Ten Things You Probably Didn't Know About DNA

Ten Things You Probably Didn't Know About DNA

by Robert T. Gonzales

It may be the basis of all life on Earth, but we're betting there's still a lot you don't know about deoxyribonucleic acid. Who discovered it? What makes it "right-handed"? And what does it have to do with LSD? Find out after the jump.

10. James Watson and Francis Crick did not discover DNA

Neither did Rosalind Franklin or Maurice Wilkins, for that matter. In actuality, the credit for discovering DNA goes to one Friedrich Miescher. In 1869, the Swiss biochemist was inspecting the pus on used surgical bandages (yay, science!) when a substance he didn't recognize passed into his microscope's field of view. He called the substance "nuclein," because, he noted, it was located within the nuclei of cells.

9. Good Call, Miescher

Which is funny, because you can actually find a fair bit of DNA in mitochondria, as well. What's interesting, though, is that out of all your DNA, it's the stuff in your nuclei that play the most important role from a hereditary standpoint; remarkably, Miescher would later speculate in a letter to his uncle that this mysterious "nuclein" might actually play a role in heredity.

8. It took decades to prove Miescher's hunch was right

Miescher's insight was years, if not decades, ahead of its time. By the turn of the 20th century, scientists had begun to strongly suspect that chromosomes — densely packed structures of DNA and protein — were involved in the transmission of traits from one generation to the next, but it wasn't until researcher Thomas Hunt Morgan showed that molecular differences in chromosomes actually corresponded to heritable physical characteristics in fruit flies that anybody truly appreciated the fundamental role of said chromosomes in the transfer of genetic information.

7. Wait... what genetic information?

What's interesting about the phrase "genetic information" is that even as late as 1933, the year Morgan received a Nobel Prize for his groundbreaking work on chromosomes, many scientists still doubted the existence of so-called "genes" — information, presumably housed within chromosomes, that gave rise to the physical traits Morgan had observed in his experiments. At the time, Morgan wrote that there was no consensus "as to what the genes are — whether they are real or purely fictitious."

The concept of genes only really found its footing in 1944, when molecular biologist Oswald Avery (pictured here) showed thatgenes were not only real, but that they were composed of DNA (and not, for example, proteins, which — also being contained in chromosomes — many scientists had assumed comprised our true "genetic" blueprint).

6. LSD May have played a role in the discovery of DNA's structure

Just nine years after Avery's discovery, James Watson and Francis Crick published an article in Nature describing the double helical structure of DNA — a structure which, according to some accounts, Crick claims to have perceived while high on LSD.

5. Why is it Watson and Crick and not Crick and Watson?

Joe Hanson actually posed this excellent question last week on It's Okay to be Smart:

How did they decide whose name would come first on their paper? That's where we get the comfortable meter of their paired and classic name pairing from. I mean, did they flip a coin? It was a fairly even collaboration, and I don't know why their names weren't on the paper in alphabetical order.

I mean, just think of that. What if it had been Crick & Watson? A huge part of the biological lexicon would be changed:

"Well Steve, you can clearly see the canonical Crick & Watson base-pairing there in the hairpin."

It turns out they did just flip a coin, though to hear James Watson tell it, it sounds like he felt he deserved to be first author, anyway.

4. DNA is Right-Handed

When you see DNA depicted as a double helix, you can clearly see that its structure is twisted. That twist makes DNA a "chiral" molecule, meaning it is asymmetric in such a way that a DNA molecule and its mirror image are not superimposable. Examples of chirality are everywhere. Take your hands, for example. For all intents and purposes, your left hand and right hand are mirror images of one another, but no matter how you twist or position either hand, you'll find that it is impossible to orient the two of them in exactly the same way. Chirality is the reason you can't shake a person's right hand with your left, or wear your left shoe on your right foot.

Chiral molecules are said to possess "handedness," and in DNA, that handedness is characterized by the direction of its twisting strands. DNA's right-handedness can be identified by a simple trick involving your hands. Take your right hand and, with your thumb pointing upward, imagine grasping the spiral pictured here (in this diagram there is only one helix... in DNA there are two, but this rule still applies). Now imagine your hand twisting around the outside of the spiral, tracing its grooves in the direction that your fingertips are pointing. Your hand should rotate upward along the helix. If you try this trick with your left hand, again grasping the helix with your thumb pointing up, you'll notice that following the rotation of the helix in the direction your fingertips are pointing will cause your hand to move downward.

That means that if you're reading an article online or in a magazine and it features a picture of a left-handed double helix, that picture is wrong, wrong, wrong.

3. Except when it isn't

Yes, most DNA is right-handed. The DNA molecule that Watson and Crick described, for example, was right-handed. But DNA can actually exist in a variety of biologically active helical conformations. The one most people are familiar with is called B-DNA (depicted at center in the image shown here). On the far left is another conformation of DNA, (called A-DNA) that is also right-handed, but more tightly wound than B-DNA. On the far right, however, is a left-handed conformation, known (awesomely) as Z-DNA. So before you go on a pedantic rampage about left- and right-handed DNA, make sure you're not getting all bent out of shape over some Z-DNA (or a plot point in the upcoming Spider-Man movie... watch for the left-handed helices around 1:30).

2. DNA can exist in a variety of bizarre and unfamiliar forms

You want a triple helix? You got it. A transient, four-stranded super-molecule (that just happens to be the lynchpin step in the process of genetic recombination)? Coming right up. How about a smiley face, a map of the Americas, or a nanodrug-carrying box, complete with lock and key? Yeah, we've got those, too. For years, DNA has been growing in popularity as a nano-scale building material for applications in everything from medicine to technology. And we've only just begun to appreciate what these DNA nanomachines are capable of. [DNA tetrahedron via]

1.   We can make synthetic DNA

Strands of DNA and RNA are formed by stringing together long chains of molecules called nucleotides. A nucleotide is made up of three chemical components: a phosphate (labeled here in red), a five-carbon sugar group (labeled here in yellow, this can be either a deoxyribose sugar - which gives us the "D" in DNA - or a ribose sugar - hence the "R" in RNA), and one of five standard bases (adenine, guanine, cytosine, thymine or uracil, labeled in blue).

By swapping out artificial molecules in place of any of these chemical components, researchers can actually make synthetic DNA. One of the most commonly created forms of synthetic DNA is XNA, which swaps out the sugar group for any number of artificially produced molecules. Just last month, researchers succeeded in creating a genetic system that allowed this XNA to replicate and evolve. And to top it all off, this "alien" XNA is actually stronger than the real thing.

Top image and XNA via Shutterstock; all other images via Wikimedia commons unless otherwise indicated

 

From io9 @ http://io9.com/5907275/ten-things-you-probably-didnt-know-about-dna

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World's first GM babies born

World's first GM babies born

 

by MICHAEL HANLON

The world's first genetically modified humans have been created...

The disclosure that 30 healthy babies were born after a series of experiments in the United States provoked another furious debate about ethics.

So far, two of the babies have been tested and have been found to contain genes from three 'parents'.

Fifteen of the children were born in the past three years as a result of one experimental programme at the Institute for Reproductive Medicine and Science of St Barnabas in New Jersey.

The babies were born to women who had problems conceiving. Extra genes from a female donor were inserted into their eggs before they were fertilised in an attempt to enable them to conceive.

Genetic fingerprint tests on two one-year- old children confirm that they have inherited DNA from three adults --two women and one man.

The fact that the children have inherited the extra genes and incorporated them into their 'germline' means that they will, in turn, be able to pass them on to their own offspring.

Altering the human germline - in effect tinkering with the very make-up of our species - is a technique shunned by the vast majority of the world's scientists.

Geneticists fear that one day this method could be used to create new races of humans with extra, desired characteristics such as strength or high intelligence.

Writing in the journal Human Reproduction, the researchers, led by fertility pioneer Professor Jacques Cohen, say that this 'is the first case of human germline genetic modification resulting in normal healthy children'.

Some experts severely criticised the experiments. Lord Winston, of the Hammersmith Hospital in West London, told the BBC yesterday: 'Regarding the treatment of the infertile, there is no evidence that this technique is worth doing . . . I am very surprised that it was even carried out at this stage. It would certainly not be allowed in Britain.'

John Smeaton, national director of the Society for the Protection of Unborn Children, said: 'One has tremendous sympathy for couples who suffer infertility problems. But this seems to be a further illustration of the fact that the whole process of in vitro fertilisation as a means of conceiving babies leads to babies being regarded as objects on a production line.

'It is a further and very worrying step down the wrong road for humanity.' Professor Cohen and his colleagues diagnosed that the women were infertile because they had defects in tiny structures in their egg cells, called mitochondria.

They took eggs from donors and, using a fine needle, sucked some of the internal material - containing 'healthy' mitochondria - and injected it into eggs from the women wanting to conceive.

Because mitochondria contain genes, the babies resulting from the treatment have inherited DNA from both women. These genes can now be passed down the germline along the maternal line.

A spokesman for the Human Fertilisation and Embryology Authority (HFEA), which regulates 'assisted reproduction' technology in Britain, said that it would not license the technique here because it involved altering the germline.

Jacques Cohen is regarded as a brilliant but controversial scientist who has pushed the boundaries of assisted reproduction technologies.

He developed a technique which allows infertile men to have their own children, by injecting sperm DNA straight into the egg in the lab.

Prior to this, only infertile women were able to conceive using IVF. Last year, Professor Cohen said that his expertise would allow him to clone children --a prospect treated with horror by the mainstream scientific community.

'It would be an afternoon's work for one of my students,' he said, adding that he had been approached by 'at least three' individuals wishing to create a cloned child, but had turned down their requests.

Neanderthal Babies All Around:

Synthetic Biology Is Closer Than You Think

Photograph by Wendy Maeda/The Boston Globe via Getty Images

George Church, genetics professor, at Harvard Medical School in Boston, 2011

George Church — he of the beard, tall man’s lope and overwhelming credentials — has hit the circuit to promote a new book: Regenesis: How Synthetic Biology Will Reinvent Nature and Ourselves. As the title explains, the book explores the field of synthetic biology, which centers on how man can program DNA to create things ranging from new fuels to seeds that grow into fully-formed houses. This subject often veers into the fanciful, and Church keeps up that tradition. Yet when he says things about bringing Neanderthals back to life, you have to take notice instead of chuckling.

For about the last 35 years, Church has been at the cutting edge of genetics and radical biology in academic and entrepreneurial settings. Today, he’s the professor of genetics at Harvard Medical School, the super-sought-after adviser to more than 20 companies in genetics and synthetic biology, and co-founder of a handful of companies. Church, 58, relishes the academic side of his work and has scores of researchers doing cutting-edge stuff at his Harvard lab. That said, he likes to make sure that people see him as a man of action and not just some big brain in an ivory tower. “I still do things with my own hands,” he says.

Regenesis opens with some fairly fantastic notions. For one, there’s talk of going all Jurassic Park on the world and bringing mammoths and other creatures back from extinction. Why would we want to do such a thing? Well, it turns out that mammoths clomped around in the tundra and stopped trees from growing and taking over vast grasslands. The increase in trees since their disappearance has contributed to warmer temperatures because the trees don’t reflect light or consume carbon dioxide as well as grass. “We need practical reasons as well as inspirational ones with this technology,” Church says.

The thought experiment turns more intriguing when the subject of Neanderthals comes up. Church has tests running in the lab around Neanderthal cells as he tries to determine what this species might have looked and acted like. “I am 3.8 percent Neanderthal,” says Church, who has had his genome sequenced. “One of my ancestors mated with a Neanderthal, and I am not embarrassed by that.”

Church figures it’s only a matter of time and proven safety before people start picking out traits for their offspring and cloning entire children. “Almost all technology in this area is banned until it works,” Church says. “In vitro fertilization was banned, and now it is immoral to deny an infertile couple their birthright to have a child produced by their bodies. At some point, someone will come up with an airtight argument as to why they should have a cloned child. At that point, cloning will be acceptable. At that point, people will already be choosing traits for their children. What politician will tell a parent that they can’t spend their hard-earned money on getting an extra 50 SAT points for their child as long as it’s safe?”

Right, but what about the Neanderthals? I can’t let that one go.

“We have lots of Neanderthal parts around the lab. We are creating Neanderthal cells. Let’s say someone has a healthy, normal Neanderthal baby. Well, then, everyone will want to have a Neanderthal kid. Were they superstrong or supersmart? Who knows? But there’s one way to find out.”

While controversy often accompanies such talk, Church says he’s avoided slings and arrows throughout his career. “I’ve been bracing for the backlash for 20 years,” he says. It’s important to have discussions about these complex issues early and in a rational manner before the technology gets ahead of the talk, he adds. “Let’s do some safety engineering first and come up with some solutions to problems,” he says.

How far off is this brave new world? Well, according to Church, probably not far at all. “The cheap human genome was supposed to arrive 50 years from now,” he says. “It arrived this year. What if a cheap Neanderthal or mammoth arrives 50 years ahead of time?”

Church reckons that training seeds to grow into chairs or houses should be well within in our reach. “Trees are essentially growing chairs,” he says. “There are lots of primates that sit and sleep in them. That’s not visionary.”

Bringing back species from the dead or modifying species will take a bit more work. “You basically have to design a dinosaur from an ostrich because of limitations with old DNA,” he says. “You have to find a way to return the teeth and tails and arms. We will get there. I wouldn’t put anything out into the next century. We just got a 1-million-fold improvement in reading and writing DNA in the last six years. I think the developmental biology that we’re talking about is something we could knock off in much less than a century. The same goes for eliminating disease and making a big dent in aging and poverty.”

Vance is a technology writer for Bloomberg Businessweek.

From the Daily Mail @ http://www.dailymail.co.uk/news/article-43767/Worlds-GM-babies-born.html and
Business Week @ http://www.businessweek.com/articles/2012-11-01/neanderthal-babies-all-around-synthetic-biology-is-closer-than-you-think


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Artificial Life Forms Created that Evolve Intelligence

Artificial Life Forms Created that Evolve Intelligence

Michigan State University (MSU) researchers have developed “digital organisms” called Avidians that were made to evolve memory, and could eventually be used to generate intelligent artificial life and evolve into symmetrical, organized artificial brains that share structural properties with real brains.

Avidians are not imaginary sci-fi alien life forms. They are the digital creations of Charles Ofria and colleagues at Michigan State University (MSU) in East Lansing. Although they "live" in a computer world called Avida, and replicate using strings of coded computer instructions instead of DNA, they are similar to real life microbes: they compete with each other for resources, replicate, mutate, and eventually evolve to become artificially intelligent life forms. Unlike real-life Darwinian microbes, their evolution can be stopped at any time, reversed, repeated, and the precise sequence of mutations that led to the new trait can be dissected. 
{Illustration: A growing population of digital organisms, started from one individual, colonizes an initially empty space (black). As it does so, the population evolves by random mutation and selection, based on each organism's resulting phenotype. Every colored square represents one digital organism, with different colors reflecting different fitness levels. The speed, control, and ease of data collection in the Avida digital evolution platform permits experiments that would be difficult or even impossible with natural organisms, such as the present study (Clune et al., doi:10.1371/journal.pcbi.1000187) on the evolution of mutation rates. (Kaben Nanlohy, Michigan State University)}
In the image above, a growing population of digital organisms, started from one individual, colonizes an initially empty space (black). As it does so, the population evolves by random mutation and selection, based on each organism's resulting phenotype. Every colored square represents one digital organism, with different colors reflecting different fitness levels. The speed, control, and ease of data collection in the Avida digital evolution platform permits experiments that would be difficult or even impossible with natural organisms. Tens of thousands of generations down the line, some of the descendents will evolve memory
MSU researcher Jeff Clune works with a system called HyperNEAT, which uses principles of developmental biology to grow a large number of digital neurons from a small number of instructions. He translated the artificial neurons into code that could control a Roomba robot.
You can build complex brains from a relatively small number of computerized instructions, or “genes,” he says. Their brains have millions of connections, yet still perform a task well, and that number could be pushed higher yet. “This is a sea change for the field. Being able to evolve functional brains at this scale allows us to begin pushing the capabilities of artificial neural networks up, and opens up a path to evolving artificial brains that rival their natural counterparts.”
by Casey Kazan 
From http://www.dailygalaxy.com/my_weblog/2010/08/artificial-life-forms-created-that-evolve-intelligence-1.html

Watch different organisms evolve and compete for space

@ http://www.youtube.com/watch?v=apANCQmPmL0

For HyperNEAT see http://eplex.cs.ucf.edu/hyperNEATpage/HyperNEAT.html
For Avida see http://avida.devosoft.org/

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