GENETICS: Unlocking Humanity's Past and Future

Stormer0628 · Feb 6, 2017

WITH ADVANCES IN SCIENCE, specifically biotechnology, scientists are now planning to bring back to life animals back from extinction, and there are a few already on the list.

Over the millennia, animals have gone extinct on Earth for many different reasons. Sometimes it's because of a dramatic shift in the climate. Other times it was because of human intervention.

Generally, it helps if there is a species still alive today that is genetically similar to the extinct animal, like elephants for woolly mammoths or cows for aurochs.

There are also certain criteria to consider, as bringing an animal back from the grave has a lot of biological and ecological implications.

Scientists must be able to show that the species is desirable, such as having an important ecological function or being beloved by humans. And they also must consider practical matters, such as whether we have access to tissue that could give us good quality DNA samples.

Most importantly, though, the animals must also be able to be reintroduced into the wild in the first place, so sufficient habitats, food, and limited contact with humans are pretty important.

Unfortunately, dinosaurs score badly on all of these points, so there probably isn't ever going to be a real Jurassic Park. However, plenty of animals are still on the table.

Here are some of them from the list of candidate species for de-extinction from the Long Now Foundation, which was founded by biologist and writer Stewart Brand, plus some others added from our own research.

1. Caspian Tigers

During their prime, Caspian tigers could be found in Turkey and through much of Central Asia, including Iran and Iraq, and in Northwestern China as well, but they went extinct in the 1960s.

Some scientists want to bring them back by reintroducing the nearly-identical Siberian tiger to its old habitats, where they expect it to adapt.

2. Aurochs

The aurochs is an ancestor of domestic cattle that lived throughout Europe, Asia, and North Africa.

Scientists want to bring them back through selective breeding of cattle species that carry some aurochs DNA. To this end, European teams have been selectively breeding cattle since 2009.

3. The Carolina Parakeet

The Carolina Parakeet was a small, green parrot with a bright yellow head and orange face that was native to the eastern United States.

The last wild one died in 1904 in Florida, but the genes that made them still linger in close relatives in Mexico and the Caribbean.

4. The Cuban Macaw

The vibrant Cuban macaw lived in Cuba and went extinct in 1885 due to hunting, trading and being captured as pets.

Aviculturalists are rumoured to have bred birds that are similar in appearance, but slightly bigger, because they had similar genes.

5. The Dodo

The dodo is perhaps the most famous extinct animal. It evolved without any natural predators, but the humans that arrived on their home island, Mauritius, took advantage of this and killed them all for food.

In 2007, scientists found the best-preserved dodo skeleton ever, which may hold valuable DNA samples.

6. Woolly Mammoth

Woolly Mammoth carcases have been frozen and preserved, which has allowed scientists to access well-preserved DNA.

The last isolated population of woolly mammoths lived on Wrangel Island in the Arctic Ocean until 4,000 years ago, but scientists contest whether we were to blame for their extinction.

7. The Labrador Duck

The Labrador Duck was always rare but disappeared between 1850 and 1870.

Supposedly it didn't taste good, so it wasn't hunted extensively for food, but scientists believe we are responsible for their extinction nonetheless. This is why they want to bring them back.

8. Woolly Rhinoceros

The woolly rhinoceros was common throughout Europe and Asia.

It had stocky legs and a thick woolly coat that made it well suited for the cold tundra environment during the ice age. Human hunting is often blamed for their extinction, so scientists want to re-introduce them to make up for it.

9. The Heath Hen

The Heath Hen lived in coastal North America up until 1932.

They made for delicious dinners, and were likely the foundation of the Pilgrims' first Thanksgiving. We practically ate them all, which makes them another candidate for de-extinction.

to be continued...

Stormer0628 · Feb 7, 2017

10. The Ivory-billed Woodpecker

The Ivory-billed Woodpecker lived in 'virgin forests' of the southeastern United States, but there hasn't been a confirmed sighting of the bird since the 1940s.

The Cornell Lab of Ornithology even offered a $50,000 reward for someone who could lead researchers to a living specimen.

11. The Imperial Woodpecker

The Imperial Woodpecker may actually still be alive, but hasn't been seen in more than 50 years.

It is officially listed as "critically endangered (possibly extinct)" because a lot of its habitat was destroyed by humans. If it is extinct, scientists want to bring it back to make up for that.

12. The Moa

The Moa were a giant flightless bird from New Zealand that reached 12 feet tall and weighed more than 500 pounds.

They died out because of over hunting by the Maori by 1400, and their closest relatives have been found to be the flighted South American tinamous, which could hold some of their genes.

13. The Elephant Bird

This giant, flightless Elephant bird was found only on the island of Madagascar and died out by the 17th century.

It is widely believed that they went extinct as a result of human activity, so we want to make up for that too.

14. The Pyrenean Ibex

The Pyrenean ibex lived in Southern France and the Northern Pyrenees, but died out in January 2000.

Scientists tried to clone one using DNA from one of the last females, but it died shortly after being born.

15. The Quagga

This extinct species of plains Zebra, the Quagga, once lived in South Africa.

The last wild one was shot in 1870 and the last in captivity died in 1883. The Quagga Project, started in 1987, is an attempt to bring them back from extinction.

16. The Freshwater Dolphin

This freshwater dolphin is known as the Baiji and lived in the Yangtze River in China.

It was declared extinct a decade ago, but scientists claimed to spot one in the river late last year. If some still are alive, conservation efforts will attempt to bring their populations up again.

17. The Tasmanian Tiger

The Thylacine, or Tasmanian Tiger, is the only marsupial to make the list. It's also probably not like any other marsupial you can name.

Although it once lived on mainland Australia and New Guinea - it eventually was limited to Tasmania until the 1930s when it died out.

Tasmanian devils may carry some of its DNA.

18. Irish Elk

Irish elks were one of the largest deer ever to walk the Earth.

The most recent remains of the species have been carbon dated to about 7,700 years ago in Siberia. Red deer or fallow deer might have some similar genes.

19. The Caribbean Monk Seal

The Caribbean monk seal was hunted to extinction for use as oil, and they were out-competed for fish by humans and died out in 1952.

They were closely related to Hawaiian monk seals, which live around the Hawaiian Islands, and Mediterranean monk seals, which are both endangered.

Stormer0628 · Feb 7, 2017

20. The Huia

The Huia was a large species of New Zealand wattlebird.

It went extinct in the 20th century because of hunting to make specimens for museums and private collectors.

The female had a long, curved beak, while the male's was shorter. Very little is known about their actual biology, so bringing them back would be fascinating.

21.The Moho

The Moho are a genus of extinct birds from Hawaii. Most of them died out because of habitat loss and hunting.

The Hawaiian Moho seen here died out in 1934, but some birds like waxwings and the palmchat might carry remnants of their DNA.

22. The Steller's Sea Cow

The Steller's sea cow is related to the manatee and dugong, the two remaining species of sea cow.

They were once abundant in the North Pacific, but within 27 years were hunted to extinction. Dugongs might still be carrying some of its DNA, which could be how scientists bring them back.

23. Passenger Pigeons

With so many pigeons around, it's hard to imagine a species going extinct. But that's what happened to the passenger pigeons, which died out after living in enormous flocks throughout the 20th century.

It was hunted as food for slaves on a massive scale until the last one died in 1914. Passenger pigeons have several living relatives, including the 17 pigeons in the group Patagioenas.

24. The Gastric-brooding Frog

This is the gastric-brooding frog, which swallowed its eggs and hatched them out of its mouth.

It became extinct in 1983, but in 2013, scientists were able to implant a 'dead' cell nucleus into a fresh egg from another frog species.

25. The Great Auk

The Great Auk went extinct in the mid-19th century. They lived in the North Atlantic from Northern Spain through Canada.

They died off because of a combination of climate changes during the Little Ice Age that brought predatory polar bears into their territories, and human hunting. So again, partially our fault.

Stormer0628 · Feb 11, 2017

HOW MUCH OF HUMAN CULTURE and civilization is really due to human free will, cognition, reflection, and introspection?

Multidisciplinary works in psychology, neurology, biology, philosophy, and other disciplines are turning in a frightening response: a dubious chunk of it.

Consider the following:

We humans are more bacteria than human: bacterial cells outnumber human cells 8:1
Bacteria, viruses, parasites are now found to communicate through complex electromagnetic mechanisms, establishing communities, sorting out friends, allies and foes within our bodies.
Bacteria, viruses, parasites are known to affect human psychology and decisions: the vicious ways parasites take over the minds of their victims are now found also happening in humans, not just wasps, ants, and other animals.
The pioneering work of Julian Jaynes through his book, The Bicameral Mind, tells us that human introspection is relatively new to the human species, in effect since a mere 3000 years in the past.
Before human introspection, the left and right hemispheres of the human brain worked as one, the right hemisphere directly overseeing the functions of the left hemisphere. The right hemisphere gives orders thru “inner voices,” something that characterizes schizophrenic individuals even now.
The introduction of human speech in the left hemisphere is the one responsible for human reflection and introspection, finally enabling full cognition in some humans. However, much of human civilization and culture retain the artifacts of pre-introspecting humanity. Much of human religion tell the story.
Schizophrenia is now recognized as the effect of parasitism in the human body—parasites freely taking over the human mind without the knowledge of affected humans. The infection could be as low as 20 percent in some population, to as high as 81 percent in some, as seen in France. The global average is 30 to 40 percent.

We may think we’re independent, capable individuals, calling the shots in our lives from a place of personal freedom, but a new breed of research offers a somewhat terrifying counter argument to this belief. Incredibly, microbes can have a profound effect on our personalities and behavior — and even cause us to be more accident prone.

While quite a bit of focus has been on the gut microbiome — and how it shapes our overall cognitive and mental health — recent discoveries have led scientists to believe this influence extends to viruses and parasites as well. Which brings us to the question: are these microscopic creatures controlling our behavior without us knowing about it?

Microbes Made Me Do It

Now, I think this is part of what makes parasites so sinister and so compelling. We place such a premium on our free will and our independence that the prospect of losing those qualities to forces unseen informs many of our deepest societal fears. Orwellian dystopias and shadowy cabals and mind-controlling super villains — these are tropes that fill our darkest fiction, but in nature, they happen all the time.
~ Ed Yong in Suicidal Wasps, Zombie Roaches and Other Parasite Tales

Roughly half the world’s population carry Toxoplasma gondii — a parasite that infects both wild and domestic cats, along with many warm-blooded mammals, including humans. Toxoplasma is also known for severely changing the behavior of rats, to the point where they seek out cat urine, which makes them an easy meal for felines. Here’s the brilliance of the parasite: it can infect pretty much any mammal, but is only able to reproduce in cats. In order for the parasite to survive, it’s developed an ingenious mechanism to alter the region of a rats brain that governs fear, anxiety and sexual arousal. “It has two genes that allow it to crank up production of the neurotransmitter dopamine in the host brain,” said Glenn McConkey of the University of Leeds, United Kingdom. Dopamine regulates the fear, pleasure and attention centers in the brain. The neurotransmitter is associated with schizophrenics as well, who have higher than normal levels.

Researchers in the Czech Republic believe T. gondii may have subtle, but far-reaching implications for human hosts — and even cultural norms. Behavioral changes caused by the parasite manifest differently in men and women. Males who are infected tend to be more introverted, oblivious to other people’s opinions of them, inclined to disregard rules, emotionally less stable and easily upset. While females are more intelligent, rule and image conscious, conforming, moralistic, outgoing, attentive to others, kindly and easygoing. On top of that, infected men have less fear and take more risks, leading to a statistically higher chance of having an auto accident.

People that live in humid, low altitude regions, where freezing and thawing are infrequent, are at greater risk of infection — largely because T. gondii cysts live longer in these climates. The cysts can be found in cat feces, soil, raw or undercooked meat, water, unpasteurized milk and unwashed vegetables. The United States, Scandinavian countries and England have relatively low infection rates, whereas countries like France, where consuming undercooked meat is common, have a higher instance of infection. Tropical regions of Latin America and sub-Saharan Africa are also prone to high rates.

Still not convinced that parasites can act as microscopic puppeteers? Consider this: according to Dr. E. Fuller Torrey, Associate Director for Laboratory Research at the Stanley Medical Research Institute, there is a clear association between toxoplasma and schizophrenia in genetically susceptible humans.

When humans are infected with T. gondii, glial cells that surround and support neurons are damaged. Schizophrenia is linked with damage to glial cells.
Pregnant women who test positive for high levels of antibodies for T. gondii have a greater chance of giving birth to children who will develop schizophrenia.
Human cells infected with T. gondii in lab tests respond to the drug haloperidol, which halts the parasite’s growth. Haloperidol is an antipsychotic used to treat schizophrenia.

Moreover, Dr. Torrey and a team of Oxford scientists ran an experiment to see if haloperidol would alter the behavior of T. gondii parasite controlled rats, which it did. The antipsychotic drug proved to be as effective as pyrimethamine — a pharmaceutical specifically used to eliminate toxoplasma.

Behavior-Bending Parasites in the Wild

Beyond the question of whether or not parasites influence a humans’ personality, scientists have no doubt that they can radically change behavior in animals, fish, crustaceans and insects.

One of the most well known examples is the rabies virus. When a dog is about to die from a rabies infection, the virus stirs the animal into a rage, causing it to bite another mammal, where the virus will continue to live on. What’s interesting is that, while the virus is causing a neurological meltdown in the dog, it simultaneously migrates from the nervous system to the animals’ saliva, ensuring the virus will be transferred to a different host through a bite.

The blue wasp, called the crypt-keeper wasp, could take the crown as the most horrific parasite of parasites. The parasite compels other parasites to shove their heads into holes … and then eats them. It’s a stunning example of a hyperparasite—a parasite whose host is also a parasite. This lifestyle is surprisingly common, especially among wasps. Many species lay eggs in the bodies of other insects, only to have other wasps lay eggs in their young. And sometimes, hyperparasites can be parasitized by other hyperparasites, creating hierarchies of bodysnatching that can grow to four tiers.

Here’s another unsettling example of parasitic mind control. Kathleen McCauliffe writes in The Atlantic:

Polysphincta gutfreundi, a parasitic wasp that grabs hold of an orb spider and attaches a tiny egg to its belly. A wormlike larva emerges from the egg, and then releases chemicals that prompt the spider to abandon weaving its familiar spiral web and instead spin its silk thread into a special pattern that will hold the cocoon in which the larva matures. The “possessed” spider even crochets a specific geometric design in the net, camouflaging the cocoon from the wasp’s predators.

But it isn’t all a complete horror show — there’re plenty of instances where these hitchhiking microbes can enrich our lives. A case in point is a study where women who consumed a probiotic laden yogurt displayed less brain activity in the regions that process emotions, compared to those who ate yogurt without probiotics. Another clinical trial showed that patients suffering from irritable bowel syndrome had reduced feelings of depression when given probiotics. And beneficial bacteria help our immune system, assist with digesting food and generate vitamins. You can read more about this bizarre and compelling world in Ed Yong’s book, I Contain Multitudes: The Microbes Within Us and a Grander View of Life

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

We humans set a premium on our own free will and independence … and yet there’s a shadowy influence we might not be considering. As science writer Ed Yong explains in this fascinating, hilarious and disturbing talk, parasites have perfected the art of manipulation to an incredible degree. So are they influencing us? It’s more than likely.

Here's how parasites could be influencing the way you think

They're messing with us.

Given recent events around the world, you could be forgiven for thinking that people have been acting in a very odd and unpredictable manner.

There has been much research across psychology and economics to explain why we behave the way we do and to explore what our motivations may be. But what if there are other unseen influences at play?

As science uncovers more about the influence of parasites and bacteria on human behaviour, we may well begin to see how they also shape our societies.

Mind control is a very real and prevalent threat to humans. We already know it is used by many organisms throughout the animal kingdom and how essential it is for the transmission and reproduction of many diverse parasitic species.

The Cordyceps fungus, for example, infects ants before making them travel to the top of the tree canopy where they die. The fungus then reproduces and its offspring float down to the forest floor to infect more ants.

Nematomorph worms, meanwhile, make their cricket hosts commit suicide by jumping into water and drowning in order to get back to where they normally live.

And parasitic trematodes infect snails so that their eyestalks bulge and change colour to red, blue and yellow. The next host, a bird, sees a juicy maggot and pecks off the eyestalks so the trematode can complete its lifecycle in the bird's gut.

These horror stories are not restricted to invertebrates – and humans are not immune.

When we learned how to farm and select strains of crops that grew best in certain environments, we sometimes made a surplus that could be stored for the future. This brought wild mice and rats and with them cats and a hidden danger: the protozoan parasite, Toxoplasma gondii.

This parasite can't complete its lifecycle in humans, but we can be infected by it through coming into contact with cat faeces (or eating uncooked meat).

The percentage of people estimated to be infected worldwide is between 30 and 40 percent. France has an infection level of a staggering 81 percent, Japan 7 percent, and the US 20 percent.

T. gondii does strange things to rats and mice to make sure they come into contact with cats. They lose their inhibition of cats and cat urine. They become more exploratory and spend more time in daylight.

But even stranger things happen when humans inadvertently come into contact with T. gondii. Men are more likely to be in car crashes due to riskier behavior. They also are more aggressive and more jealous.

Women, meanwhile, are more likely to commit suicide. It has even been suggested that T. gondii could potentially be involved in dementia, bipolar disorder, obsessive-compulsive disorder and autism.

There is even evidence from more than 40 studies that people suffering from schizophrenia have elevated levels of IgG antibodies against T. gondii.

So how does this tiny organism cause such extreme reactions? The full answer is still to be discovered but there are tantalising results that show it influences the levels of neurotransmitters such as dopamine.

Cysts (bradyzoites) are found throughout the infected brain in clumps or individually in specific places such as the amygdala, which has been shown to control fear response in rats.

Interestingly, an imbalance in dopamine levels is thought to be a characteristic of people that have schizophrenia.

Analysis of the T. gondii genome has discovered two genes that encode tyrosine hydroxylase, an enzyme that produces a precursor to making dopamine, called L-DOPA.

And there is experimental evidence to support how this might go on to affect behaviour.

Primarily, dopamine levels are high in infected mice, and their T. gondii-related behaviour can be reduced if the antagonist of dopamine (haloperidol) is administered.

Microbial mind controllers

There are many more mini puppet masters. It has recently been shown that the microbes that are plentiful on and in our bodies may also exert an influence on our behaviour.

We are covered in microbes and our human cells are outnumbered by bacterial cells eight to one. In fact, we are more microbe than human.

This microbiome has been shown to regulate, not just the digestion and breakdown of food, but many different processes, too.

Alterations to the gut microbiome can lead to susceptibility to conditions such as diabetes, neurological conditions, cancer, and asthma.

But it was recently shown that the gut microbes that break down food can directly affect the production of another neurotransmitter (serotonin) in the colon and blood, which can then in turn affect communicative, anxiety-like and nerve-related (sensorimotor) behaviours.

In the future, there may be the possibility of treating anxiety or depression by administering a 'healthy' microbiome, and recent research altering the microbiomes of patients suffering from Clostridium infections has shown excellent results via faecal transplantation from healthy individuals.

With further research we will begin to unravel just how these microscopic overlords are manipulating our decisions – and their influence on society, culture and politics should not be underestimated.

REFERENCES:
The Ultimate Mind Control: Researchers Suspect Bacteria, Viruses and Parasites Influence Human Behavior, Culture
How parasites could be influencing the way you think
The Parasite That Compels Other Parasites to Shove Their Heads Into Holes

poorpost · Feb 13, 2017

yung woolly mammoth, eto ba yung icoclone nla?
kahit maging successful ang pag balik ng wollies hindi parin cla makaka.adapt sa panahon ngayon
nag.evolve cla through the ice age at mag.adapt sa panahong yun
btw hypothesis lng naman

what if parasites will the key para mapabagal ang aging ng tao?

Stormer0628 · Feb 15, 2017

Scientists' ability to create organisms through synthetic biology is getting easier and cheaper fueling the start of a new era in biology.
Synthetic biology has already led to some innovations such as lab-grown meat, advancement in medicine, and even helping to bring back extinct species.

AND SO IT HAS COME TO THIS.

We have learned how to manipulate the code of life. Why this hasn’t received more attention is beyond me—or are people just evading an issue that they cannot be sure to meet head on themselves?

Synthetic Biology is a multidisciplinary field that often defies definition. Yet despite its complexity, it is a remarkably easy field to apply once you’ve learned the science behind it. From a computer, you can input your desired genetic sequence, print it out, glue it together, put it into a cell and then watch whatever you have created sprout.

Even more astonishingly is that it has also helped provide us with our best insights into how life on earth began, answering questions that have been with us from the beginning. Reason enough to learn a little more about it.

THE FUTURE OF LIFE
The amount of people and money pouring into this field is growing incredibly fast. This is being further expedited by the emergence of DIY bio (do it yourself biology). Labs are springing up all over the world as the tools required are getting cheaper and more ubiquitous. Now almost anyone with a decent enough understanding of the subject can build their own synthetic biology lab and start hacking away at life.

We have also recently discovered new bases that will allow us to do things we never would have dreamed of. All life that we know is made from DNA containing primarily four bases: A, C, T, and G. We have now added X and Y, opening the door for us to create things never before thought possible.

We are already seeing some of what it can do. Lab-grown meat, de-extinction, new biochemicals and medicines, the list goes on and on. Before long it is believed that we will be able to synthetically recreate humans.

We have been altering the genomes of various species since the agricultural revolution, the difference now is in our ability to select specific lines from the code of life and swap them or delete them or put new lines in. This will have a wide range of implications as we learn more about the roles of specific genes while also allowing us to direct and accelerate evolution.

Glowing microbes grown by Dr. Scott Pownall at Open Science Network; he
took the genes from glowing jellyfish and inserted them into Escherichia coli cells.

The 20th century saw a series of breakthroughs in our understanding of Physics that redefined what we were capable of. It brought about the atomic age, allowed us to explore our solar system, and opened up insights into the universe that fundamentally changed our understanding of reality.

Biology seems to be experiencing a similar paradigm shift. It is allowing us to manipulate the building blocks of life and redefine the natural world, all of which will radically alter our collective fate.

SOURCE

poorpost said:
yung woolly mammoth, eto ba yung icoclone nla?
kahit maging successful ang pag balik ng wollies hindi parin cla makaka.adapt sa panahon ngayon
nag.evolve cla through the ice age at mag.adapt sa panahong yun
btw hypothesis lng naman

what if parasites will the key para mapabagal ang aging ng tao?

Yes, and at the rate the ice is melting again because of current global warming, we could imagine these to-be revived mammoths living inside special snow cubicles for museum or carnival piece.

There are many insights now to aging. Perhaps I'll do that next.

Stormer0628 · Feb 19, 2017

Humans Are Programmed to Die
In a small laboratory in Philadelphia, Penn., in 1965, a curious young biologist conducted an experiment that would revolutionize the way we think about aging and death. The scientist who conducted that experiment, Dr. Leonard Hayflick, would later lend his name to the phenomenon he discovered, the Hayflick limit.

Dr. Hayflick noticed that cells grown in cultures reproduce by dividing. They produce facsimiles of themselves (by a process known as mitosis) a finite number of times before the process stops for good and the cell dies. In addition, cells frozen during their lifetimes and later returned to an active state had a kind of cellular memory: The frozen cells picked up right where they left off. In other words, interrupting the cells' life span did nothing to lengthen it.

Hayflick found that cells go through three phases. The first is rapid, healthy cell division. In the second phase, mitosis slows. In the third stage, senescence, cells stop dividing entirely. They remain alive for a time after they stop dividing, but sometime after cellular division ends, cells do a particularly disturbing thing: Essentially, they commit suicide. Once a cell reaches the end of its life span, it undergoes a programmed cellular death called apoptosis.

When a new cell is born from an older one through cell division, it begins its own life span. This span appears to be governed by DNA, located in the nucleus of a cell. A student of Hayflick's later found that when he removed the nucleus of an old cell and replaced it with the nucleus of a young cell, the old cell took on a new life. The old cell's life span took on that of a young cell. Like any other cell (except for stem cells), it divided most rapidly early in its lifetime, eventually slowing cellular division as it aged, before stopping altogether and undergoing apoptosis.

The implications of the Hayflick limit are staggering: Organisms have a molecular clock that's inexorably winding down from the moment we're born.

When all of the cells created in the human body before birth (and all of the cells these cells produce) are multiplied by the average time it takes for cells to reach the end of their lives, you get roughly 120 years. This is the ultimate Hayflick limit—the maximum number of years that a human can possibly live.

When Dr. Leonard Hayflick performed his experiments using human cells grown in a culture, he managed to pull back the curtain on an ancient process that essentially prevents immortality. The process of cellular death exists within our genetic code. The nucleus of a diploid cell (a cell with two sets of chromosomes) is comprised of DNA information contributed by each of an organism's parents. Since the key to the Hayflick limit is found in the cell's nucleus, we are basically programmed to die. Why is this?

There are several reasons why a cell should be programmed to die after a certain point. In the developmental stages, for example, human fetuses have tissue that creates some webbing between our fingers. As we gestate, this tissue undergoes apoptosis that ultimately allows our fingers to form. Menstruation—the monthly process of shedding the lining of the uterus—is also carried out through apoptosis. Programmed cellular death also combats cancer (defined as uncontrolled cellular growth); a cell that turns cancerous still has a life span like any other cell and will die out eventually. The drugs used in chemotherapy are meant to accelerate this process by triggering apoptosis in cancerous cells.

Apoptosis is the result of several signals from both inside and outside a cell. When a cell stops receiving the hormones and proteins it needs to function or sustains enough damage to stop functioning properly, the process of apoptosis is triggered. The nucleus explodes and releases chemicals that act as signals. These chemicals attract phospholipids that engulf the cell fragments, degrade the individual chromosomes and carry them out of the body as waste.

Clearly, apoptosis is an intensely regulated and highly refined process. How, then, could we ever possibly thwart it?

Telomerase and the Possibility of Cellular Immortality
The discovery of the Hayflick limit represented a radical change in the way science looked at cellular reproduction. Before the doctor's discovery, cells were thought to be capable of immortality. Although the phenomenon of the Hayflick limit has been studied only in vitro, it eventually came to generally be accepted in the scientific community as fact. For decades, it looked like the limit was insurmountable, and it still appears that way.

In 1978, however, the discovery of a segment of non-replicating DNA in cells called telomeres shed light on the possibility of cellular immortality.

Telomeres are repetitive strings of DNA found at the ends of chromosome pairs within diploid cells. These strings are usually compared to the plastic ends of shoelaces (called aglets) that keep the laces from fraying. Telomeres provide the same protection to chromosomes, but the telomere on the end of each chromosome pair is shortened with each cellular division. Eventually, the telomere is depleted, and apoptosis begins.

The discovery of telomeres supported the Hayflick limit; after all, it was the physical mechanism by which cells entered senescence.

Just under a decade later, however, another breakthrough in cellular aging was uncovered. Telomerase is a protein that's found in all cells, but in normal cells, it's turned off—it doesn't do anything. In abnormal cells like tumors and germ cells, however, telomerase is quite active: It contains an RNA template capable of producing new telomeres on the ends of chromosomes in aging cells.

Telomerase has the aging research community excited for two reasons. First, since it's naturally active in tumors and can be detected in urine samples, testing for the presence of telomerase can lead to more effective testing of cancer patients. Second, researchers have figured out how to extract telomerase and synthesize it. Potentially, if active telomerase is added to normal adult cells, they'll continue to replicate long beyond their Hayflick limit. In one study that supports this notion, researchers reported that cells to which they'd introduced telomerase had replicated 20 more times than their normal life span would indicate—and were still dividing.

Turning on Immortality: The Debate Over Telomerase Activation
The role of telomerase in allowing the immortal growth of reproductive cells is now well established in the scientific literature.

In the laboratory dish, the introduction of telomerase into cultured human cells transforms otherwise aging mortal cells into immortal cells without transforming them into cancer cells. On the heels of this discovery, small molecule activators of telomerase are being developed for use in treating cellular aging and at least one nutritional supplement is being marketed for the treatment of aging.

The arguments for and against those telomerase treatments are discussed HERE.

Fusing Aging Theories: Telomere Shortening Leads to Mitochondrial Dysfunction
New research is adding insight and linking three theories of aging—one that suggests telomere shortening governs lifespan, and two others that suggest dysfunctional mitochondria or oxidative stress leads to aging.

At Harvard-affiliated Dana-Farber Cancer Institute, scientists have gathered data suggesting telomere shortening is the cause of mitochondrial dysfunction and diminished antioxidant defenses. Together, they decrease the body’s energy and diminish organ function, both characteristic of old age.

As telomeres—protective caps at the end of cell chromosomes—shorten with age and begin to fray, cells activate the p53 gene, which signals an “emergency shutdown” chain of events that turns off normal cell growth and division and compromise antioxidant defenses. Going one step further, data from the carefully orchestrated mouse study, published in Nature, show that the p53 gene also represses PGC1-alpha and PGC1-beta. These PCGs are considered the master regulators of metabolism and mitochondrial function.

Repressing PCGs increases the number of dysfunctional mitochondria (with mutated mitochondrial DNA) and leads to a decrease in functional mitochondria distributed throughout in muscles and organs. The dysfunctional mitochondria in aged tissues leak greater amounts of reactive oxygen species and the lack of functional mitochondria hinders normal energy production from cell respiration (the body’s main producer of ATP energy).

“What we have found is the core pathway of aging connecting several age-related biological processes previously viewed as independent from each other,” said Ronald A. DePinho, M.D., a cancer geneticist and senior author of the paper, in a press release.

“Because telomere dysfunction weakens defenses against damage by free radicals, or reactive oxygen species,” Dr. DePinho said, “we think this exposes telomeres to an accelerated rate of damage which cannot be repaired and thereby results in even more organ deterioration. In effect, it sets in motion a death spiral.”

In an article also published in the same issue Nature, Daniel P. Kelly, M.D., scientific director and professor at Burnham Institute for Medical Research-Lake Nona, Orlando, Florida, said that the “intriguing study… unveils a potentially unifying mechanism for cellular ageing.”

Mitigating the Toll of Aging
The new study further supports current thinking that the best defense against aging is to reduce the adverse affects of overproduction of free radicals produced from dysfunctional mitochondria, which cause additional oxidative stress.

Dr. DePinho said, “The findings bear strong relevance to human aging, as this core pathway can be directly linked to virtually all known genes involved in aging, as well as current targeted therapies designed to mitigate the toll of aging on health.”

Those current targeted therapies include boosting the human body’s antioxidant defenses by eating a healthy diet, reducing calories (by around 25 percent), and supplementing with antioxidant vitamins C and E, as well as with green tea, CoQ10 and resveratrol. These practices not only help to protect against oxidative stress, thereby protecting against telomere shortening, but also help boost generation of new, healthy mitochondria.

When we asked telomere biologist Bill Andrews, Ph.D., to comment on the new study, he answered that it was “tremendous news,” as it supports the need for more research into management of telomeres by activating the genetic expression of the enzyme telomerase, which re-lengthens telomeres.

Dr. Andrews wrote, “It’s the best support ever for the fact that telomere elongation’s role in aging far exceeds the roles played by mitochondria and oxidative stress.” In effect, telomere shortening is the root cause of the others.

Mitochondria become dysfunctional when telomeres shorten and fray, a new study suggests. In an article to be published in a forthcoming issue of IsaNews magazine, Dr. Andrews writes, “Mitochondrial dysfunction causes aging—but telomere shortening has turned out to be the primary cause of mitochondrial dysfunction. And humans’ natural defenses against oxidative stress are really quite exceptional (for example, our cells produce ten times more superoxide dismutase, a potent natural antioxidant, than mice)—until telomere shortening begins to degrade those defenses inside our bodies.”

He added that while “anti-aging therapies of years past merely treated the symptoms of aging, new research is devoted to identifying a new class of therapies that treat aging at its root cause, and hold great promise of one day allowing us to feel young and healthy at 120 years of age and beyond.”

An earlier study, of which Dr. DePinho was also the senior author, gives testimony to the benefits of telomerase, as found in mice that were genetically engineered to produce the enzyme. The study found that when the telomerase was restored in the mice, their age-related symptoms disappeared and several organs including the brain were rejuvenated.

Stormer0628 · Feb 25, 2017

Woody Alen famously quipped that he doesn’t want to accomplish immortality through his work but through not dying. But we are often told that death is natural. Much of the time the statement is left hanging without support as if it is totally obvious. Occasionally, someone will go the extra mile by repeating the (Buddhist?!) mantra that everything and everyone born will die and become food and/or raw material for the next generation – the proverbial great circle of life.

But the above claim is at best incomplete. And, at worse, totally false. First of all it doesn’t acknowledge or explain the great variability of life spans we find out there in the “natural world.” Why, for example, some creatures live many times the average human life? What is it that makes them better, more natural, more suited to or worthy of longer lives than us? Why is it natural for a sea shell or a sponge to live for 400 or 1,500 years respectively, while humans are “naturally” capped at 100 or so?

Secondly, and more importantly, what about the growing list of organisms that have skipped the philosophical debate altogether and have already embraced different versions of biological immortality?! Is that a sign that, having realized they will never achieve immortality through their work, those organisms had no other option but to go for the real thing?!

If death is natural then why do some organisms seem to be immortal?

If you are not familiar with those creatures here is a short list:

1. The Turritopsis Nutricula aka the Immortal Jellyfish: Technically known as a hydrozoan, it is the only known animal that is capable of reverting completely to its younger self. The jellyfish does this through the cell development process of transdifferentiation. Scientists believe the cycle can repeat indefinitely, rendering it potentially immortal. [The main issue often raised by critics with this process is one of identity – is the offspring considered to be the same specimen or not. Most biologists argue that it isn’t. In fact, bacteria are also said to be biologically immortal, but only at the level of the colony, since the two daughter bacteria resulting from cell division of a parent bacterium can be regarded as unique individuals.]

2. The Hydra is a genus of small, simple, fresh-water animals that possess radial symmetry. Hydra are predatory animals belonging to the phylum Cnidaria and the class Hydrozoa. They can be found in most unpolluted fresh-water ponds, lakes, and streams in the temperate and tropical regions and can be found by gently sweeping a collecting net through weedy areas. They are multi-cellular organisms which are usually a few millimeters long and are best studied with a microscope. Biologists are especially interested in Hydra due to their regenerative ability; and that they appear not to age or to die of old age.

3. Tardigrades (commonly known as waterbears or moss piglets) are small, water-dwelling, segmented animals with eight legs. Tardigrades are notable for being one of the most complex of all known polyextremophiles. (An extremophile is an organism that can thrive in a physically or geochemically extreme condition that would be detrimental to most life on Earth.) For example, tardigrades can withstand temperatures from just above absolute zero to well above the boiling point of water, as well as pressures greater than any found in the deepest ocean trenches, ionizing radiation — at doses hundreds of times higher than would kill a person and have lived through the vacuum of outer space. They can go without food or water for nearly 120 years, drying out to the point where they are 3% or less water, only to rehydrate, forage, and reproduce. And they basically turn themselves to biological glass to protect against dehydration. Amazingly, as much as 20% of tardigrade genome have been shown to be snatched from foreign DNA.

4. Planarian flatworms: Planarian flatworms appear to exhibit an ability to live indefinitely and have an “apparently limitless [telomere] regenerative capacity fueled by a population of highly proliferative adult stem cells.”

Planaria can be cut into pieces, and each piece can regenerate into a complete organism. Cells at the location of the wound site proliferate to form a blastema that will differentiate into new tissues and regenerate the missing parts of the piece of the cut planaria. It’s this feature that gave them the famous designation of being “immortal under the edge of a knife.”

Very small pieces of the planarian, estimated to be as little as 1/279th of the organism it is cut from, can regenerate back into a complete organism over the course of a few weeks. New tissues can grow due to pluripotent stem cells that have the ability to create all the various cell types. These adult stem cells are called neoblasts, which comprise around 20% of cells in the adult animal. They are the only proliferating cells in the worm, and they differentiate into progeny that replace older cells. In addition, existing tissue is remodeled to restore symmetry and proportion of the new planaria that forms from a piece of a cut up organism. The organism itself does not have to be completely cut into separate pieces for the regeneration phenomenon to be witnessed. In fact, if the head of a planaria is cut in half down its centre, and each side retained on the organism, its possible for the planaria to regenerate two heads and continue to live.

5. Lobsters: Because they are prized as a delicacy seafood, most people are familiar with those large marine crustaceans – they have long bodies with muscular tails, and live in crevices or burrows on the sea floor. Three of their five pairs of legs have claws, including the first pair, which are usually much larger than the others. What most people don’t know, however, is that older lobsters are more fertile than younger lobsters. Lobsters also keep growing throughout life, don’t show any signs of ageing and have been reported to live 100 or even 200 hundred years before ending on someone’s dinner table.

In addition to the above five examples, there are a few other potential candidates that may have accomplished biological immortality. Some of the best known applicants are the Rougheye Rockfish, the Aldabra Giant Tortoise, the sea anemone and others. And chances are that we will continue to discover other similarly fascinating biologically immortal organisms.

Now, we have to be clear that biological immortality doesn’t mean actual immortality. There is a full spectrum of other causes that can lead to death. [For example, you can be a 200 year old fish or lobster and still get caught and eaten.] It is with this recognition in mind that Dr. Aubrey de Grey is very careful with the language he uses when describing his work – prolonging healthy life-span, defeating ageing etc. De Grey often stresses that he is not working on immortality because, for example, perfectly healthy people can and do get run over and killed by cars every day. So Aubrey insists on being clear that his work focuses on the internal, biological factors, and not the external ones, which are outside of his control. And it is the former that are usually associated with “the natural causes for death.”

But if they are so “natural” then why do some organisms seem to avoid them altogether?! And, more generally:

If death is natural then why are some biologically immortal?

SOURCE

BONUS

Stormer0628 · Mar 2, 2017

With technology like CRISPR making gene editing easier than ever before, society is divided on the ethical implications of using the tech to alter simply “unwanted” genes.
Given the potential of gene editing to drastically change humanity, it is timely that we're having this discussion on what and who it should be used for right now.

GENETIC EDITING FOR ALL

We are all subject to the genetic lottery. That’s how it’s always been, and for a while, we thought that was how it would always be.

Then, in 2014, a gene-editing technology called CRISPR was introduced. With CRISPR, geneticists could edit sections of the genome to alter, add, or remove parts of the DNA sequence. To date, it is by far the easiest way we’ve found to manipulate the genetic code, and it is already paving the way for more efficient and effective treatments of conditions with a genetic component. However, the technology brings with it the potential to manipulate and remove simply “unwanted” genes.

While most of the proposed CRISPR applications are focused on editing somatic (non-reproductive) cells, altering germline (reproductive) cells is also a very real possibility. This prospect of editing germline cells and making changes that would be passed on from generation to generation has sparked a heated ethical debate.

The potential to change someone’s DNA even before they are born has led to claims that CRISPR will be used to create “designer babies.” Detractors were appalled at the hubris of science being used to engineer the human race. Supporters, on the other hand, are saying this ability should be a human right.

RIGGING THE GAME

To be fair, most advocates of genetic editing aren’t rallying for support so CRISPR can be used to create a superior human race. Rather, they believe people should have free access to technology that is capable of curing diseases. It’s not about rigging the genetic game — it’s about putting the technique to good use while following a set of ethical recommendations.

To that end, a panel made up of experts chosen by the National Academy of Sciences and the National Academy of Medicine released a series of guidelines that essentially gives gene editing a “yellow light.” These guidelines supports gene editing on the premise that it follows a set of stringent rules and is conducted with proper oversight and precaution.

Obviously, genetic enhancement would not be supported under these guidelines, which leaves some proponents miffed. Josiah Zaynor, whose online company The ODIN sells kits allowing people to conduct simple genetic engineering experiments at home, is among those who are adamant that gene editing should be a human right. He expressed his views on the subject in an interview with The Outline:

We are at the first time in the history of humanity where we can no longer be stuck with the genes we are dealt. As a society we have begun to see how choice is a right, but for some reason when it comes to genetics, some people think we shouldn’t have a choice. I can be smart and attractive, but everyone else should be ugly, fat, and short because those are the genes they were dealt and they should just deal with it.

However, scientific institutions continue to caution against such lax views of genetic editing’s implications. Apart from the ethical questions it raises, CRISPR also faces opposition from various religious sects and legal concerns regarding the technology. Governments seem divided on the issue, with nations like China advancing research, while countries like the U.K., Germany, and the U.S. seem more concerned about regulating it.

The immense potential of gene editing to change humanity means the technology will continue to be plagued by ethical and philosophical concerns. Given the pace of advancement, the time is right to have this discussion on what and who it should be used for right now.

SOURCE

Stormer0628 · Mar 4, 2017

To put that in perspective, consider that by 2020 humanity should be creating all 44 trillion gigabytes worth of data. According to the study, this method should allow for 215,000,000 gigabytes—215 petabyte—on one gram of DNA. Error-free.

Scientists have been talking about using DNA to store data for years, but the application's been limited so far by high cost and errors in the data. Just recently, in a study published in Science, researchers announced they've made the process 100 per cent error-free and 60 per cent more efficient compared to previous results—approaching the theoretical maximum for DNA storage. The authors estimate that their original order of DNA would be good for over 10[SUP]15[/SUP] reads of the data

Even so, a few hurdles remain until this becomes a regular data storage solution. For one thing, it's still quite time-consuming and expensive—the authors estimate that at a brain-exploding $3,500 per MB—and you thought SSDs were pricey, huh. And each time you want to read the data, you need to be prepared to wait about a day. But remember if we can get this far in the technology, it might not be a surprise if the solution comes right next week.

Ten years ago, if you wanted to back up some old photos, you might have stored them on a big, clunky external hard drive that weighed a couple of pounds and was a pain to lug around. Ten years from now, you might back up all the data from your entire life on just a few grams of DNA.

DNA as a storage medium makes sense—after all, it already stores the billions of letters that code for life. It is compact and durable. Unlike the floppy disk or that five pound hard drive you used to lug around, it will never go obsolete. Instead of 1 and 0s, code is written in As, Gs, Cs and Ts. Using DNA, you could store all the data in the world in a nice-sized walk-in closet and keep it there for thousands and thousands of years.

This is not the first time scientists have turned to the double helix for storage. In 2011, Harvard University geneticist George Church pioneered the use of DNA for electronic data storage, encoding his own book, some images, and a Javascript program in the molecules. A year later, researchers European Bioinformatics Institute improved the method, and uploaded all of Shakespeare’s sonnets, a clip of Martin Luther King’s “I have a dream” speech, a PDF of the paper from James Watson and Francis Crick that detailed the structure of DNA, and a photo of their institute into a tiny speck of DNA. In July, a team from Microsoft and University of Washington also managed to store a record 200 megabytes of data in DNA.

But it was difficult to encode more than a few hundred letters with data without it turning into an undecipherable mess of gobbledygook.

In their new paper out Friday in Science, Yaniv Erlich and Dina Zielinski, from the New York Genome Center and Columbia University, respectively, detail a major improvement. Their new method, dubbed “DNA Fountain,” riffs off what’s known as fountain code, which slices data into chunks and then reassembles it, allowing, say, a large file like a movie to be flawlessly streamed over a lousy connection. Using their new method, they were able to store total over two megabytes of data in 72,000 DNA strands and easily retrieve it. One of Erlich’s Twitter followers was even able to crack the code and retrieve the Amazon gift card. The 215 petabytes of data on a single gram of DNA is already 100 times more than Church did just a few years back.

The new method works like a simple Sudoku puzzle, essentially using hints to keep any lost data from ruining the overall picture. "Even if you don't get all the numbers, you can still solve the Sudoku puzzle," Yaniv Erlich, co-author of the paper and a professor of computer science at Columbia University, said.

The DNA Fountain technique is remarkable in its resistance to errors and ability to maximize the storage capacity of DNA.

Before we’re all walking around with bits of DNA on our key rings instead of flash drives, however, sequencing will have to become significantly cheaper. But that might happen sooner than we realize. This year, Illumina announced plans to bring the cost of sequencing an entire human genome sequencing down to $100. Sequencing a few megabytes of data would cost a small fraction of that.

And if you find this crazily interesting, keep in mind that this is complemented by another research direction: turning DNA into computers that would even be faster than quantum computers! And the field is humming about just nicely.

imadandam · Mar 5, 2017

Ammazzing. Thanks for the info

poorpost · Mar 5, 2017

Hindi ko pa nababasa
TIA

Stormer0628 · Mar 7, 2017

Lasers Flesh Out Dino-Bird Profile

A new technique harnessing high-powered lasers is probing dinosaur fossils and helping unmask the prehistoric creature’s transition from being a small feathered dinosaur into an actual flying bird.

Scientists used the method on fossils of the dinosaur Anchiornis, a four-winged, feathered dino that was located in China around 160 million years earlier. The laser beams fleshed out a novel view of the long-extinct animals, revealing their drumstick-shaped legs, bird-like arms, and a long and slender tail.

This Jurassic creature is not exactly classified as a bird, but it maintained a number of skeletal and soft tissue qualities found in bird and lived around the time birds diverged from their closely resembling dinosaur predecessors. The Archaeopteryx, lived around 150 million years ago, has been long deemed the earliest-living bird.

Laser Technology At Work
The technique, known as laser-stimulated fluorescence (LSF), directed high-powered laser at the fossils in a dark place to bring out a glow in concealed soft tissues such as skin. It successfully created the first detailed body figure of the dinosaur — a “real landmark in our understanding of avian origins,” said co-lead author and University of Hong Kong paleontologist Michael Pittman in a Reuters report.

Dinosaur fossils are largely made up of bones, which are the ones best preserved over millions of years. But the fossil analysis method offered a new possibility.

“This is a new way to actually see the dinosaur, besides the bone,” reported the technique’s pioneer, Thomas Kaye.

Light particles or photons interact with atoms and molecules in different ways. Once they hit a molecule, they are emitted back in a different color based on the molecule’s makeup.

In the case of fossils, various fossilized tissue types will cause laser light to re-emit at different wavelengths, producing a glow in varying colors. Kaye said the glow does not dictate what the exact part is, but clearly notes that it is different — paleontologists can then investigate more closely using other methods.

Can They Fly Or Glide?
Apart from the animal’s leg and arm characteristics, the laser-initiated probe also showed astoundingly bird-like footpads as well as a shallow site of soft tissue fronting the elbow, known as the propatagium. The latter is important in bird flight, thus it is a piece of the puzzle of whether the Anchiornis could fly, glide, or neither.

“So it seems like Anchiornis had a somewhat more primitive wing than modern birds,” Kaye told Christian Science Monitor. “Maybe that type of wing was an intermediate stage in the evolution of the modern bird wing, or maybe it was a totally separate experiment in dinosaur flight.”

For the authors, the creature probably maintained some aerodynamic ability. Some scientists thought it could glide, while other disagreed due to its flight feathers not being well-suited for flight.

While the new findings may not necessarily change scientists’ current view of avian evolution, Kaye believes that they provided new observations from actual physical evidence. The next step for them, he shared, is to fly the lasers on a drone for new discoveries.

The findings were discussed in the journal Nature Communications.

DINOSAURS: 5 Things You May Not Know Video

SOURCE

Stormer0628 · Mar 11, 2017

Gaia Vince discovers that analyzing the genetics of ancient humans means changing ideas about our evolution.

The Rock of Gibraltar appears out of the plane window as an immense limestone monolith sharply rearing up from the base of Spain into the Mediterranean. One of the ancient Pillars of Hercules, it marked the end of the Earth in classical times. Greek sailors didn’t go past it. Atlantis, the unknown, lay beyond.

In summer 2016, Gibraltar is in the throes of a 21st-century identity crisis: geographically a part of Spain, politically a part of Britain; now torn, post Brexit, between its colonial and European Union ties. For such a small area – less than seven square kilometres – Gibraltar is home to an extraordinarily diverse human population. It has been home to people of all types over the millennia, including early Europeans at the edge of their world, Phoenicians seeking spiritual support before venturing into the Atlantic, and Carthaginians arriving in a new world from Africa.

But I’ve come to see who was living here even further back, between 30,000 and 40,000 years ago, when sea levels were much lower and the climate was swinging in and out of ice ages. It was a tough time to be alive and the period saw the species that could, such as birds, migrate south to warmer climes, amid plenty of local extinctions. Among the large mammal species struggling to survive were lions, wolves and at least two types of human: our own ‘modern human’ ancestors, and the last remaining populations of our cousins, the Neanderthals.

By understanding more about these prehistoric people, we can learn about who we are as a species today. Our ancestors’ experiences shaped us, and they may still hold answers to some of our current health problems, from diabetes to depression.

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Everyone of European descent has some Neanderthal DNA in their genetic makeup

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I’m picked up outside my hotel by archaeologists Clive and Geraldine Finlayson, in a car that itself looks fairly ancient. Typical for this crowded little peninsula, they are of diverse origins – he, pale-skinned and sandy-haired, can trace his ancestry back to Scotland; she, olive-skinned and dark-haired, from the Genoese refugees escaping Napoleon’s purges. How different we humans can look from each other. And yet the people whose home I am about to visit truly were of a different race.

We don’t know how many species of humans there have been, how many different races of people, but the evidence suggests that around 600,000 years ago one species emerged in Africa that used fire, made simple tools from stones and animal bones, and hunted big animals in large cooperative groups. And 500,000 years ago, these humans, known as Homo heidelbergensis, began to take advantage of fluctuating climate changes that regularly greened the African continent, and spread into Europe and beyond.

By 300,000 years ago, though, migration into Europe had stopped, perhaps because a severe ice age had created an impenetrable desert across the Sahara, sealing off the Africans from the other tribes. This geographic separation enabled genetic differences to evolve, eventually resulting in different races, although they were still the same species and would prove able to have fertile offspring together. The race left behind in Africa would become Homo sapiens sapiens, or ‘modern humans’; those who evolved adaptations to the cooler European north would become Neanderthals, Denisovans and others whom we can now only glimpse with genetics.

Neanderthals were thriving from Siberia to southern Spain by the time a few families of modern humans made it out of Africa around 60,000 years ago. These Africans encountered Neanderthals and, on several occasions, had children with them. We know this because human DNA has been found in the genomes of Neanderthals, and because everyone alive today of European descent – including me – has some Neanderthal DNA in their genetic makeup. Could it be that their genes, adapted to the northerly environment, provided a selective advantage to our ancestors as well?

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It was like Neanderthal City

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After driving through narrow tunnels on a road that skirts the cliff face, we pull up at a military checkpoint. Clive shows the guard our accreditation and we’re waved through to park inside. Safety helmets on to protect from rockslides, we leave the car and continue on foot under a low rock arch. A series of metal steps leads steeply down the cliff to a narrow shingle beach, 60 metres below. The tide is lapping the pebbles and our feet must negotiate the unstable larger rocks to find a dry path.

I’ve been concentrating so hard on keeping my footing that it is something of a shock to look up and suddenly face a gaping absence in the rock wall. We have reached Gorham’s Cave, a great teardrop-shaped cavern that disappears into the white cliff face and, upon entering, seems to grow in height and space. This vast, cathedral-like structure, with a roof that soars high into the interior, was used by Neanderthals for tens of thousands of years. Scientists believe it was their last refuge. When Neanderthals disappeared from here, some 32,000 years ago, we became the sole inheritors of our continent.

I pause, perched on a rock inside the entrance, in order to consider this – people not so different from myself once sat here, facing the Mediterranean and Africa beyond. Before I arrived in Gibraltar, I used a commercial genome-testing service to analyse my ancestry. From the vial of saliva I sent them, they determined that 1 per cent of my DNA is Neanderthal. I don’t know what health advantages or risks these genes have given me – testing companies are no longer allowed to provide this level of detail – but it is an extraordinary experience to be so close to the intelligent, resourceful people who bequeathed me some of their genes. Sitting in this ancient home, knowing none of them survived to today, is a poignant reminder of how vulnerable we are – it could so easily have been a Neanderthal woman sitting here wondering about her extinct human cousins.

Gorham’s Cave seems an oddly inaccessible place for a home. But Clive, who has been meticulously exploring the cave for 25 years, explains that the view was very different back then. With the sea levels so much lower, vast hunting plains stretched far out to sea, letting people higher on the rock spot prey and signal to each other. In front of me would have been fields of grassy dunes and lakes – wetlands that were home to birds, grazing deer and other animals. Further around the peninsula to my right, where the dunes gave way to shoreline, would have been clam colonies and mounds of flint. It was idyllic, Clive says. The line of neighbouring caves here probably had the highest concentration of Neanderthals living anywhere on Earth. “It was like Neanderthal City,” he adds.

Deep inside the cave, Clive’s team of archaeologists have found the remains of fires. Further back are chambers where the inhabitants could have slept protected from hyenas, lions, leopards and other predators. “They ate shellfish, pine seeds, plants and olives. They hunted big game and also birds. There was plenty of fresh water from the springs that still exist under what is now seabed,” Clive says. “They had spare time to sit and think – they weren’t just surviving.”

He and Geraldine have uncovered remarkable evidence of Neanderthal culture in the cave, including the first example of Neanderthal artwork. The ‘hashtag’, a deliberately carved rock engraving, is possibly evidence of the first steps towards writing. Other signs of symbolic or ritualistic behaviour, such as the indication that Neanderthals were making and wearing black feather capes or headdresses as well as warm clothes, all point to a social life not so different to the one our African ancestors were experiencing.

Clive shows me a variety of worked stones, bone and antler. I pick up a flint blade and hold it in my hand, marvelling at how the same technology is being passed between people biologically and culturally linked but separated by tens of thousands of years. Other sites in Europe have uncovered Neanderthal-made necklaces of strung eagle talons dating back 130,000 years, little ochre clamshell compacts presumably for adornment, and burial sites for their dead.

These people evolved outside of Africa but clearly had advanced culture and the capability to survive in a hostile environment. “Consider modern humans were in the Middle East perhaps 70,000 years ago, and reached Australia more than 50,000 years ago,” says Clive. “Why did it take them so much longer to reach Europe? I think it was because Neanderthals were doing very well and keeping modern humans out.”

But by 39,000 years ago, Neanderthals were struggling. Genetically they had low diversity because of inbreeding and they were reduced to very low numbers, partly because an extreme and rapid change of climate was pushing them out of many of their former habitats. A lot of the forested areas they depended on were disappearing and, while they were intelligent enough to adapt their tools and technology, their bodies were unable to adapt to the hunting techniques required for the new climate and landscapes.

“In parts of Europe, the landscape changed in a generation from thick forest to a plain without a single tree,” Clive says. “Our ancestors, who were used to hunting in bigger groups on the plains, could adapt easily: instead of wildebeest they had reindeer, but effectively the way of capturing them was the same. But Neanderthals were forest people.

“It could’ve gone the other way – if instead the climate had got wetter and warmer, we might be Neanderthals today discussing the demise of modern humans.”

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This is why ancient genetics and ancient genomics
are so powerful – you can look at an individual
and say, "Did they have this gene or not?"

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Although the Neanderthals, like the Denisovans and other races we are yet to identify, died out, their genetic legacy lives on in people of European and Asian descent. Between 1 and 4 per cent of our DNA is of Neanderthal origins, but we don’t all carry the same genes, so across the population around 20 per cent of the Neanderthal genome is still being passed on. That’s an extraordinary amount, leading researchers to suspect that Neanderthal genes must be advantageous for survival in Europe.

Interbreeding across different races of human would have helped accelerate the accumulation of useful genes for the environment, a process that would have taken much longer to occur through evolution by natural selection. Neanderthal tweaks to our immune system, for example, may have boosted our survival in new lands, just as we prime our immune system with travel vaccines today. Many of the genes are associated with keratin, the protein in skin and hair, including some that are linked to corns and others that play a role in pigmentation – Neanderthals were redheads, apparently. Perhaps these visible variants were considered appealing by our ancestors and sexually selected for, or perhaps a tougher skin offered some advantage in the colder, darker European environment.

Some Neanderthal genes, however, appear to be a disadvantage, for instance making us more prone to diseases like Crohn’s, urinary tract disorders and type 2 diabetes, and to depression. Others change the way we metabolise fats, risking obesity, or even make us more likely to become addicted to smoking. None of these genes are a direct cause of these complicated conditions, but they are contributory risk factors, so how did they survive selection for a thousand generations?

It’s likely that for much of the time since our sexual encounters with Neanderthals, these genes were useful. When we lived as hunter-gatherers, for example, or early farmers, we would have faced times of near starvation interspersed with periods of gorging. Genes that now pose a risk of diabetes may have helped us to cope with starvation, but our new lifestyles of continual gorging on plentiful, high-calorie food now reveal harmful side-effects. Perhaps it is because of such latent disadvantages that Neanderthal DNA is very slowly now being deselected from the human genome.

While I can (sort of) blame my Neanderthal ancestry for everything from mood disorders to being greedy, another archaic human race passed on genes that help modern Melanesians, such as people in Papua New Guinea, survive different conditions. Around the time that the ancestors of modern Europeans and Asians were getting friendly with Neanderthals, the ancestors of Melanesians were having sex with Denisovans, about whom we know very little. Their surviving genes, however, may help modern-day Melanesians to live at altitude by changing the way their bodies react to low levels of oxygen. Some geneticists suspect that other, yet-to-be-discovered archaic races may have influenced the genes of other human populations across the world.

Interbreeding with Neanderthals and other archaic humans certainly changed our genes, but the story doesn’t end there.

I am a Londoner, but I’m a little darker than many Englishwomen because my father is originally from Eastern Europe. We are attuned to such slight differences in skin colour, face shape, hair and a host of other less obvious features encountered across different parts of the world. However, there has been no interbreeding with other human races for at least 32,000 years. Even though I look very different from a Han Chinese or Bantu person, we are actually remarkably similar genetically. There is far less genetic difference between any two humans than there is between two chimpanzees, for example.

The reason for our similarity is the population bottlenecks we faced as a species, during which our numbers dropped as low as a few hundred families and we came close to extinction. As a result, we are too homogeneous to have separated into different races. Nevertheless, variety has emerged through populations being separated geographically – and culturally, in some cases – over thousands of years. The greatest distinctions occur in isolated populations where small genetic and cultural changes become exaggerated, and there have been many of them over the 50,000 years since my ancestors made the journey out of Africa towards Europe.

According to the analysis of my genome, my haplogroup is H4a. Haplogroups describe the mutations on our mitochondrial DNA, passed down through the maternal line, and can theoretically be used to trace a migratory path all the way back to Africa. H4a is a group shared by people in Europe, unsurprisingly, and western Asia. It is, the genome-testing company assures me, the same as Warren Buffet’s. So what journey did my ancestors take that would result in these mutations and give me typically European features?

--------------------------------------------------

There exists an uneasy relationship between biology and culture

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to be continued....

Stormer0628 · Mar 12, 2017

“I was dumped by helicopter in the wilderness with two other people, a Russian and an indigenous Yukaghir man, with our dogs, our guns, our traps, a little food and a little tea. There we had to survive and get food and furs in the coldest place on Earth where humans live naturally – minus 60 degrees.”

Eske Willerslev lived for six months as a trapper in Siberia in his 20s. Separately, his identical twin brother Rane did the same. When they were teenagers, their father had regularly left them in Lapland to survive alone in the wilderness for a couple of weeks, fostering a passion for the remote tundra and the people who live there, and they went on increasingly lengthy expeditions. But surviving practically alone was very different. “It was a childhood dream, but it was the toughest thing I have ever done,” Eske admits.

These experiences affected the twins deeply, and both have been driven towards a deeper understanding of how the challenge of survival has forged us as humans over the past 50,000 years. It led Eske into the science of genetics, and to pioneering the new field of ancient DNA sequencing. Now director of the Centre for GeoGenetics at the Natural History Museum of Denmark, Eske has sequenced the world’s oldest genome (a 700,000-year-old horse) and was the first to sequence the genome of an ancient human, a 4,000-year-old Saqqaq man from Greenland. Since then, he has gone on to sequence yet more ancient humans and, in doing so, has fundamentally changed our understanding of early human migration through Europe and beyond. If anyone can unpick my origins, it is surely Eske.

First, though, I go to meet his twin Rane, who studied humanities, went into cultural anthropology and is now a professor at Aarhus University. He’s not convinced that his brother’s genetic approach can reveal all the answers to my questions: “There exists an uneasy relationship between biology and culture,” he tells me. “Natural scientists claim they can reveal what sort of people moved around, and they are not interested in having their models challenged. But this cannot tell you anything about what people thought or what their culture was.”

To put this point to Eske, I visit him in his delightful museum office, opposite a petite moated castle and in the grounds of the botanic gardens – there could scarcely be a more idyllic place for a scientist to work. Greeting him for the first time, just hours after meeting Rane, is disconcerting. Identical twins are genetically and physically almost exactly the same – looking back, many years from now, at DNA left by the brothers, it would be all but impossible to tell them apart or even to realise that there were two of them.

Eske tells me that he is increasingly working with archaeologists to gain additional cultural perspective, but that genetic analysis can answer questions that nothing else can. “You find cultural objects in certain places and the fundamental question is: Does that mean people who made it were actually there or that it was traded? And, if you find very similar cultural objects, does that mean there was parallel or convergent cultural evolution in the two places, or does that mean there was contact?” he explains.

“For example, one theory says the very first people crossing into the Americas were not Native Americans but Europeans crossing the Atlantic, because the stone tools thousands of years ago in America are similar to stone tools in Europe at the same time. Only when we did the genetic testing could we see it was convergent evolution, because the guys carrying and using those tools have nothing to do with Europeans. They were Native Americans. So the genetics, in terms of migrations, is by far the most powerful tool we have available now to determine: was it people moving around or was it culture moving around? And this is really fundamental.”

What Eske went on to discover about Native American origins rewrote our understanding completely. It had been thought that they were simply descendants of East Asians who had crossed the Bering Strait. In 2013, however, Eske sequenced the genome of a 24,000-year-old boy discovered in central Siberia, and found a missing link between ancient Europeans and East Asians, the descendants of whom would go on to populate America. Native Americans can thus trace their roots back to Europe as well as East Asia.

And what about my ancestors? I show Eske the H4a haplotype analysed by the sequencing company and tell him it means I’m European. He laughs derisively. “You could be and you could be from somewhere else,” he says. “The problem with the gene-sequencing tests is that you can’t look at a population and work back to see when mutation arose with much accuracy – the error bars are huge and it involves lots of assumptions about mutation rates.

“This is why ancient genetics and ancient genomics are so powerful – you can look at an individual and say, ‘Now we know we are 5,000 years ago, how did it look? Did they have this gene or not?’”

--------------------------------------------------

While ancient genomics can help satisfy
curiosity about our origins, its real value may
be in trying to unpick different health risks

--------------------------------------------------

The things that we thought we understood about Europeans are coming unstuck as we examine the genes of more ancient people. For example, it was generally accepted that pale skin evolved so we could get more vitamin D after moving north to where there was little sun and people had to cover up against the cold. But it turns out that it was the Yamnaya people from much further south, tall and brown-eyed, who brought pale skins to Europe. Northern Europeans before then were dark-skinned and got plenty of vitamin D from eating fish.

It is the same with lactose tolerance. Around 90 per cent of Europeans have a genetic mutation that allows them to digest milk into adulthood, and scientists had assumed that this gene evolved in farmers in northern Europe, giving them an additional food supply to help survive the long winters. But Eske’s research using the genomes of hundreds of Bronze Age people, who lived after the advent of farming, has cast doubt on this theory too: “We found that the genetic trait was almost non-existent in the European population. This trait only became abundant in the northern European population within the last 2,000 years,” he says.

It turns out that lactose tolerance genes were also introduced by the Yamnaya. “They had a slightly higher tolerance to milk than the European farmers and must have introduced it to the European gene pool. Maybe there was a disaster around 2,000 years ago that caused a population bottleneck and allowed the gene to take off. The Viking sagas talk about the sun becoming black – a major volcanic eruption – that could have caused a massive drop in population size, which could have been where some of that stock takes off with lactose.”

While ancient genomics can help satisfy curiosity about our origins, its real value may be in trying to unpick some of the different health risks in different populations. Even when lifestyle and social factors are taken into account, some groups are at significantly higher risk of diseases such as diabetes or HIV, while other groups seem more resistant. Understanding why could help us prevent and treat these diseases more effectively.

It had been thought that resistance to infections like measles, influenza and so on arrived once we changed our culture and started farming, living in close proximity with other people and with animals. Farming started earlier in Europe, which was thought to be why we have disease resistance but Native Americans don’t, and also why the genetic risks of diabetes and obesity are higher in native Australian and Chinese people than in Europeans.

“Then,” says Eske, “we sequenced a hunter-gatherer from Spain, and he showed clear genetic resistance to a number of pathogens that he shouldn’t have been exposed to.” Clearly, Europeans and other groups have a resistance that other groups don’t have, but is this really a result of the early agricultural revolution in Europe, or is something else going on?

Eske’s analysis of people living 5,000 years ago has also revealed massive epidemics of plague in Europe and Central Asia, 3,000 years earlier than previously thought. Around 10 per cent of all skeletons the team analysed had evidence of plague. “Scandinavians and some northern Europeans have higher resistance to HIV than anywhere else in the world,” Eske notes. “Our theory is that their HIV resistance is partly resistance towards plague.”

It could be that the cultural changes we have made, such as farming and herding, have had less influence on our genes than we thought. Perhaps it is simply the randomness of genetic mutation that has instead changed our culture. There’s no doubt that where mutations have occurred and spread through our population, they have influenced the way we look, our health risks and what we can eat. My ancestors clearly didn’t stop evolving once they’d left Africa – we’re still evolving now – and they have left an intriguing trail in our genes.

At the Gibraltar Museum, a pair of Dutch archaeology artists have created life-size replicas of a Neanderthal woman and her grandson, based on finds from nearby. They are naked but for a woven amulet and decorative feathers in their wild hair. The boy, aged about four, is embracing his grandmother, who stands confidently and at ease, smiling at the viewer. It’s an unnerving, extraordinarily powerful connection with someone whose genes I may well share, and I recall Clive’s words from when I asked him if modern humans had simply replaced Neanderthals because of our superior culture.

“That replacement theory is a kind of racism. It’s a very colonialist mentality,” he said. “You’re talking almost as if they were another species.”

===============

Professor Eske Willerslev is a research associate at the Wellcome Trust Sanger Institute, which is funded by a core grant from the Wellcome Trust, which publishes Mosaic.

This article first appeared on Mosaic and is republished here under a Creative Commons licence.

Stormer0628 · Mar 15, 2017

After scientists have successfully implemented an error-free DNA storage, the next step, of course, is a DNA computer. And what a computer it would be! We think quantum computers would be fast, but even those are no match for DNA computers!

Like living DNA, the new type of computer would be self-replicating, one that replaces silicon chips with processors made from DNA molecules, and it would be faster than any other form of computer ever proposed—yes, faster than even quantum computers.

Called a nondeterministic universal Turing machine (NUTM), it's predicted that the technology could execute all possible algorithms at once by taking advantage of DNA's ability to replicate almost perfect copies of itself over billions of years.

The basic idea is that our current electronic computers are based on a finite number of silicon chips, and we're fast approaching the limit for how many we can actually fit in our machines.

To address this limitation, researchers are currently working on making quantum computers a reality—superpowerful devices that replace the bits of electronic computers with quantum-entangled particles called qubits.

Unlike regular bits that can only take on the form of 1 or 0 in the binary code, qubits can take the form of 0, 1, or a superposition of the two simultaneously, which allows them to perform many different calculations at once.

Obviously this would result in a huge boost in speed, but quantum computers are an incredibly difficult thing to get right, because of how complicated it is to create the exact conditions for not one quantum-entangled particle, but a whole lot of them.

Despite concerted efforts all over the world, no one has managed to build a fully functioning quantum computer.

But the secret third option here is a DNA-based machine that gets all the benefits of a quantum computer, without the headache of quantum weirdness, because it's based on DNA doing what DNA does best—replicating.

"DNA is an excellent medium for information processing and storage," the team involved in the project from the University of Manchester in the UK explains.

"It is very stable, as the sequencing of ancient DNA demonstrates. It can also reliably be copied, and many genes have remained virtually unchanged for billions of years."

To give you an idea of the difference such a device could make in the world, imagine you've got a computer program searching a maze, and it reaches a fork in the road.

A regular electronic computer would have to decide which path to follow, but a DNA-based computer wouldn't need to choose - it could replicate itself and follow both paths at the same time.

With both paths covered, the program would figure out which one leads to the end of the maze far quicker than an electronic computer that could only test one at a time.

"Our computer's ability to grow as it computes makes it faster than any other form of computer, and enables the solution of many computational problems previously considered impossible," says one of the team, Ross D. King.

"Quantum computers are an exciting other form of computer, and they can also follow both paths in a maze, but only if the maze has certain symmetries, which greatly limits their use."

Not only that, but imagine no longer being constrained by the physical limits of using silicon chips, which are pretty damn small right now, but are nowhere near the size of a single DNA molecule.

"As DNA molecules are very small, a desktop computer could potentially utilize more processors than all the electronic computers in the world combined - and therefore outperform the world's current fastest supercomputer, while consuming a tiny fraction of its energy," says King.

While DNA-based computers have been proposed since the 1990s, King and his team say this is the first time the feasibility of a DNA-based nondeterministic universal Turing machine (NUTM) has been established.

"We demonstrate that this design works using both computational modelling and in vitro molecular biology experimentation," the team reports.

"The current design has limitations, such as restricted error-correction. However, it opens up the prospect of engineering NUTM-based computers able to outperform all standard computers on important practical problems."

The researchers propose using DNA molecules to represent information based on the four-character genetic alphabet - A [adenine], G [guanine], C [cytosine], and T [thymine] - rather than the binary alphabet of 1s and 0s.

They say that regular computers - which are classified as universal Turing machines (UTM) - can be converted into nondeterministic universal Turing machines (NUTM) using a programming language called Thue.

Invented by software engineer John Colagioia in early 2000, Thue programming language can take strings of alphabet symbols and rewrite them in different orders to create completely separate strings for a self-replicating form of data processing.

"The application of a Thue rule to a string therefore produces a new string - equivalent to change of state in a UTM," the researchers explain.

Because multiple Thue rules can be applied to a single string, and individual Thue rules can be applied to multiple positions in a string, the computing possibilities are virtually endless.

The team has also demonstrated that DNA is physically strong enough to act as processors in this set-up—something that previous experiments have also shown—and say it's now up to someone to actually build this thing for real.

When that happens—you know you have a road map to the sickest, strangest, and most intimidating computer system ever.

You think you're ready for it?

===================
The research has been published in the Journal of the Royal Society Interface, and you can read it for free at arXiv.org.

rapidox · Mar 15, 2017

haha parang nagbabasa lang ako nang tabloid, DNA computers. :rofl:

Pero malay mo, yung akala nang iba nakakatawa ngayun possible pala sa future.

Pero yung na imagine ko lang na purpose nang DNA sa computer ay bio-hardware, kung saan nag self replicate yung computer mo into a bigger computer just like human growth. ex. from a child to an adult = from a DNA Personal computer to DNA super computer

Stormer0628 · Mar 16, 2017

rapidox said:
haha parang nagbabasa lang ako nang tabloid, DNA computers.

Pero malay mo, yung akala nang iba nakakatawa ngayun possible pala sa future.

Pero yung na imagine ko lang na purpose nang DNA sa computer ay bio-hardware, kung saan nag self replicate yung computer mo into a bigger computer just like human growth. ex. from a child to an adult = from a DNA Personal computer to DNA super computer

The theory is solid, confirmed by ongoing research and experiments. The biggest issue is lack of proper program algorithm to probe foreseeable complexities.

With Trump and his gang of pseudoscientists, Brexit at EU, scientists are suddenly made aware to improve their media presentations and narrative to secure that suddenly elusive funding now. They would be wise to heed the advice of Hari Sheldon of Asimov's Foundation: "Always account for mutants in your social forecasts. Those will throw you back years behind or forward in your target." It's behind in their case now. Too bad for those in the twilight of their careers though. Rogue politics will leave such bad taste in their mouths like nothing can.

I'm sure the field would come up with more palatable term for DNA computing along the way. It's a bit off as it stands right now.

rapidox · Mar 16, 2017

We think quantum computers would be fast, but even those are no match for DNA computers!

dito lng tlga ako tumawa, parang tabloid news lng. Yes it is a solid theory, sorry pero ganun din yun ginawa ni Bush Jr. sa cold fusion dati ginawa nya itong media hype pero mapa hanggang ngayun nasa primative stage parin yung research.

Trump ok'd Elon Musk and other radical science projects, not really surprised since Trump is also a venture capitalist but in luxury properties business.

Stormer0628 · Mar 16, 2017

rapidox said:
dito lng tlga ako tumawa, parang tabloid news lng. Yes it is a solid theory, sorry pero ganun din yun ginawa ni Bush Jr. sa cold fusion dati ginawa nya itong media hype pero mapa hanggang ngayun nasa primative stage parin yung research.

Trump ok'd Elon Musk and other radical science projects, not really surprised since Trump is also a venture capitalist but in luxury properties business.

Yes. Media is no saints when it comes to trying to draw in viewership and click share. Most of the time I try to tone down some of these sources. Most, not all the time. :lol:

Fusion might have more trouble containing and retaining fusion reactions and meeting its targets than these scientists involved in dna computing though. Computing research has proven it could progress by large leaps and bounces than any other field. And there is that ballistic electrons that might offer a more manageable energy option than superconductor and fusion researches right now. Nice transition tech perhaps.

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