DNA is a vestige of formation of liquid crystal order

Finding: Scientists have discovered liquid crystals of ultrashort DNA molecules immersed in water, providing a new scenario for a key step in the emergence of life on Earth.

The research 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.

The conventional View Random formation of DNA is not possible.
If the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, then what are the effective ways for simple molecules to spontaneously self-select, "chain-up" and self-replicate.

What the study shows
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.

Even tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules. 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.

What are Liquid Crystals?
Liquid crystals are organic materials related to soap that exhibit both solid and liquid properties. They are commonly used for information displays in computers, flat-panel televisions, cell phones, calculators and watches.

What affects liquid crystals?
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. 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.

How short is short?
A series of experiments were conducted to see how short the DNA segments could be and still show liquid crystal ordering. 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.

What does this mean?
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.

Columnar Stacking is possible if the nanoDna can form duplexes
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. 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.

Complementary and noncomplementary DNA segments
Additional tests by the team involved mixed solutions of complementary and noncomplementary DNA segments. 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.

Significance for DNA molecules
The significance is 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.

DNA is a vestige of formation of liquid crystal order
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.

Environmental Setting Of Human Migrations In The Circum-Pacific Region

Finding: The expansion of modern human populations into the circum-Pacific region occurred in at least four pulses, in part controlled by climate and sea level changes in the Late Pleistocene and Holocene epochs. Modern humans migrated into eastern Asia via a southern coastal route.

A new study adds insight into the migration of anatomically modern humans out of Africa and into Asia less than 100,000 years before present (BP).

Phase 1 45,000 to 40,000 BP Stable climate and sea level

The initial "out of Africa" migration was thwarted by dramatic changes in both sea level and climate and extreme drought in the coastal zone. A period of stable climate and sea level 45,000-40,000 years BP gave rise to the first major pulse of migration, when modern humans spread from India, throughout much of coastal southeast Asia, Australia, and Melanesia, extending northward to eastern Russia and Japan by 37,000 years BP.

33,000 to 16,000 BP Climate change - sea level and cold climate change
The northward push of modern humans along the eastern coast of Asia stalled north of 43° N latitude, probably due to the inability of the populations to adjust to cold waters and tundra/steppe vegetation.

The ensuing cold and dry Last Glacial period, ~33,000-16,000 year BP, once again brought dramatic changes in sea level and climate, which caused abandonment of many coastal sites.

Phase 2 16,000 to 8,000 BP Climate Warming

After 16,000 years BP, climates began to warm, but sea level was still 100 m below modern levels, creating conditions amenable for a second pulse of human migration into North America across an ice-free coastal plain now covered by the Bering Sea.

Phase 3 8,000 to 6,000 BP climate stabilization

The stabilization of climate and sea level in the early Holocene (8,000-6,000 years BP) supported the expansion of coastal wetlands, lagoons, and coral reefs, which in turn gave rise to a third pulse of coastal settlement, filling in most of the circum-Pacific region.

A drop in sea level in the western Pacific in the mid-Holocene (~6,000-4,000 year BP), caused a reduction in productive coastal habitats, leading to a brief disruption in human subsistence along the then densely settled coast.

Phase 4 3,500 to 1,000 BP

This disruption may have helped initiate the last major pulse of human migration in the circum-Pacific region, that of the migration to Oceania, which began about 3,500 years BP and culminated in the settlement of Hawaii and Easter Island by 2000-1000 years BP.

Gene comparison between Human and mammals

Finding: By comparing portions of the human genome with those of other mammals, researchers have discovered almost 300 previously unidentified human genes, and found extensions of several hundred genes already known.

Behind the discovery
The fundamental is the idea that as organisms evolve, sections of genetic code that do something useful for the organism change in different ways.

What is the human genome?
The complete sequence of the human genome was accomplished several years ago. That means that the 3 billion or so chemical units, called bases, that make up the order of the genetic code is known. What is not known is the identification of the exact location of all the short sections that code for proteins or perform regulatory or other functions.

The genes make proteins...the basic chemical component needed for building cells. More than 20,000 protein-coding genes have been identified. This finding is important because it shows there still could be many more genes that have been missed using current biological methods. These existing methods are very effective at finding genes that have a wide expression but may miss those that are expressed only in certain tissues or at early stages of embryonic development.

Using evolution for gene discovery
This method involves using evolution to identify these genes. Gene comparision follows evolution; it has been doing this experiment for millions of years. There are many similarities between genes of the two species. The differences can be identified. Using a computer is the microscope to observe the results.

Four different bases -- commonly referred to by the letters G, C, A and T -- make up DNA. Three bases in a row can code for an amino acid (the building blocks of proteins), and a string of these three-letter codes can be a gene, coding for a string of amino acids that a cell can make into a protein.

Conserved genes
Siepel and colleagues set out to find genes that have been "conserved" -- that are fundamental to all life and that have stayed the same, or nearly so, over millions of years of evolution.
The researchers started with "alignments" discovered by other workers -- stretches up to several thousand bases long that are mostly alike across two or more species.

Over millions of years, individual bases can be swapped -- C to G, T to A, for example -- by damage or miscopying. Changes that alter the structure of a protein can kill the organism or send it down a dead-end evolutionary path. But conserved genes contain only minor changes that leave the protein able to do its job. The computer looked for regions with those sorts of changes by creating a mathematical model of how the gene might have changed, then looking for matches to this model.

Migration of Early Humans From Africa Aided By Wet Weather

Finding: Migrations out of Africa 200,000 to 150,000 was dependent on the the wet climate in the presently hyper-arid Saharan-Arabian desert.

Conventional thinking
This migration was dependent on the occurrence of wetter climate in the region. There is good evidence that the southern and central Saharan-Arabian desert experienced increased monsoon precipitation during this period (200,000 to 150,000), but there is no unequivocal evidence for a corresponding rainfall increase in the northern part of the migration corridor, including the Sinai-Negev land bridge between Africa and Asia.

Passage through this "bottleneck" region would have been dependent on the development of suitable climate conditions.

Uranium series dating method - Speleothems
Scientists a reconstruction of paleoclimate in the Negev Desert based on absolute uranium series dating of carbonate cave deposits (speleothems). Speleothems only form when rainwater enters the groundwater system and vegetation grows above a cave.

Today the climate in the Negev Desert is very arid and speleothems do not form, but their presence in a number of caves clearly indicates that conditions were wetter in the past. Scientists have dated 33 speleothem samples from five caves in the central and southern Negev Desert.

Increased Rainfall in the central and Southern Negev Desert
The ages of these speleothems show that the last main period of increased rainfall occurred between 140,000 and 110,000 years ago. The climate during this time consisted of episodic wet events that enabled the deserts of the northeastern Sahara, Sinai, and the Negev to become more hospitable for the movement of early modern humans.

Wet periods in the North and South parts of the Saharan-Arabian desert
The simultaneous occurrence of wet periods in the northern and southern parts of Saharan-Arabian desert may have led to the disappearance of the desert barrier between central Africa and the Levant.

The humid period in the Negev Desert between 140,000 and 110,000 years ago was preceded and followed by essentially unbroken arid conditions; thus creating a climatic "window" for early modern human migration to the Levant.

Evolution Is Deterministic, Not Random -- Multi-species Study

Finding: Biologists in an international team have concluded that developmental evolution is deterministic and orderly, an not the random sequence operation many previously believed based on a study of different species of roundworms.

If organs do not change, how does evolutionary development work in those organs?

Enter the study involving the female copulatory and egg-laying organ, the vulva, found in nearly 50 species of roundworms. The conventional wisdom is that because the vulva does not significantly change across species, one might predict that there would be little variation in vulva development. But that is not the case. Researchers found a lot of developmental variation. They concluded that this variation, since it did not affect the final adult vulva, could not have evolved in a random, fashion.

The research team looked at more than 40 characteristics of vulva development, including cell death, cell division patterns, and related aspects of gonad development. They plotted the evolution of these traits on a new phylogenetic tree, which illustrates how species are related to one another and provides a map as to how evolutionary changes are occurring.

Unidirectional changes

Their results showed an even greater number of evolutionary changes in vulva development than they had expected. But they found that evolutionary changes among these species were unidirectional in nearly all instances.

The decline of cell divisions

For example, they concluded that the number of cell divisions needed in vulva development declined over time instead of randomly increasing and decreasing.

The decline of number of rings

In addition the number of rings used to form the vulva consistently declined during the evolutionary process.

These results demonstrate that, even where you might expect evolution to be random, it is not.

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

Finding: Scientists have 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.

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.

Since the formation of molecular chains as uniform as DNA by random chemistry is essentially impossible, 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.

Tiny fragments of double helix DNA can spontaneously self-assemble into columns that contain many molecules. 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.

Teams at CU-Boulder and University of Milan began a series of experiments to see how short the DNA segments could be and still show liquid crystal ordering. The teams 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.

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 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. 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. 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.

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.

Fantasy Hero's and Intelligent Design

A lot of Intelligent design proponents question the slow and methodical evolutionary march to sophistication. They believe that sophistication came all at once, that it was designed that way...because the designer knew before hand what the final design was to look like, so there was no need for an intermediary step.

OK. Prove it!

This reminds me of the time when I was young and believed in superheroes and superhuman feats. If you start with the comic book heroes like Superman, The Fantastic Four and the like they all had extra-ordinary gifts and abilities. I soon realized that such fantasy powers couldn't come true. So I substituted those comic book fantasy powers for other fantasy powers, like hitting .500 in baseball, or throwing 6 touchdowns per game without an interception, or carrying a ball for an average of 8 yards per carry. It soon dawned on me why most hitters were hitting .260, why most Quarterbacks throw only 2 touchdowns passes and also throw picks; and that most runners only have a 2.5 yard per carry average. Reality bites.

The intelligent design argument is much like believing in the fantasy world of the comic books. It is a fine world, but reality bites. If you want to produce a scientific basis for Intelligent design, as a viable alternative to Evolution, I and most other scientists would be glad to listen.

So develop a scientific theory of Intelligent Design...prove it!.

Simple to complex then simple to complex

There has been one rule that evolutionary biologists felt they could cling to: the amount of complexity in the living world has always been on the increase. Now even that is in doubt.

The Tree of Life
In recent years, genetic analysis has forced biologists to consider the possibility that organisms such as the sea squirt might have lost some of the complexity of their ancestors. Yet even now, few recognise the full implications of loss as a key player in evolution. The entire tree of life has been built on the assumption that evolution entails increasing complexity. So, for example, if two groups of animals were considered close because both had a particular prominent feature, then someone discovered a third, intermediate line that lacked that feature but shared many other aspects of the two groups, traditional phylogenists would conclude that the feature had arisen independently in the two outlying groups, by a process known as convergent evolution.

They often did not even consider the alternative explanation: that the feature in question had evolved just once in an ancestor of all three groups, and had subsequently been lost in the intermediate one. Now a handful of molecular biologists are considering that possibility.

Instead of simply looking to see whether two species share certain genes, the new approach involves taking the "molecular fingerprint" of different types of cells. It identifies the unique combination of transcription factors - molecules that control which of a cell's genes are turned on and when - that specify the make-up of a cell, including the molecular signals it transmits and receives.

If two groups of organisms share the same type of cells, with the same molecular fingerprint, giving rise to similar features in both, then it is extremely unlikely that these features evolved twice. So any intermediate groups of organisms that lack that feature would most likely have lost it during the course of evolution. Only now, with the ability to explore at the molecular level how morphological features have been lost, gained and modified over time, is the true extent of evolutionary loss coming to light.

Finding: In genetic variation - an ancestor may develop certain traits, only to be followed by generations of child variants that lose the trait, and then redevelop the trait.

500 million year old Jellyfish

Finding: Using "fossil snapshots" found in rocks more than 500 million years old, three University of Kansas researchers have described the oldest definitive jellyfish ever found. This is significant because the fossil record is biased against soft-bodied life forms such as jellyfish, because they leave little behind when they die. That means that scientists are still working to solve the evolutionary development of many soft-bodied animals. But now they have a clear picture of what the soft-body form looked like when it comes to Jelly-Fish.

Here is what happened: researchers describe four types of cnidarian fossils preserving traits that allow them to be related to modern orders and families of jellyfish. The specimens are about 200 million years older than the oldest previously discovered jellyfish fossils.

Rapid Species diversification
Research jellyfish the group describes, found in Utah, offer insights into the puzzle of rapid species diversification and development that occurred during the Cambrian radiation, a time when most animal groups appear in the fossil record, beginning roughly 540 million years ago. The fossil record reveals much less about the origin and early evolution of animals such as jellyfish than it does about animals with hard shells or bones.

The Problem resolution:
The fossil record is full of circular shaped blobs, some of which are jellyfish. That's one of the reasons the fossils we describe are so interesting, because you can see a distinct bell-shape, tentacles, muscle scars and possibly even the gonads. The jellyfish left behind a film in fine sediment that resembles a picture of the animal. Most jellyfish do not leave such a clear impression behind because they are often preserved in coarse sand.

With the discovery of the four different types of jellyfish in the Cambrian, however, provide enough detail to assert that the types can be related to the modern orders and families of jellyfish. The specimens show the same complexity. That means that either the complexity of modern jellyfish developed rapidly roughly 500 million years ago, or that the group is even older and existed long before then.

The jellyfish described in the article are also unique because they push the known occurrence of definitive jellyfish back from 300 million to 505 million years, a huge jump, and show more detail than anything previously described that is younger.