What “junk DNA” does

A major discovery:

It turns out that “junk DNA”, once thought to comprise most of the genetic material packed into our cells, isn’t junk. Instead, it plays a complicated — and still shadowy — role in regulating our genes.

That’s the essential insight of a five-year project to study the 98 percent of the human genome that is not, strictly speaking, genes. It now appears that more than three-quarters of our DNA is active at some point in our lives.

“This concept of ‘junk DNA’ is really not accurate. It is an outdated metaphor to explain our genome,” said Richard Myers, one of the leaders of the 400-scientist Encyclopedia of DNA Elements Project, nicknamed Encode.

“The genome is just alive with stuff. We just really didn’t realize that before,” said Ewan Birney of the European Bioinformatics Institute in England.

The new insights are contained in six papers published Wednesday in the journal Nature. More than 20 related papers from Encode are appearing elsewhere.

The human genome consists of about 3 billion DNA “letters” strung one to another in 46 chains called chromosomes. Specific stretches of those letters (whose formal name is “nucleotides”) carry the instructions for making specific proteins. Those proteins, in turn, build the cells and tissues of living organisms.

The Human Genome Project, which identified the correct linear sequence of those letters, revealed that human cells contain only about 21,000 genes — far fewer than most biologists predicted. Furthermore, those genes took up only 2 percent of the cell’s DNA. The new research helps explain how so few genes can create an organism as complex as a human being.

The answer is that regulating genes — turning them on and off, adjusting their output, manipulating their timing, coordinating their activity with other genes — is where most of the action is.

The importance and subtlety of gene regulation is not a new idea. Nor is the idea that parts of the genome once thought to be “junk” may have some use. What the Encode findings reveal is the magnitude of the regulation.

It now appears that at least 4 million sections of the genome are involved in manipulating the activity of genes. Those sections act like switches in a wiring diagram, creating an almost infinite number of circuits.

“There is a modest number of genes and an immense number of elements that choreograph how those genes are used,” said Eric D. Green, director of the National Human Genome Research Institute, the federal agency that paid for the research.

via ‘Junk DNA’ concept debunked by new analysis of human genome – The Washington Post.

So every cell of every living organism contains not just genetic information but a whole system for activating, directing, timing, and animating that information.

We sure are lucky that millions of years of random mutations and natural selection evolved into something so infinitely complex.

Oh, wait.  All of that had to be in place in order to make reproduction possible; that is, before natural selection could happen.

How Quantum Physics refutes materialism

Physics professor Stephen M. Barr explains how quantum physics makes the world view of materialism–the assumption of most of today’s atheists–scientifically impossible.

Materialism is an atheistic philosophy that says that all of reality is reducible to matter and its interactions. It has gained ground because many people think that it’s supported by science. They think that physics has shown the material world to be a closed system of cause and effect, sealed off from the influence of any non-physical realities — if any there be. Since our minds and thoughts obviously do affect the physical world, it would follow that they are themselves merely physical phenomena. No room for a spiritual soul or free will: for materialists we are just “machines made of meat.”

Quantum mechanics, however, throws a monkey wrench into this simple mechanical view of things.  No less a figure than Eugene Wigner, a Nobel Prize winner in physics, claimed that materialism — at least with regard to the human mind — is not “logically consistent with present quantum mechanics.” And on the basis of quantum mechanics, Sir Rudolf Peierls, another great 20th-century physicist, said, “the premise that you can describe in terms of physics the whole function of a human being … including [his] knowledge, and [his] consciousness, is untenable. There is still something missing.”

Barr goes on to explain in a technical but pretty lucid manner why this is the case, going into the mathematics of probability and why the observer has an intrinsic impact on the system being observed.   I can’t summarize it.  Read it yourself.  Here is his conclusion:

If the mathematics of quantum mechanics is right (as most fundamental physicists believe), and if materialism is right, one is forced to accept the Many Worlds Interpretation of quantum mechanics. And that is awfully heavy baggage for materialism to carry.

If, on the other hand, we accept the more traditional understanding of quantum mechanics that goes back to von Neumann, one is led by its logic (as Wigner and Peierls were) to the conclusion that not everything is just matter in motion, and that in particular there is something about the human mind that transcends matter and its laws. It then becomes possible to take seriously certain questions that materialism had ruled out of court: If the human mind transcends matter to some extent, could there not exist minds that transcend the physical universe altogether? And might there not even exist an ultimate Mind?

via Does Quantum Physics Make it Easier to Believe in God? | Big Questions Online.

HT:  Anna Williams

Sunday’s landing on Mars

Remember those spunky little rovers that were landed on Mars, sending back pictures of the Red Planet for years on end?  Well, another rover is scheduled to touch down on Mars this Sunday, August 6.

It’s the size of an SUV, with massive digging arms, lasers, and automated laboratories that may settle the question of Martian life once and for all.  The plan is for this 2000 pound vehicle, named “Curiosity,” to be dropped inside a Martian crater that appears to have once held water.  The difficulty of this landing, requiring pin-point precision of all systems, is being described as “seven minutes of terror” for the NASA team trying to pull this off.

If it works, we will greatly expand our knowledge of Mars.  And have some sublime photos of another world.

With Mars mission and rover Curiosity, NASA hunts building blocks of life – The Washington Post.

Children as cure for the common cold

More counter-intuitive mysterious health findings:

A new study says that parents are less apt to the common cold than those without children.

Researchers at Carnegie Mellon University found that those with kids were half as likely to develop colds with that number increasing with each additional child in the household.

Yet, the study shows that a strengthened immune system is not what protects parents.

Rather, researchers say that “mental toughness” stemming from parenthood helps them to fight off the virus, reported the Daily Mail. . .

Researchers found that those people who had children were 52 percent less likely to get a cold.

Medical News Today said that the study also found that the risk of parents contracting a cold was even lower when the parents did not live with their children – 73 percent less likely.

Interestingly, when researchers controlled for factors such as immunity and exposure to the cold virus, parents still fought off the virus better than non-parents, pointing to psychological factors that may offer protection.

“Although parenthood was clearly protective, we were unable to identify an explanation for this association,” said study author Sheldon Cohen of Carnegie Mellon University in a press release.

“Because we controlled for immunity to the virus, we know that these differences did not occur just because the parents were more likely to have been exposed to the virus through their children.”

The study was published in the journal Psychosomatic Medicine.

via Parents less apt to common cold than non-parents, says study.

One would assume that having kids would expose parents to all kinds of bugs their offspring bring home with them.  But that having kids reduces the number of colds?  And that the more kids you have the more protected you are against colds?  And more so if your  offspring aren’t around?  It’s hard to imagine the connecting factors.  That parents have greater “mental toughness”?  May be, but since when does toughmindedness protect a person from viruses?

Any theories about why this should be?

We are a little world made cunningly

The ancients talked about the human body as a microcosm, as a little world.  Now scientists have shown just how true that is, how each of us is a world with millions of inhabitants:

They live on your skin, up your nose, in your gut – enough bacteria, fungi and other microbes that collected together could weigh, amazingly, a few pounds.

Now scientists have mapped just which critters normally live in or on us and where, calculating that healthy people can share their bodies with more than 10,000 species of microbes.

Don’t say “eeew” just yet. Many of these organisms work to keep humans healthy, and results reported Wednesday from the government’s Human Microbiome Project define what’s normal in this mysterious netherworld.

One surprise: It turns out that nearly everybody harbors low levels of some harmful types of bacteria, pathogens that are known for causing specific infections. But when a person is healthy – like the 242 U.S. adults who volunteered to be tested for the project – those bugs simply quietly coexist with benign or helpful microbes, perhaps kept in check by them. . . .

Already the findings are reshaping scientists’ views of how people stay healthy, or not.

“This is a whole new way of looking at human biology and human disease, and it’s awe-inspiring,” said Dr. Phillip Tarr of Washington University at St. Louis, one of the lead researchers in the $173 million project, funded by the National Institutes of Health.

“These bacteria are not passengers,” Tarr stressed. “They are metabolically active. As a community, we now have to reckon with them like we have to reckon with the ecosystem in a forest or a body of water.”

And like environmental ecosystems, your microbial makeup varies widely by body part. Your skin could be like a rainforest, your intestines teeming with different species like an ocean.

Scientists have long known that the human body coexists with trillions of individual germs, what they call the microbiome. Until now, they’ve mostly studied those that cause disease: You may recall health officials saying about a third of the population carries Staphylococcus aureus harmlessly in their noses or on their skin but can infect others.

But no one knew all the types of microbes that live in healthy people or where, and what they do. Some 200 scientists from nearly 80 research institutions worked together for five years on this first-ever census to begin answering those questions by unraveling the DNA of these microbes, with some of the same methods used to decode human genetics. The results were published Wednesday in a series of reports in the journals Nature and the Public Library of Science. . . .

Our bodies are thought to be home to about 10 bacterial cells for every human cell, but they’re so small that together microbes make up about 1 percent to 3 percent of someone’s body mass, explained Dr. Eric Green, director of NIH’s National Human Genome Research Institute. That means a 200-pound person could harbor as much as 6 pounds of bacteria.

There are about 22,000 human genes. But the microbes add to our bodies the power of many, many more – about 8 million genes, the new project estimated.

Those bacterial genes produce substances that perform specific jobs, some of which play critical roles in the health and development of their human hosts, said Dr. Bruce Birren of the Broad Institute of MIT and Harvard, another of the project’s investigators. Genes from gut bacteria, for example, lead to digestion of certain proteins and fats. They also produce certain beneficial compounds, like inflammation-fighting chemicals.

Another surprise: There isn’t one core set of bacteria that perform those functions. A wide variety can do the same jobs, the researchers found.

That’s fortunate considering people carry a customized set of microbes, one that varies dramatically depending on where you live, your diet and a host of other factors. Your microbial zoos also can change, such as when taking antibiotics that kill infection-causing germs as well as good intestinal bacteria that may be replaced with different but equally effective bugs.

“We don’t all have the same bacteria although they all seem to have been organized to do the same things,” Birren said. It may be that our lifestyle and environment “induces each of us to have arrived at a solution that works for us.”

With this first snapshot of what normal looks like, studies now are under way to see how the microbes differ in people with certain diseases, in hopes of learning how to prevent or treat the illnesses.

via News from The Associated Press.

Yes, this could be considered disgusting, but I agree with the researcher who finds it awe-inspiring.  So even individual human beings are actually a community of separate creatures.  Reminds me of the co-inherence of the Trinity.

P.S.:  Who can identify the allusion in the title to this post?  Without Googling it?

The weird science of Light

More mind-blowing discoveries from quantum physics:

In the quantum optical laboratories at the Niels Bohr Institute, researchers have conducted experiments that show that light breaks with the classical physical principles. The studies show that light can have both an electrical and a magnetic field, but not at the same time. That is to say, light has quantum mechanical properties.

via Breaking the limits of classical physics.

 


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