Tiny DNA Molecules Show Liquid Crystal Phases, Pointing To New Scenario For First Life On Earth

A microscope image showing that a solution of tiny DNA molecules has formed a liquid-crystal phase. The DNA molecules pair to form DNA double helices, which, in turn, stack end-to-end to make rod-shaped aggregates that orient parallel to one another. Image by Michi Nakata, University of Colorado.
A team led by the University of Colorado at Boulder and the University of Milan has discovered some unexpected forms of liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth.
CU-Boulder physics Professor Noel Clark said the team found that surprisingly short segments of DNA, life's molecular carrier of genetic information, could assemble into several distinct liquid crystal phases that "self-orient" parallel to one another and stack into columns when placed in a water solution. Life is widely believed to have emerged as segments of DNA- or RNA-like molecules in a prebiotic "soup" solution of ancient organic molecules.
A paper on the subject was published in the Nov. 23 issue of Science. The paper was authored by Clark, Michi Nakata and Christopher Jones from CU-Boulder, Giuliano Zanchetta and Tommaso Bellini of the University of Milan, Brandon Chapman and Ronald Pindak of Brookhaven National Laboratory and Julie Cross of Argonne National Laboratory. Nakata died in September 2006.
Since the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, Clark said, scientists have been seeking effective ways for simple molecules to spontaneously self-select, "chain-up" and self-replicate. The new study shows that in a mixture of tiny fragments of DNA, those molecules capable of forming liquid crystals selectively condense into droplets in which conditions are favorable for them to be chemically linked into longer molecules with enhanced liquid crystal-forming tendencies, he said.
"We found that even tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules," Clark said. "Our vision is that from the collection of ancient molecules, short RNA pieces or some structurally related precursor emerged as the molecular fragments most capable of condensing into liquid crystal droplets, selectively developing into long molecules."
Liquid crystals - organic materials related to soap that exhibit both solid and liquid properties - are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches. Most liquid crystal phase molecules are rod-shaped and have the ability to spontaneously form large domains of a common orientation, which makes them particularly sensitive to stimuli like changes in temperature or applied voltage.
RNA and DNA are chain-like polymers with side groups known as nucleotides, or bases, that selectively adhere only to specific bases on a second chain. Matching, or complementary base sequences enable the chains to pair up and form the widely recognized double helix structure. Genetic information is encoded in sequences of thousands to millions of bases along the chains, which can be microns to millimeters in length.
Such DNA polynucleotides had previously been shown to organize into liquid crystal phases in which the chains spontaneously oriented parallel to each other, he said. Researchers understand the liquid crystal organization to be a result of DNA's elongated molecular shape, making parallel alignment easier, much like spaghetti thrown in a box and shaken would be prone to line up in parallel, Clark said.
The CU-Boulder and University of Milan team began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering, said Clark. The team found that even a DNA segment as short as six bases, when paired with a complementary segment that together measured just two nanometers long and two nanometers in diameter, could still assemble itself into the liquid crystal phases, in spite of having almost no elongation in shape.
Structural analysis of the liquid crystal phases showed that they appeared because such short DNA duplex pairs were able to stick together "end-to-end," forming rod-shaped aggregates that could then behave like much longer segments of DNA. The sticking was a result of small, oily patches found on the ends of the short DNA segments that help them adhere to each other in a reversible way -- much like magnetic buttons -- as they expelled water in between them, Clark said.
A key characterization technique employed was X-ray microbeam diffraction combined with in-situ optical microscopy, carried out with researchers from Argonne and Brookhaven National Laboratories. The team using a machine called the Argonne Advanced Photon Source synchrotron that enabled probing of the "nano DNA" molecular organization in single liquid crystal orientation domains only a few microns in size. The experiments provided direct evidence for the columnar stacking of the nano DNA pieces in a fluid liquid crystal phase.
"The key observation with respect to early life is that this aggregation of nano DNA strands is possible only if they form duplexes," Clark said. "In a sample of chains in which the bases don't match and the chains can't form helical duplexes, we did not observe liquid crystal ordering."
Subsequent tests by the team involved mixed solutions of complementary and noncomplementary DNA segments, said Clark. The results indicated that essentially all of the complementary DNA bits condensed out in the form of liquid crystal droplets, physically separating them from the noncomplementary DNA segments.
"We found this to be a remarkable result," Clark said. "It means that small molecules with the ability to pair up the right way can seek each other out and collect together into drops that are internally self-organized to facilitate the growth of larger pairable molecules.
"In essence, the liquid crystal phase condensation selects the appropriate molecular components, and with the right chemistry would evolve larger molecules tuned to stabilize the liquid crystal phase. If this is correct, the linear polymer shape of DNA itself is a vestige of formation by liquid crystal order."

Germanic Sacred Places and Objects in Britain

The Germanic invaders of the British Isles seem to have been less concerned with magic and with the aura of particular places in this world than were the Celts. The primary religious places among the non-Christian Northern Europeans were mythological: Yggdrasill or Von, the River of Expectation, formed by the slaver of the great wolf Fenrir. One exception might be burial mounds such as the one at Sutton Hoo in Suffolk, a place associated with King Raedwald, who was converted to Christianity during a visit to the court of King Ethelbert, who himself had been converted by Augustine, the founder of what was to become one of the holiest of British Christian centers, the monastery and cathedral at Canterbury. Of the fifteen burial mounds at Sutton Hoo, the largest, containing an eighty-nine-foot Anglo-Saxon boat, is thought to have been a memorial to Raedwald, who died in about 625 ce. The Sutton Hoo excavations brought to light an amazing collection of valuable objects of primarily “pagan” or non-Christian origin. We know that Raedwald’s wife was an adamant follower of the old Germanic religion and that her husband, even after his conversion, placed both Christian and non- Christian objects and altars in his place of worship.

The Anglo-Saxon Victory Tree: The Holy Rood

The Ruthwell Cross, Ruthwell church

The Germanic conception of the world tree, along with the practice of venerating sacred groves and mighty trees, found a new mode of expression in Anglo-Saxon Christianity. The development of the Cult of the Cross was widespread throughout Christendom, to be sure, but it found particularly fertile soil in Britain, where its expression also was peculiarly Germanic and often martial in some aspects. As was mentioned in connection with The Dream of the Rood, the Germanic understanding of Christ as a young hero echoed Anglo-Saxon sensibilities concerning the nature of the Savior, both as God and as man; likewise, Anglo-Saxon perceptions of the Cross often recast it into a battle-standard of Christ Triumphant and of the hope of salvation. In this way the Anglo-Saxons of Britain put a uniquely Germanic spin on a Mediterranean and Near eastern cult of veneration.

Before the fourth century ce, the cross was not widely embraced as a sign of Christianity, symbolizing as it did the gallows of a criminal. This changed after the conversion of the Emperor Constantine; as the story goes, in a dream before a great battle against overwhelming odds, Constantine saw a shining cross in the night sky and heard a voice pronounce, “by this sign ye shall conquer.” He hastened to heed these words, and the Roman troops the following day were preceded by banners of the cross; they won a great victory over the host of Huns at the Battle of Milvian Bridge on the Danube, and Constantine ended the persecution of Christians, and converted before he died. It is worth noting that Constantine’s mother, Helen, is reputed to have found the True Cross on a pilgrimage to the Holy Land, and that one of the great Anglo- Saxon narrative poems, Elene, has to do with this discovery. Whether or not the story of Constantine’s vision is apocryphal, it is certain that after his conversion a great deal of prestige accrued to the cross, and it was eventually adopted as the primary Christian symbol.

The Cross became an object of great devotion in the East, and soon various ceremonies, cults, traditions, and relics sprang up as a result of this veneration. This popularity had migrated to Western Europe by the end of the seventh century, and before the middle of that century a number of cross legends are known to have been circulating in Britain. It is during this period that the Cult of the Cross took on a peculiarly British flavor, a flavor that combined subtle hints of Celtic and Germanic pagan traditions along with the predominant eastern Christian taste. In 633 ce Oswald of Northumbria erected a giant wooden cross before the Battle of Heavenfield in a none-toosubtle attempt to co-opt Constantine’s strategy for success; he prevailed, and for ages after this date miracles were attributed to fragments of that battle standard. The success of the Cult of the Cross in Anglo-Saxon England was likewise assured.

The most notable and idiosyncratic Anglo-Saxon outgrowth of the Cult of the Cross was the widespread popularity of large, standing stone crosses, which became objects and locations of worship. By the mid-eighth century these icons had become so popular that Boniface complained that they were taking the place of regular churches; perhaps, indeed, the worshipers were hearkening back to the days of sacred groves and trees, and it is certain that the Rood of Christ was often likened to a tree. The poet who wrote The Dream of the Rood emphasized the cross’s identity as a tree, and also as a battle standard: he even called it “The Victory Tree.” Over 1,500 standing stone crosses survive in Britain to this day, and it is reasonable to assume that many more made of wood are lost to us. The most significant of these remaining roods is the Ruthwell Cross.

Standing nearly twenty feet high, the Ruthwell Cross is a striking combination of Celtic artistic traditions (intricate vine patterns known as interlace, interwoven with human and animal figures), biblical scenes, and Germanic runes and warrior conception of Christ, all bound together in an overtly Christian symbol. A number of other British crosses likewise blend cultural and mythic elements, perhaps most notably that at Gosforth. Particularly, the runic inscription running along the east and west faces of the Ruthwell Cross includes a passage from The Dream of the Rood describing Christ’s mounting of the Rood, and his death thereon; it has been noted that this passage is one that most emphasizes the Christ Militant of Anglo- Saxon belief. It also has been argued that this particular selection resonates with the scene of the death of Baldr. The lone manuscript known to contain The Dream of the Rood dates from the ninth century or so, but the Ruthwell Cross itself dates from the height of the Cult of the Cross in Britain— perhaps around the year 700—and therefore some early form of the poem must have, as well. This conception of the Tree of Christ—with all its pagan echoes and warrior ethos—thus predates the beginning of the Viking raids by almost a century, and therefore the Germanic aspects both of the poem and of the Ruthwell Cross are likely to be of mostly pure Anglo- Saxon derivation.

Alexander and Bucephalus

ALEXANDER, the son of Philip of Macedon, became king in 336 B.C. The queen-mother adored her brave son and dreamed of the great things he would do when he became a man. She did all she could to awake his ambition, telling him that he was descended from Achilles, the hero of Troy, and bidding him, when he was older, strive to do nobler deeds than his great ancestor had done. One of his tutors called the young prince Achilles, while he named himself Phoenix, after the tutor of the old Greek hero.

The Iliad of Homer, which tells of the deeds of Achilles, Alexander knew by heart. When he was a man he always carried a copy with him on his campaigns. It is said that he slept with it as well as his sword beneath his pillow.

Alexander might almost have been a Spartan boy, so simple was his training. He learned to ride, to race, to swim, but he never cared to wrestle as did most lads of his time. Nor would he offer prizes for such contests at the games which were held each year.

When the prince was asked if he would run in the Olympic Games, for he was fleet of foot, he answered, "Yes, if I could have kings to race with me."

Even as a lad he was eager to win glory, and when he heard of a great victory gained by his royal father, or of a town that had been subdued by him, he was more sorry than glad, and said to his companions, "My father will make so many conquests that there will be nothing left for me to win."

One day, while Alexander was still a boy, a Greek from Thessaly arrived at the court of Macedon, bringing with him a noble horse, named Bucephalus, which he offered to sell for £2600.

Philip went with his son and his courtiers to look at the horse and to test its powers. But when any one approached or tried to mount, Bucephalus reared and kicked, and became so unmanageable that the king, growing angry, bade the Thessalian take the animal away.

The prince had been watching the horse keenly, and as he was being led away, the lad exclaimed, "What an excellent horse do they lose for want of skill and courage to manage him!"

Philip heard what his son said, but at first he took no notice of his words. But when the prince said the same thing again and again, he looked at Alexander, and saw that he was really sorry that the horse was being sent away.

Then, half mocking, the king said, "Do you reproach those who are older than yourself, as if you knew more and were better able to manage him than they?"

"I could manage the horse better than others have done," answered the prince.
"And if you fail what will you forfeit?" asked the king.

"I will pay the whole price of the horse," said Alexander quickly.

The courtiers laughed at the confidence of the prince, but paying no attention to them, he ran toward the horse and seizing the bridle turned Bucephalus, so that he faced the sun. For the prince had noticed that the steed was afraid of his own shadow as it flitted backward and forward with his every movement.

THE LEGEND OF SAVADDAN LAKE

Not far from the foot of the Black Mountains of Brecon, in a low lovely fertile valley, under the shadow of Mount Troedd, lies Savaddan Lake (the Llangorse Lake of our maps). The following tradition is told regarding it.

Many years ago, when all the surrounding country was under Prince Tewdryg, the bed of the lake was occupied by Savaddan, a town identified with the Roman Loventium. It was, at the time of our story, ruled by a maiden, the beautiful and high-spirited Gwenonwy, who was under Tewdryg’s suzerainty. From far and wide came suitors for her hand and throne, but none found such favor as the noble Gruffydd, youngest son of a neighboring prince named Meigyr. He was all that her heart could desire, yet the maiden Princess dared not wed him, for her father on his deathbed had demanded, and received her promise, never to become the bride of one who was not her equal both in birth and fortune.

She was a rich and powerful Princess, while he, though of good birth, was poor. After long delays Gruffydd determined to bring matters to a crisis, and went one night to the Princess’s bower and urged her to forget her oath and wed him, regardless of her promise.

‘‘Never,’’ replied the Princess, ‘‘shall it be said that the daughter of the noble Ieuan broke her word. I love you, Gruffydd; but my honor is dearer to me than even your love. You, too, are a Prince, and of a noble family. Use your good arm and sword as your fathers have done, and gain wealth as they did, and come to me a year hence my equal as well in fortune as in rank. For a year and a day I will wait and pray for you; return to me within that time a bridegroom worthy of Gwenonwy’s hand, or return no more.’’

The Prince then left Savaddan and his love, and went to the court of Tewdryg, and for ten months fought under his banner against Madoc, the rebel lord of Skenpeth, gaining much honor but little wealth. At last the war ended, and Gruffydd resolved to make a final appeal to the love of Gwenonwy. Leaving Tewdryg’s capital, he arrived on the third day of his journey at Bryn-yr-Allt, a monastery on the mountain side overlooking Savaddan. Here he asked and obtained shelter for the night. He had not slept long when he was awakened by the sound of voices in the refectory, which was separated from his room only by a thin wooden partition.

He overheard a conversation between Owen the Sub-Prior and another monk, Father Aeddan, from which he learnt that the Prior was expected to return next day, bringing with him mules laden with precious stones and jeweled robes, bequeathed to the monastery by Howell, Prince of Cwmdu, whom he had attended on his deathbed. Gruffydd determined, on hearing this, to waylay and rob the Prior. He went to a spring, named Codvan’s Well, by which the Prior must pass, attacked him and left him for dead, and carried off his mules with their loads to Savaddan.

He told Gwenonwy his story, and was received by her with favor. Meanwhile the monks who had gone out to meet the Prior found him lying insensible, but he recovered sufficiently to tell them who the murderer was before he died. That night an order arrived from Princess Gwenonwy that a monk from the monastery should attend that night at the Palace to unite her to Gruffydd, Prince of Bronllys. In the evening a vast assembly thronged the royal chapel to witness the marriage.

Father Owen performed the ceremony, and as the young pair knelt before him for the final benediction, the priest stepped forward, and in a loud authoritative tone exclaimed, ‘‘Rise, Gruffydd of Bronllys, thou murderer; and thou, too, lady accomplice in his crime, inasmuch as thou hast not avenged it. Wedded, yet unblest, hear God’s decree. Thou, Prince, hast shed sacred blood, and thou, Princess, rejoicest in the unholy deed. Therefore God shall visit you with a great and terrible punishment. In His mercy He will bear with you for a time, but in the fourth generation the blow will fall not only on yourselves, but on all your unblest seed. It shall be; God hath spoken it.’’

Without the blessing of the Church upon her union, the kneeling Princess rose in a rage, and, turning to her guards, she said, ‘‘This presumptuous man has dared to offer an insult to a Princess of Savaddan within her own palace walls. Hence with him to the guard tower. Let him there await the fulfillment of his prophecy. Should he still live at the fourth generation, and his words prove vain, he shall die. It shall be; I have spoken it.’’

Many long and weary years the good father spent in a lonely cell at Savaddan, while the town and Court were given up to debauchery and vice.

Meanwhile Gruffydd and Gwenonwy, now growing old, saw springing up around them a goodly family of children and grandchildren. Soon Myvig, their eldest grandson, married, and in due course a child was born. This was the longdreaded advent of the fourth generation; still there was no evidence of the predicted punishment.

On the fortieth day from the birth of Myvig’s son, the Princess, persuading herself that Owen’s curse was merely an idle threat, summoned all her family and friends to a great banquet in honor of the young prince’s birth. On the appointed day the great hall of the palace was full. The feast was at its height, and wine was flowing freely, when four guards entered, leading the venerable Sub-Prior.

The Prince taunted him with the non-fulfillment of his prophecy, but he only repeated that vengeance was at hand unless the guilty ones repented. The Prince ordered that he be shut up in the topmost room of the watch-tower, which should then be burnt to the ground. And this was done.

Father Aeddan, now Prior, heard of what had happened, and from the monastery above watched the town and flames of the burning tower shoot up towards the sky. After the tower had fallen, a mist came down upon the valley and hid the town. While the Prior prayed the mist gradually rose, and the valley was seen entirely filled with a vast lake. No trace of the lost town ever appeared save a cradle containing a sleeping child, the infant son of Myvig, the last of the princes of Savaddan.

Lifting the child from its cradle, Father Aeddan bore it to the monastery. Naming it Gastayn, he taught it all that the good monks could teach. Gastayn afterwards expressed a desire to embrace the ascetic life, and built a hut on the lake’s edge in a sheltered spot. There he spent a life of great piety and rigor, in continual prayer for the souls of his wicked progenitors. His holiness and learning was so famed that one of the royal princes of South Wales entrusted his sons to Gastayn’s care. Following in the footsteps of their pious tutor, they became renowned for the purity and sanctity of their lives, some of them, indeed, even obtaining the glorious crown of martyrdom. Gastayn, at his death, was buried in his hermitage, where in after years a church was built which to this day bears the name of the ‘‘Church of St. Gastayn.’’

Such is the legend told by the country folk in the neighborhood, who still gravely tell you that on a calm summer’s day it is possible to see the church tower through the waters of the lake, and even to hear the bells ring!

Asperatus Cloud

Photograph courtesy Merrick Davies

An "asperatus" cloud rolls over New Zealand's South Island in an undated picture.

This apparently new class of clouds is still a mystery. But experts suspect asperatus clouds' choppy undersides may be due to strong winds disturbing previously stable layers of warm and cold air.

Asperatus clouds may spur the first new classification in the World Meteorological Organization's International Cloud Atlas since the 1950s, Gavin Pretor-Pinney said.

Since the last addition to the atlas, the emergence of satellite imagery has pushed meteorologists to take a much broader view on weather and focus less on small-scale cloud formations.

But "the tide is turning back again," in part because the humble cloud is seen as a "wild card" in climate-change prediction, Pretor-Pinney said.

LeMone agreed that clouds are a "big unknown" in climate change, mostly because climate-change models do not provide a high-enough resolution to determine what clouds' impacts will be on a changing world.

An undated picture could be examples of the first new type of cloud to be recognized since 1951. Or so hopes Gavin Pretor-Pinney, founder of the Cloud Appreciation Society.

The British cloud enthusiast said he began getting photos of "dramatic" and "weird" clouds (including the above) in 2005 that he didn't know how to define.

A few months ago he began preparing to propose the odd formations as a new cloud variety to the UN's World Meteorological Organization, which classifies cloud types.

Pretor-Pinney jokingly calls it the "Jacques Cousteau cloud," after its resemblance to a roiling ocean surface seen from below. But the cloud fan has proposed a "formal," Latin name: Undulatus asperatus--roughly, "a very turbulent, violent, chaotic form of undulation," explained Pretor-Pinney, author of the new Cloud Collector's Handbook.

Margaret LeMone, a cloud expert with the National Center for Atmospheric Research in Boulder, Colorado, said that she has taken photos of asperatus clouds intermittently over the past 30 years.

It's likely that the cloud will turn out to be a new variety, LeMone said.

"Having a group of people enthusiastic about clouds can only help the field of meteorology," she added.

Asked how has such a striking cloud type could go unrecognized, Pretor-Pinney cites its rarity--and the proliferation and portability of digital cameras. "Technology has allowed us to have this new perspective on the sky."

The Earth Shall Bleed

What, you thought I was kidding about the Dark Eclipse coming right before the Earth starts bleeding? What kind of horrible jackass would joke about something like that?

This is a picture of a place called Blood Falls in Antarctica. Here’s the actual explanation: “2 million years ago the Taylor Glacier sealed off a small body of water that contained a community of microbes. This small pool of wild animals has not seen oxygen, sunlight or heat since that time. As the earth warmed and the glaciers in Antarctica melted away, these organisms have been independently evolving for eons without any outside contact. Until now, when they’ve suddenly sprung forth from the glacier. The frothy water is rich in iron, which gives it the striking red color. These strangely alien microbes may exist nowhere else on earth, and they give scientists an idea of what kind of life may survive after the earth becomes uninhabitable by almost all other life forms.”

So, there’s a place called Blood Falls, located on the frozen, cruel and empty continent of Antarctica, that contains strange life forms which have been sealed away for untold ages, and have now awoken and spilled forth onto the world. Oh yeah, and they’ll probably be the last things alive on the planet.