsuit has been dismissed, a group of Christian schools has appealed Otero's rulings to the Ninth U.S. Circuit Court of Appeals in San Francisco...

Advice for a zealous atheist

Zealotry is not a behavior limited to religous individuals. Atheists can also be zealots. Take the case of P.Z. Myers:

...Myers is a biologist at the University of Minnesota at Morris who has a national following for Pharyngula, the blog on which he regularly exposes and lambastes efforts by creationists to undermine the teaching of evolution. A few weeks ago, he wrote a blog entry in which he defended a University of Central Florida student who protested the presence of religious groups on his campus by taking a Eucharist — the small wafer blessed in Roman Catholic services and then seen as the body of Christ — and removing it from the service rather than consuming it. Myers, in an entry entitled “It’s a Frackin’ Cracker” — questioned why this was such a big deal.

Ever since, Myers and his university have been bombarded by e-mail and other messages attacking him and calling for the university to punish him for insulting Catholic teachings.

On Thursday, Myers responded by staging what he called a “great desecration.” For the desecration, he took a communion wafer (sent to him by a supporter in the United Kingdom, who removed it from a church there), and pierced it with a rusty nail. ("I hope Jesus’s tetanus shots are up to date,” Myers quipped on the blog.) He then threw it in the garbage with a banana peel and coffee grounds, symbols of refuse. But to show that he wasn’t picking on Catholics, Myers added to his mixture some ripped out pages of the Koran. As a proud atheist, Myers isn’t a member of a faith that he could desecrate at the same time so he took a text he does cherish — The God Delusion, by Richard Dawkins — and tore some pages out and added them to the trash...

Atheist like Professor Myers should keep in mind that many fellow scientists are making the case that religion itself is an evolutionary phenomenon. David Sloan Wilson, for one, has taken on none other than Richard Dawkins for his derision of 'God' delusionists.

In the search for greater understanding, which should be the primary goal of any scientists, an appreciation for religion - both its contributions and its detractions to our humanity - should inform the rhetoric.

There is something to be said for the psychology inherent within the old adage: You attract more bees with honey than with vinegar. Ridicule of religon may just activate a primative 'fight' response rather than the rational, disspassionate critical thinking atheists should be striving for.

Reproducible Evidence of Evolution

Bacteria make major evolutionary shift in the lab (HT: Instapundit):

22:00 09 June 2008
NewScientist.com news service
Bob Holmes

A major evolutionary innovation has unfurled right in front of researchers' eyes. It's the first time evolution has been caught in the act of making such a rare and complex new trait.

And because the species in question is a bacterium, scientists have been able to replay history to show how this evolutionary novelty grew from the accumulation of unpredictable, chance events.

Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.

Profound change

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity...

...Evidence of evolution

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve.

Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories.