55 replies to this topic

[Lazarus Long]

I am posting this article to spark a debate on numerous ancillary aspects implied by these findings. One that I am interested in is the importance of specific DNA sequences surviving beyond the "individual", another that cannot be overlooked is if there exists in certain environments, naturally occurring "Gene Banks" that preserve DNA across long periods and from which, at least microbial genetics can access pre-existing advantageous episomal information to enhance the efficacy of environmental mutational adaptation.

This last conjecture is just to stimulate talk but I suggest this is a finding that will come back into discussion with reference to many areas from environmental ecology to cryogenics.

Also the links back at the original article are too important to ignore and I suggest that all "serious students" go to that page just to data mine it.



http://www.nature.co.../030414-11.html

Siberia yields oldest authenticated DNA
400,000-year-old plant sequence pulled from the permafrost.
18 April 2003
REX DALTON

Sediments from glacial deposits could hold DNA data for whole ecosystems. © Science


References
Willerslev, E. et al. Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments Science published online, doi:10.1126/science1084114|Article|
Poinar, H. N. et al. Molecular Coproscopy: Dung and Diet of the Extinct Ground Sloth. Science, 281, 5375, (1998). |Homepage|
Cooper, A. & Poinar, H. N. Ancient DNA: Do it Right or Not at All. Science, 289, 5482, (2000). |Homepage|
Hoss, M. & Paabo, S. Mammoth DNA sequences. Nature, 370, 333, (1994). |Homepage|

Edited by Bates, 23 July 2005 - 06:22 PM.

[Lazarus Long]

And here is one article that overlaps my hypothesis that we can overtake laboratory based nanotech by utilizing adapted genetic models as well as the mechanism by which, the conjecture for the existience of genetic "banking" can influence future generations of adaptive evolution. I will return to creating designer viruses later as an aspect of the tools fro imroved transcriptase and synthetic programmable antibodies as well.

By the way there are also great links on this page that overlap many areas of genetic discussion and application.

http://www.nature.co...4/020204-2.html

DNA downloads alone
The information in DNA can be copied into new molecules without proteins' help.
05 February 2002
PHILIP BALL


Two million years ago life looked like this. Four billion years ago it was a different story. © SPL

Chemists have reproduced the basic process of information transfer central to all life without the catalysts that facilitate it in living cells.1

They show that DNA alone can pass its message on to subsequent generations. Many researchers believe that DNA-like molecules acted thus to get life started about four billion years ago - before catalytic proteins existed to help DNA to replicate.

The experiment, carried out by David Lynn and co-workers at Emory University in Atlanta, Georgia, might create a new basis for the precise synthesis of useful polymer materials. It may even hasten the advent of synthetic biology: the creation of life from scratch.

History repeats itself

Synthetic self-replicating molecules have been made in the lab at least three times before. But in all these cases the replicating molecules were given a substantial helping hand.

Before, each molecule acted as a template on which its copy was constructed from two ready-made halves. In other words most of the information in the copy was present already in the fragments from which it was made. It was rather like reproducing the information in this sentence simply by pasting it together from two already-written halves.

In contrast, Lynn and colleagues paste each letter in place, one by one. They make, not a copy, but a complementary molecule, containing the same information but in a different code. It is rather like making a copy of one of these sentences but translated into French.

In the cell, DNA itself contains two such complementary molecules, each one a chain of molecular units, stuck together in the double helix. When DNA replicates before a cell divides, these complementary strands part and each acts as a template to guide the synthesis of a fresh strand.

Each DNA strand contains all the information needed to make a new strand. There are four different kinds of molecular unit, and the sequence of these along the strand determines the sequence of units assembled in the new strand. Enzymes drive this assembly process.

Stranded

Lynn's group has found a way to do without the enzymes, so that a single strand of DNA can act as a template for the assembly of its complementary strand. Scientists have achieved this before, but imperfectly: only one of the four types of DNA unit acted as a template, and the complementary strand wasn't always the same length as the template.

The Emory group uses a new trick to join the components together on a DNA template. The chemical links between successive units in the new strand aren't like those in DNA itself. Instead they are amide linkages, like those that unite proteins' molecular units, which are also chain-like molecules laden with information. This makes the assembly of the new strand more accurate.

Amide-linked DNA chains can help units of true DNA to join together. So the researchers hope to achieve the reverse process of templating DNA using amide-linked DNA. This might then enable the two kinds of molecule to support their mutual replication, allowing the possibility of molecular evolution and the appearance of life-like complexity.


References
Li, X., Zhan, Z.-Y. J., Knipe, R. & Lynn, D. G. DNA-catalyzed polymerization. Journal of the American Chemical Society, 124, 746 - 747, (2002).


Missing links made simple
How life got the upper hand
A whole old world
Origins of life
© Nature News Service / Macmillan Magazines Ltd 2002

Edited by Lazarus Long, 01 June 2003 - 09:30 PM.

[Cyto]

Not Junk After All

Wojciech Makalowski

Repetitive elements called Alu elements constitute more than 10% of the human genome yet do not appear to code for proteins. In his Perspective, Makalowski discusses new work (Lev-Maor et al.) that sheds light on how Alu elements become inserted into the coding regions of genes resulting in the formation of new proteins and thus contributing to evolution.

Section of article from Science...

From bacteria to mammals, the DNA content of genomes has increased by about three orders of magnitude in just 3 billion years of evolution (1). Early DNA association studies showed that the human genome is full of repeated segments, such as Alu elements, that are repeated hundreds of thousands of times (2). The vast majority of a mammalian genome does not code for proteins. So, the question is, "Why do we need so much DNA?" Most researchers have assumed that repetitive DNA elements do not have any function: They are simply useless, selfish DNA sequences that proliferate in our genome, making as many copies as possible. The late Sozumu Ohno coined the term "junk DNA" to describe these repetitive elements. On page 1288 of this issue, Lev-Maor and colleagues (3) take junk DNA to new heights with their analysis of how Alu elements in the introns of human genes end up in the coding exons, and in so doing influence evolution.

[Cyto]

And today theres more...for free!

Survival of the fittest before the beginning of life: Selection of the first oligonucleotide-like polymers by UV light

Armen Y Mulkidjanian , Dmitry A Cherepanov and Michael Y Galperin

BMC Evolutionary Biology 2003 3:12 (published 28 May 2003)

PDF is FREE HERE at BMC.

Overall RNA would have survived due to the nitrogenous bases absorbing UV light. While this can hurt us it would protect RNA since mutation existsed but to the point where any of it would have been helpful. So could the protection value of selected for the bases we currently have now? We will see in later experiments.

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Well this was something I wasn't aware of but meh, I'm not an evolution researcher.

A simple dependence between protein evolution rate and the number of protein-protein interactions

Hunter B Fraser , Dennis P Wall and Aaron E Hirsh

BMC Evolutionary Biology 2003 3:11 (published 23 May 2003)

Here is the sum up...


Background

It has been shown for an evolutionarily distant genomic comparison that the number of protein-protein interactions of proteins correlates negatively with their rates of evolution. However the generality of this observation has recently been challenged. Here we examine this problem using protein-protein interaction data from the yeast Saccharomyces cerevisiae and genome sequences from two other yeast species.

Results

In contrast to a previous study that used an incomplete set of protein-protein interactions, we observed a highly significant correlation between number of interactions and evolutionary distance to either Candida albicans or Schizosaccharomyces pombe. This study differs from the previous one in that it includes all known protein interactions from S. cerevisiae, and a larger set of protein evolutionary rates. In both evolutionary comparisons, a simple monotonic relationship was found across the entire range of the number of protein-protein interactions. In agreement with our earlier findings, this relationship cannot be explained by the fact that proteins with many interactions tend to be important to yeast. The generality of these correlations in other kingdoms of life unfortunately cannot be addressed at this time, due to the incompleteness of protein-protein interaction data from organisms other than S. cerevisiae.

Conclusions

Protein-protein interactions tend to slow the rate at which proteins evolve. This may be due to structural constraints that must be met to maintain interactions, but more work is needed to definitively establish the mechanism(s) behind the correlations we have observed.

PDF For FREE.

[Lazarus Long]

{Reworking post under construction only edit by prior consult} [ph34r]

Multicellular organisms arose from colonies of identical cells acting in concert. The grouping of cells provided for resource sharing. Cell type specialization was a later phenomenon that further cemented the dominance of multicellular organisms, but it was not the driving force for multicellularity.
Peter (Ocsrazor)
Evolution And Its Implications For Aging...
http://www.imminst.o...&f=67&t=155&hl=

I began this as a response to Peter’s post in the thread shown above but as I developed the response it overlapped into a crucial theoretic aspect of the formulation of the Theory of Human Selection I have been trying to write down for some time and so I am reworking the series of posts into this one to be placed here where it belongs.

In this hypothesis I propose that the example of symbiotic convergence of different species of single celled organisms acting in concert and coming to share genetic information is a pragmatic reality with complex aspects both passive and dynamic that have made a vital contribution to and continue influencing the evolution of life on Earth and not only for simpler single celled organisms but as a subtler and more longer term aspect of genetic mutation as a less destructive mechanism than the commonly understood models of toxic and radiation induced mutations that have extremely high rates of concordant failure associated with them.

This mechanism is more complex and should be understood as represented by two distinct but overlapping phases, the first when bacteria and Eukaryotes merged and second as a consequence of bacterial episomes/plasmid formation the creation of a secondary genetic interactive medium for the exchange of genotypic information through viruses, when I suggest some plasmids maintained their viability independent of the original donor DNA and become the earliest proto-viruses.

Cyanobacteria in plants lead to and are incorporated still into plant genetics for chlorophyll production and mitochondria. It is not only an example of merged species that have retained their own unique genes in plants & animals but one that provided a significant advantage both for the energy needs of complex multicellular differentiation & organization and as the means of “sudden acquisition” of necessary competitive characteristics without the necessity of drastic mutation.

The other great contribution of the cyanobacteria is the origin of plants. The chloroplast with which plants make food for themselves is actually a cyanobacterium living within the plant's cells. Sometime in the late Proterozoic, or in the early Cambrian, cyanobacteria began to take up residence within certain eukaryote cells, making food for the eukaryote host in return for a home. This event is known as endosymbiosis, and is also the origin of the eukaryotic mitochondrion.
http://www.ucmp.berk...cyanointro.html

Yes the process you describe also takes place and may have been more common as single celled organisms began to assemble into larger "colony" like formation with subtle differentiation though painstakingly slow and error prone mutation that form cellular variation and shared function but the process of symbiotically adapting was also occurring all the while and this too even occurs at the most basic level through the sharing of genetic information across species limits with plasmids. And it was this that allowed some species to adopt and adapt a characteristic that was actually the advantageous mutation of a different species. We see this most often today in the rapid ability of many pathogens to "acquire" resistance from common bacteria like staphylococcus while not in themselves actually a member of that species.

The point is that this capacity to merge abilities and benefit through specialization of cellular role predicated upon symbiosis is also an important reason that multicellular organization could rapidly evolve by improving the odds on "Random Mutation” and Natural Selection and basically offsetting specific species weakness through cooperative synergy.

If my strength offsets your weakness and visa versa then together we comprise a significantly more powerful species to our adversaries especially if we can add a mutually beneficial behavior and not just externally defensive/offensive ones (like sharing sustenance) and over time our separate characteristics are lost as the genes merge to combine what were different species into one species with cellular differentiation.

Peter goes on to say:
The engulfment of the organisms that became mitochondria and chloroplasts predates the formation of multicellular organisms by a huge expanse of time and is not a good metaphor for what happened in the transition from single cells to multicelled organisms. If multicellular organisms had formed from multiple species of single cells, even closely related ones, our genes or cell structures would bear the markers of this merger. No such markers exist.

Actually one such marker clearly does exist; Mitochondrial DNA. But aside from that the symbiosis of these two species creates both a physical advantage that fosters the subsequent cellular differentiation process by dramatically increasing the energy production ability of the cell to offset the needs of other cell to specialize for function. In other words this symbiosis makes "possible” the latter multicellular evolution that takes the cumulative colony building behavior and catalyzes the possible mutations.

This would explain why multicellular differentiation appears to "explode" into the fossil record and is NOT seen to appear as one single organism adapting and dominating a niche and then simply remaining successful and unchanged. We see divergent evolution immediately as a consequence of the advent of multicellular organization. We see convergent evolution of competing species (a few million years) not long after that.

This engulfment is not so long before we see multicellular differentiation on a “Evolutionary Time Scale” and second as the process occurs it is by definition a prototypical example of a type of de facto cellular differentiation, especially on the microscopic scale of the engulfment.

The fact that it predates by a significant time period does not discount what I am saying in light of the temporal requirements for the process to continue to result in the subsequent evolution tha tcombines the now possible energy distribution with colony budding building adaptive differention. From my perspective this suggests the inclusion of cyanobacterium in the cell was a critically necessary adaptation for the latter complex multicellular evolution to occur as per the requirements of cellular specialization to have sufficient energy to survive the specialized behavior that makes them less able to survive environmentally independently.

Also there is a second aspect that can be shown to have developed along side the "Standard Model” of Natural selection. And this type of symbiosis/parasitism is "behavioral,” while you are correct that mitochondrial DNA is "unique" in the respect of being clearly identifiable and distinct genetically, what they clearly foster are the pathway into creating entire phyla of plant and animal species that begin to adapt through an alternative strategy of “specific” competition and this is through a combination of general selective competition and broader behavioral symbiosis/parasitism along with the introduction of a less risky aspect of mutagenesis associated with the simultaneous appearance of viruses.

We still see this in the myriad of ways plants have adapted to take advantage of animal motility for their own propagation including fruit bearing, grappling, and pollination through so many strategies the mind boggles.

Example: http://www.nature.co.../030519-13.html

Properly called Armorphophallus titanum, the blue whale of botany comes from the rainforests of western Sumatra, Indonesia. It was discovered in 1878 by the Florentine botanist Odoardo Beccari. He sent the seeds to Kew Royal Botanical Gardens in London, where the first cultivated specimen flowered in 1889. Famously, three blooms appeared at Kew last year.

Hothouse Titan Arums rarely flower, but when they do, they are hard to ignore. The colossal lily-shaped blooms smell of rotting flesh - hence the plant's nickname 'the corpse flower'. By mimicking a carcass in decay, the brownish flowers attract insects that deposit their eggs inside the plant, spreading its pollen in the process.
Nature News Service / Macmillan Magazines Ltd 2003

Yes, eukaryotes resist the insertion of genetic information but that can also be seen as by virtue of the success of having violated it in the first place and Cyanobacterium clearly are forerunners all evolution for it was their behavior as a species that provided the "terraformation” of the Earth’s surface into a less hostile environment making much of the rest of evolution possible before the kinds of speciation we later see even occurs.

Now let me make sure I am clear on this point, I do not disagree with anything that you have said about the evolution of multicellularization, but what I am suggesting is that not only was there more than one method for this process (and the resulting evidence does supports this) but second; there existed a dynamic relationship between the processes that alters the character evolution on earth by dramatically improving the ability to adapt through, and survive mutagenesis. More importantly we still see this primitive form of gene sharing as I suggested in two distinct environmental models, bacterial adaptive sexuality, and viral independence as a consequence of self replicating genes that are only quasi alive.

What is important in the second part is that the bacterial phage characteristics of viruses alter the fundamental mechanism of evolution by increasing the rate AND specificity of mutation, not only changing the “odds,” but increasing the probability of a successful adaptation to environmental conditions by creating access to a larger genome of proven genetic “subroutines” for environmental application.

http://www.nature.co.../030414-11.html

As per the article on DNA remaining viable in the environment for vastly longer extended periods than had previously been thought imaginable the organic substrate of the Earth crust may be understood to provide a “random access for selection” data bank once the interaction of the viral along with microbial flora & fauna is understood to not only utilize some of this information but as in the case of viruses may be able to insert viable DNA sequences into vastly larger complex hosts that is acquired through either accessing this “terrestrial organic substrate” or through epizootic assimilation which has come to into competition with the ancient form of what I call a “Terrestrial DNA Bank”.

It is rational to suggest this to be true because it is one of the methods pathogens are pathogenic thorough adaptive mutagenesis. And shows how the dynamic of competition symbiotic/parasitic behaviors enter the Selection process as logically dualistic interactive strategies.

While nevertheless an excruciatingly slow process by human standards it was qualitatively as distinct for a shifting “rate” of change as to say compare a snail and spaceship. At lift off the speed is only slightly more for the Space Shuttle than the snail due to its mass as it takes seconds to overcome its own inertia but then the two methods diverge as the acceleration of the newer process makes a quantum leap.

We can observe this from a grander perspective easier as the larger concept of accelerating evolution looming before us, which may be seen as converging on a specific singular event or “Omega Point” as Tipler coined the phrase but that is only one assumption. Because in the case of fossil record of evolution what this “kind” of qualitative acceleration has usually heralded is a period of new environmental access and massive Divergent and (concurrent though lagging) Convergent Evolution.

In fact we are beginning to adapt the process in a recent breakthrough utilizing viral transcription for a successful gene insertion in adult mammals. The following recent, little noticed development belongs in its own thread as it heralds a big step forward if confirmed for being able to reactivate organ morphogenesis.

It is an example of what has been sought for some time being refined into being able to insert characteristics genetically that we find desirable in the future, what it however represents is simply one of many examples of this behavior that we also see as related to a variety of “naturally” occurring examples.
We have begun to do so with teeth and now complex sensory subsystems.

The aspect of spontaneous neural attachment is a bonus that may be due to stimulus from the implanted DNA the way the placenta seems to override the mothers metabolism somewhat to regulate her body function focused on fetal development & life support. (this last conjecture is by way of analogy) and curiosity for its DNA driven externalized command ability. Fetal biogenesis is also representative of an example of when second party DNA seems to be able to override host DNA through a sort of command subroutine of the host allowing the external regulation.

http://story.news.ya...me/hearing_loss

Excerpt:
For the reported study, Raphael and colleagues worked with a gene called "Math1," which must be active for a fetus to develop the initial supply of hair cells. In a surgical procedure, they squirted a solution containing Math1 genes into cochleas of adult guinea pigs. The genes had been placed inside viruses, which acted like shuttles to get the genes into the animals' cells.

One and two months later, the researchers examined the cochleas of 14 treated animals. All showed immature hair cells, usually between 25 and 50. Apparently, the treatment had transformed some non-sensory cells into hair cells, Raphael said.

Many of the immature cells were outside the region where hair cells normally grow, so those clearly resulted from the treatment, Raphael said. Despite their odd location, it's possible that at least some of them might be able to function, he said.

http://www.jneurosci.org/

While I should say upfront this is an "artificial” procedure it is however one that exploits an already existing characteristic of viral phages, which in themselves parallel what Cyanobacteria did in the first place when it inserted itself into those first eukaryotes and changed how life evolves. Clearly we have complex interactions of genetic information that at the most primitive is somewhat clear but is perhaps affecting complex organisms in ways we haven't yet effectively included in our phylogenic modeling.

The cyanobacteria have an extensive fossil record. The oldest known fossils, in fact, are cyanobacteria from Archaean rocks of western Australia, dated 3.5 billion years old. This may be somewhat surprising, since the oldest rocks are only a little older: 3.8 billion years old!

Cyanobacteria are among the easiest microfossils to recognize. Morphologies in the group have remained much the same for billions of years, and they may leave chemical fossils behind as well, in the form of breakdown products from pigments. Small fossilized cyanobacteria have been extracted from Precambrian rock, and studied through the use of SEM and TEM (scanning and transmission electron microscopy).
http://www.ucmp.berk...ia/cyanofr.html

http://www.ucmp.berk...reedomains.html

Three Domains of Life

Until comparatively recently, living organisms were divided into two kingdoms: animal and vegetable, or the Animalia and the Plantae. In the 19th century, evidence began to accumulate that these were insufficient to express the diversity of life, and various schemes were proposed with three, four, or more kingdoms. The scheme most often used currently divides all living organisms into five kingdoms: Monera (bacteria), Protista, Fungi, Plantae, and Animalia. This coexisted with a scheme dividing life into two main divisions: the Prokaryotae (bacteria, etc.) and the Eukaryotae (animals, plants, fungi, and protists).
Recent work, however, has shown that what were once called "prokaryotes" are far more diverse than anyone had suspected. The Prokaryotae are now divided into two domains, the Bacteria and the Archaea, as different from each other as either is from the Eukaryota, or eukaryotes. No one of these groups is ancestral to the others, and each shares certain features with the others as well as having unique characteristics of its own.

Within the last two decades, a great deal of additional work has been done to resolve relationships within the Eukaryota. It now appears that most of the biological diversity of eukaryotes lies among the protists, and many scientists feel it is just as inappropriate to lump all protists into a single kingdom as it was to group all prokaryotes. Although many revised systems have been proposed, no single one of them has yet gained a wide acceptance.
A fourth group of biological entities, the viruses, are not organisms in the same sense that eukaryotes, archaeans, and bacteria are. However, they are of considerable biological importance.

I am arguing additionally that the viruses are more than a simple “consequence” of liberated genes they are also a mechanism for adaptive mutagenesis that has become environmentally stable and somewhat independently competitive but still overtly functionally parasitic, except in specific instances where the interaction of viral genetic transcription improves the odds of a successful mutation sooner in relation to environmental stress.

Obviously this is a radical theoretical departure from parochial evolutionary genetics but what I am proposing is a dynamic relationship of Selective Mutation through gene sharing that won’t show up as distinct because the original species’ full genome is not merged, only segments and these would appear as mutations not as mergers per se.

Ironically it would be analogous to the way I copy/pasted selective characteristics from different articles into this post to construct a new idea. Only I tag the source information to identify it.

If this is in fact happening with gene segments the type of marker that must be found would have to be a previous mutation within a latter mutation that is the result of such merged DNA. The carryover of the previous mutation suddenly appearing the fossil record coincident with the larger mutation would confirm my hypothesis. Sort of a DNA copyright tag )

There are some elusive examples of this and I will pursue such evidence.

Edited by Lazarus Long, 05 June 2003 - 02:40 AM.

[Lazarus Long]

I am including this brief synopsis because the aspect of their discovery in plankton also suggests another example of symbiosis. Plankton is a complex phenomenon that can be seen as a "multi species collective" within marine ecology.

It is made of subsets of larval, microbial, and algenous species that not only thrive in concert but both macroscopically and microscopically can be seen to be involved with complex multicellular activity as life support (food, shelter, oxygenation) larval synergetic competition for survival, and as complex algaes that are prototypical of primitive multicellularization. But plankton also is a critical food source for many larger marine species from shrimp to blue whales, whale sharks and sea turtles.

LL/kxs

Introduction to the Archaea

Life's extremists. . .
http://www.ucmp.berk...ea/archaea.html
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The Domain Archaea wasn't recognized as a major domain of life until quite recently. Until the 20th century, most biologists considered all living things to be classifiable as either a plant or an animal. But in the 1950s and 1960s, most biologists came to the realization that this system failed to accomodate the fungi, protists, and bacteria. By the 1970s, a system of Five Kingdoms had come to be accepted as the model by which all living things could be classified.

At a more fundamental level, a distinction was made between the prokaryotic bacteria and the four eukaryotic kingdoms (plants, animals, fungi, & protists). The distinction recognizes the common traits that eukaryotic organisms share, such as nuclei, cytoskeletons, and internal membranes.

The scientific community was understandably shocked in the late 1970s by the discovery of an entirely new group of organisms -- the Archaea. Dr. Carl Woese and his colleagues at the University of Illinois were studying relationships among the prokaryotes using DNA sequences, and found that there were two distinctly different groups.

Those "bacteria" that lived at high temperatures or produced methane clustered together as a group well away from the usual bacteria and the eukaryotes. Because of this vast difference in genetic makeup, Woese proposed that life be divided into three domains: Eukaryota, Eubacteria, and Archaebacteria. He later decided that the term Archaebacteria was a misnomer, and shortened it to Archaea. The three domains are shown in the illustration above at right, which illustrates also that each group is very different from the others.

Further work has revealed additional surprises, which you can read about on the other pages of this exhibit. It is true that most archaeans don't look that different from bacteria under the microscope, and that the extreme conditions under which many species live has made them difficult to culture, so their unique place among living organisms long went unrecognized. However, biochemically and genetically, they are as different from bacteria as you are. Although many books and articles still refer to them as "Archaebacteria", that term has been abandoned because they aren't bacteria -- they're Archaea.

Archaeans include inhabitants of some of the most extreme environments on the planet. Some live near rift vents in the deep sea at temperatures well over 100 degrees Centigrade. Others live in hot springs (such as the ones pictured above), or in extremely alkaline or acid waters. They have been found thriving inside the digestive tracts of cows, termites, and marine life where they produce methane. They live in the anoxic muds of marshes and at the bottom of the ocean, and even thrive in petroleum deposits deep underground.

Some archaeans can survive the dessicating effects of extremely saline waters. One salt-loving group of archaea includes Halobacterium, a well-studied archaean. The light-sensitive pigment bacteriorhodopsin gives Halobacterium its color and provides it with chemical energy. Bacteriorhodopsin has a lovely purple color and it pumps protons to the outside of the membrane. When these protons flow back, they are used in the synthesis of ATP, which is the energy source of the cell. This protein is chemically very similar to the light-detecting pigment rhodopsin, found in the vertebrate retina.

Archaeans may be the only organisms that can live in extreme habitats such as thermal vents or hypersaline water. They may be extremely abundant in environments that are hostile to all other life forms. However, archaeans are not restricted to extreme environments; new research is showing that archaeans are also quite abundant in the plankton of the open sea. Much is still to be learned about these microbes, but it is clear that the Archaea is a remarkably diverse and successful class of organisms.

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Edited by Lazarus Long, 01 June 2003 - 08:53 PM.

[Lazarus Long]

I will try and get back to this with the full article when I figure out how to retrieve it. Please feel free to post it anyone if you can get the text first. Oh and Helix, we have noticed a decay effect for many links and the directs all agree thereis sufficient space to post more of the full text of serious sources so don't feel like you have to truncate as much as you have been.

Later we can edit the threads to eliminate redundancy and superfluous dialogue thus establishing a better logical chain but for now let's continue to crate a fully functional open source database on the salient issues.

Does that sound reasonable to everyone?

http://www.nature.co...nrg1115_fs.html

July 2003 Vol 4 No 7 PERSPECTIVES
Nature Reviews Genetics 4, 566 -572 (2003); doi:10.1038/nrg1115


Z-DNA: THE LONG ROAD TO BIOLOGICAL FUNCTION

Alexander Rich & Shuguang Zhang

Preface

Biologists were puzzled by the discovery of left-handed Z-DNA because it seemed unnecessary. Z-DNA was stabilized by the negative supercoiling generated by transcription, which indicated a transient localized conformational change. Few laboratories worked on the biology of Z-DNA. However, the discovery that certain classes of proteins bound to Z-DNA with high affinity and great specificity indicated a biological role. The most recent data show that some of these proteins participate in the pathology of poxviruses.

RELATED LINKS
Enhanced text PDF

(These links should work if you already have access to "Nature's" archives otherwise you must pay to view)

[kevin]

Here's a link to a PDF for those who do not have the luxury of a membership or fat wallet... I tried to post the full text but it was truncated.. Is this configurable?
PDF

Edited by kperrott, 02 July 2003 - 06:20 AM.

[Lazarus Long]

Thanks Kevin

I am about to check but it looks like it got through and maybe we can do this more often this way and then I or you can except pieces when we have a chance. I can't get it to open but it does download it could be my new Adobe 6 install so I will try again later after I reboot.

[kevin]

Happy to provide... There's a move in California to make all journals public access...

I checked the link and it seems to load ok with Adobe 5... I'll e-mail the doc if you have trouble..

[Lazarus Long]

http://www.nature.co...424482a_fs.html
Nature 424, 482 - 483 (31 July 2003); doi:10.1038/424482a
Paleobiology: Setting the record straight

By analysing masses of data from fossils throughout the world, a group of palaeontologists hopes to address the big questions about the history of life on Earth. Quirin Schiermeier logs on to the Paleobiology Database.

We've never had it so good — or at least that has been the prevailing view among palaeobiologists who have tried to track the history of our planet's biodiversity. On the long road from the first stirrings of multicellular life to today's shimmering diversity, untold numbers of species have fallen by the wayside. From time to time, legions of creatures have perished together in mysterious mass extinctions. But if you examine the fossil record, the evolution of new species seems generally to have had the upper hand over extinction. Like stock indices in a bull market, plots showing the diversity of life over geological time reveal a rising trend, despite occasional setbacks.

But how can we be sure that this isn't a sampling artefact? Even high-school biology students are taught that the fossil record is far from complete. Given that younger rocks are more likely to be exposed at the surface, it is possible that the apparent rise in biodiversity merely represents the greater scrutiny that has been applied to these strata. Palaeontologists have even coined a term for this source of bias: 'the pull of the recent'. Add in the confusion caused by the varied names used to describe the same organisms, and some researchers argue that attempting to assess the history of Earth's biodiversity is a fool's quest.


John Alroy hopes the database will answer crucial fossil questions.

John Alroy, a palaeontologist at the University of California, Santa Barbara (UCSB), begs to differ. He is one of the founders of the Paleobiology Database, a project set up in 2000 with financial support from the US National Science Foundation. This freely accessible database, hosted by UCSB's National Center for Ecological Analysis and Synthesis, already holds information on more than 30,000 different fossil collections, and is still growing. Through sheer weight of numbers, and by applying various statistical tricks to account for sampling biases, Alroy and his colleagues hope to determine whether the Earth's biodiversity really has been on the rise — and to answer some other tricky questions.

The data are divided into individual collections, retrieved from specific locations and strata by particular palaeontologists. In addition to descriptions of specimens, the database includes information on the composition and age of the sediments in which they were found, and the fossils' state of preservation. "It is the multitude of easily retrievable information that makes it so useful," says Wolfgang Kiessling, a palaeontologist at the Museum of Natural History in Berlin, who is one of the 70 or so scientists authorized to enter information into the database. "It allows us to interpret the known fossil record in a more unbiased way, and we can now ask a whole host of new questions about how natural systems operate."

But some sceptics suspect that no amount of statistical sophistication will eliminate the uncertainty inherent in palaeontology. It may always be impossible to determine the degree to which the fossil record is 'known', they argue. And some fear that the Paleobiology Database will seduce unwary researchers into drawing erroneous conclusions. "No doubt palaeontology will benefit from more informed fossil data," says Andrew Smith, an invertebrate palaeontologist at London's Natural History Museum. "But you can easily be misled if you assume that all data are objective."

Multicellular life left little impression on the fossil record for around half a billion years. But at the onset of the Cambrian period, some 550 million years ago, oxygen and calcium had become sufficiently abundant in the oceans for the development of organisms with hard components. The result was the 'Cambrian explosion' of marine biodiversity. Our understanding of diversity trends since then owes a heavy debt to the work of John 'Jack' Sepkoski, a palaeontologist at the University of Chicago. In the 1970s, Sepkoski began to scour the palaeontological literature for information on the first and last appear ances of marine organisms, extrapolating the ups and downs of life in the oceans. Because individual species appear only fleetingly in the fossil record, and are often misidentified, he focused on genera — the trilobites Paradoxides bohemicus and Paradoxides gracilis, for instance, are species within the same genus, whereas Asaphus cornutus and Crozonaspis struvei belong to different genera.

Expanding knowledge
SOURCE: REF. 2

On the level: the traditional view that biodiversity has increased over time (top) is challenged by an analysis that corrects for sampling bias.

Sepkoski's work1 indicated that diversity continued to expand from the Cambrian explosion until the end of the Ordovician period, some 440 million years ago. From then on, it remained on a more or less stable plateau until the Permian–Triassic mass extinction — the most severe experienced by our planet. But Sepkoski found an upward trend in marine biodiversity after the beginning of the Triassic period, 250 million years ago, with just one significant interruption: the extinction event that put paid to the dinosaurs at the end of the Cretaceous period, some 65 million years ago (see figure, right). "Sepkoski has given us a clue about the dramatic things that happened in the history of life," says Alroy. "But we need more comprehensive data, and better analytical tools, to quantify his findings."

This is what the Paleobiology Database aims to provide. Because of the information included about individual collections, it is possible to correct for sampling biases in ways that Sepkoski, with his simple analysis of the first and last appearances of genera in the fossil record, was unable to do. For instance, within each interval being studied you can examine a fixed number of collections, in an attempt to account for variation in sampling intensity from rocks of different ages. Other corrections can be applied to account for bias in geographical coverage, and so on. Sepkoski himself realized the need to do this, and contributed to the Paleobiology Database until his death from heart failure, aged just 50, in 1999.

Initial analyses have already given some intriguing hints of discrepancies from Sepkoski's earlier conclusions. In the first major paper2 to make use of the Paleobiology Database, Alroy and 24 colleagues — including the late Sepkoski — sampled the database's marine component, which at the time contained 8,591 collections, mainly from North America and Europe. They applied four different statistical methods to correct for variation in sampling intensity in rocks of different ages. Each gave roughly the same result, suggesting that marine biodiversity has not risen over the past 150 million years, and is at a similar level to that during the period between 450 million and 300 million years ago (see figure).

If this finding is correct, it means that Sepkoski's conclusion about rising diversity since the Triassic is a sampling artefact. "This is a very important and surprising result," says Kiessling. "It is the first time evidence has been found that there may be an upper threshold to biodiversity — a maximum holding capacity of the environment." The threshold theory is controversial, however, and the picture may yet change again, as researchers consider data on other taxonomic groups or from different regions.

Indeed, a team led by palaeontologist David Jablonski of the University of Chicago has analysed the database's entries for bivalve molluscs, concluding that the pull of the recent has been overestimated in previous studies3. For this group of animals, at least, Jablonski and his colleagues argued, the increase in diversity over time does seem to be real.

Alroy and his colleagues believe that the database is the key to resolving this and other controversies surrounding the history of life on Earth, such as whether the great mass extinctions really were as dramatic as has been assumed. It should also give palaeo-ecologists a better idea of whether biodiversity is controlled by environmental parameters such as climate, volcanic activity and ocean chemistry — or whether, as a theory proposed two years ago4 suggests, it varies randomly.

Share and share alike
Getting the most out of the database may require a cultural change on the part of some palaeontologists, however. Further expansion of its scope will require researchers to make their collections available for analysis. The situation in New Zealand, where palaeontologists began three decades ago to compile and publish all fossil data in an openly searchable way, under an agreement between the Geological Society of New Zealand and the New Zealand Geological Survey, provides an ideal model. In a paper published just a few weeks ago, these data were used to study bias in measurements of mollusc diversity caused by variation in the total area of exposed rocks of different ages5. But in Europe, says Kiessling, some palaeontologists still jealously guard their own collections to maintain an advantage over their rivals.

The value of the Paleobiology Database will depend on the quality, as well as the quantity, of its information. Some experts fear that quality-control issues could cause misleading results, particularly in the hands of scientists who are not experts on the organisms that they are trying to analyse. Smith, for instance, is concerned about the potential for confusion due to problems with taxonomic nomenclature. "Names may disappear, but their last occurrence in the record does not necessarily mean extinction of a species, family or genus," he says. Despite such shortcomings, however, Smith intends to use the database and contribute to it. "But I would only work with taxa that I know," he adds.

Alroy and his colleagues are trying to address the problem that Smith has highlighted. At a meeting later this year, they plan to set up task force to resolve inconsistencies in the database. Once this group's work is done, enthusiasts claim, the database will be a powerful tool. "It will add a long-term perspective to many open questions," says Kiessling.

http://www.paleodb.org


QUIRIN SCHIERMEIER
Quirin Schiermeier is Nature's German correspondent.



References 1. Sepkoski, J. J. Jr Paleobiology 7, 36-53 (1981).
2. Alroy, J. et al. Proc. Natl Acad. Sci. USA 98, 6261-6266 (2001). | Article | PubMed | ChemPort |
3. Jablonski, D., Roy, K., Valentine, J. W., Price, R. M. & Anderson, P. S. Science 300, 1133-1135 (2003). | Article | PubMed | ChemPort |
4. Hubbell, S. P. The Unified Neutral Theory of Biodiversity and Biogeography (Princeton Univ. Press, Princeton, New Jersey, 2001).
5. Crampton, J. S. et al. Science 301, 358-360 (2003). | Article | PubMed | ChemPort |

[Lazarus Long]

Here is an interesting article that returns to the issue of DNA "code noise" apparently the consensus is that what we have is another mystery not noise, just another layer of complexity and more subtle organizational information.

LL/kxs

http://story.news.ya...ience_genome_dc
Genome Hunt Shows We're Closer to Rats Than Cats
2 hours, 31 minutes ago Science - Reuters
By Maggie Fox, Health and Science Correspondent

WASHINGTON (Reuters) - A comparison of human DNA to 12 other animals shows we share more than our genes and helps show that people are more closely related to rats than to cats, U.S. scientists reported on Wednesday.

The survey also adds to the argument that so-called "junk" DNA is nothing of the sort, but must do something important because it stays virtually identical across many species.

It also supports what is becoming increasingly clear -- that the stretches of DNA we call genes are only a small part of the genetic story.

The research team at the National Human Genome (news - web sites) Research Institute and several universities compared the same stretch of DNA in a chimpanzee, baboon, cat, dog, cow, pig, rat, mouse, chicken, zebra fish and two species of puffer fish -- the Japanese delicacy Fugu and Tetraodon -- with human DNA.

In people, this stretch of DNA it is a much-studied genetic region that contains the CFTR gene that, when mutated, causes cystic fibrosis.

"It provides some pretty definitive evidence that we are indeed closer to rodents than we are to carnivores," Dr. Eric Green, scientific director of the NHGRI and leader of the study, said in a telephone interview.

"Our data really puts the nail in the case. In the sequence you can find changes in the genome that clearly occurred in both humans and rodents but did not occur in others."

The changes come in repetitive sequences of DNA that, until just a few years ago, were believed to be junk -- useless stretches of trash that somehow got saved.

DNA is very difficult to interpret. Its long, long code is built on just four nucleotides -- the compounds known by the abbreviations A,C,T and G.


A TRICKY CODE TO BREAK

Reading the long string of four letters repeating in various combinations is proving to be even trickier than scientists thought it would be. At first they believed the genes -- the sequences that control production of the protein building blocks of the body -- would be the only functioning parts of the sequence.

But it turns out there are sequences that control the genes, and perhaps that do even more.

"It now seems that about 5 percent of our genomes are functionally important," Green said.

"Only a third of that codes for genes. That means that two-thirds of what is functionally important is not (gene) encoding DNA. We don't even know what it looks like so how are we going to find it?"

Green hopes to do so by comparing the genomes of different species.

"This is the idea that you can truly use sequences from multiple genomes and analyze them all at once to try and find the small percent that is shared among all of them," he said.

"We believe this is going to be a very valuable way to find those sequences that are very important."

Why? Because nature cannot ditch vital DNA.

"Evolution is about mixing things up. If evolution has hung on to some stretch (of DNA), even if it is repetitive, it is telling us something ... Where did (evolution) find it wasn't safe to change the genome?" he asked.

Green's team, working with researchers at Pennsylvania State University, the University of Washington and the University of California, Santa Cruz, will look at 100 different regions of the genomes of the 13 species.

This is the first region they have analyzed, they reported in Thursday's issue of the journal Nature.

"We will discover new types of functional elements in the coding DNA that we didn't even know existed," Green said.

[Lazarus Long]

I am going to go out on a limb and make a prediction that we will discover DNA is encrypted with a "quaternary mathematical language" and that is why:

(a) It assembles itself three (possibly more) dimensionally for storing/handling information and manipulating matter as we are looking for in nanotech.

(b) It can store and manipulate exponentially more data per operational volume than current computational "binary" logical methodologies.

Clues we're already aware of are the Double Helix molecular aspect as well as chromosomal archiving. Now we are beginning to perceive ever complex encryption that reflects the obvious multi-chromosomal nature of life in general and also can be seen internally in the brain (a known DNA computer) that appears to process information in a manner distinctly different from currently understood electronic binary methods.

Calling the brain an "analogue", or "parallel quantum computer" may only beg the question of defining how that would explain the level of general complexity we do observe that appears able to integrate with remarkably simple constructs for the expression/perception of thought, action, physical maintenance, and varying sensory input.

While a seemingly simple observation, it is possible that we are only scratching the surface of the possible encryption that this base 4 (binary squared) or "quaternary" system of logic may offer. It would then be no accident that there exists four base pairs of DNA and these are more than a simple yes/no logical system and could allow for perhaps a new logical model with respect to algorithmic possibility that begins to fall into what some theorize as "fuzzy logic".

Instead of simple yes/no we get "yes/no/maybe/certain" or some other rational equivalent.

[kevin]

I can see a nice segue from your previous post into the first link here which talks about how there is a language buried in our DNA... perhaps the language is a book from some alien race... telling of a history or perhaps more insights on how to get home.. whatever the case, the fact that junk DNA obeys Zipf's Law of Languages is truly remarkable.

http://www.abc.net.a...nts/s133634.htm
http://hum-molgen.or...2002/msg08.html
http://www.eurekaler...h-pop051002.php

Your proposal of a quaternary mathematical language in DNA, rather than a binary is interesting. I think it would provide further avenues for investigating some of the more perplexing issues of the way information seems to be communicated through time/space. It brings to mind the article I read in Scientific American, "Information in a Holographic Universe", where in the end the proposal was that information exchange between physical processes is more important than even space/time.

I imagine our DNA to be the physical/holographic expression of the projection into our space/time of a small part of an evolving infomational pattern existing in 5D. The world as we perceive it, is an illusion. What kind of information is stored in our DNA and how is it communicated? Does it transmit information on more than one level? I think so, between strands, chromosomes, cells, organs and by extension people, societies, species... and further without end. I believe your notion of quaternary storage allows for a mechanism that more complex information transmission requires and I assert that there are levels of information communication going on that we have NO clue about from the perspective of an ant on the back of an elephant. Further, I believe we are creating newer levels of information transmission with the use of electronics... and thus we provide information a new substrate to work with... It truly is the message and not the medium here I think.

--------------------
As an addendum to the junk DNA hypothesis.. Doesn't it makes more sense that introns must be critical to the formation of multicellular lifeforms as they aren't present in single celled organisms such as bacteria or mitochondria? Conserved intron regions between organisms will sure shed some light on which sections are evolutionarily important... VERY EXCITING!

[kevin]

Public release date: 21-Aug-2003

Contact: Amy Adams
amyadams@stanford.edu
650-723-3900
Stanford University Medical Center

Stanford researcher finds method to define genetic 'words'

STANFORD, Calif. - With the human genome in hand, scientists now know the roughly 30,000 words making up the language of the human body. But what do those words mean? Stuart Kim, PhD, associate professor of developmental biology and genetics at the Stanford School of Medicine, has created the first dictionary that defines them.

His work, published in the Aug. 21 advance online version of the journal Science, could help researchers understand the role of newly identified genes. It also provides a glimpse into how a gene's function has evolved over time. "This tool tells you which genetic words are used together. If I see a new word and I see its context, I know what that word means," Kim said.

Kim's method works because scientists already understand the role many proteins play within a cell. Of these known genes, those involved in the same process, such as cell division, all tend to be active at the same time. Relying upon context, scientists can deduce that an undefined gene active at the same time as genes with a known function is probably involved in the same process.

Kim and graduate student Joshua Stuart created their genetic dictionary from gene activity data in four organisms: humans, fruit flies, a roundworm called C. elegans and yeast. Previous experiments at Stanford have yielded a wealth of information about when and in what tissues the genes in these organisms become active.

From these data, Kim and his colleagues figured out which genes happened to be churning out protein at the same time. Their results showed groups of genes with identical patterns of activity. Some genes within these groups have known activities, providing a context for the many genes whose function was previously unknown.

Kim and his colleagues tested their resource using five genes with previously unknown functions. These genes were always active at the same time as a network of genes known to be involved in cell proliferation. These genes also happened to be extremely active in cancer cells, which fail to divide normally, adding credence to the idea that these were cell division genes. To further test the role of one gene, the researchers eliminated its function in C. elegans. Some cells in those worms began rampant division. "This tells us that the five genes really are involved in proliferation," Kim said.

"People can go to this dictionary and find out how their word is used," Kim said. His data is available online for researchers who want to learn more about their favorite undefined gene.

Kim envisions numerous uses for this resource. Researchers who study a particular cellular function may seek out novel genes that are activated in concert with their usual genetic suspects. Other researchers may want to know the function of a gene that's mutated in people with a genetic disease. Kim's database could pinpoint a role for the disease gene, guiding future research in that disorder.

Kim added that his data also could be used to identify genes that have changed function over time. He said some genes are part of the same network in all organisms from yeast to humans. These genes are often involved in very basic processes such as making proteins. Other genes, such as those involved in the nervous system, may have changed little over time, but they are activated with a different group of genes in each organism. The proteins made by these genes have taken on new roles as evolution has progressed.

Eran Segal, a graduate student in computer science, is a co-first author on the paper. Daphne Koller, PhD, associate professor of computer science at Stanford, shares contributing authorship with Kim.


###
Stanford University Medical Center integrates research, medical education and patient care at its three institutions - Stanford University School of Medicine, Stanford Hospital & Clinics and Lucile Packard Children's Hospital at Stanford. For more information, please visit the Web site of the medical center's Office of Communication & Public Affairs at http://mednews.stanford.edu

[kevin]

Just like the discovery of RNA interference began with the the activity of small RNA pieces in plants, this discovery is the harbinger of bigger things to come in the animal kingdom as well. Small RNA's have already been implicated in the switching on and off of genes in embryogenesis.
--------------------------------------------------------------


MicroRNAs - Tiny molecules shape up plants

A team of German and US scientists demonstrates that development and growth of plants is controlled by tiny pieces of RNAs

Small RNA molecules have big effects on plant shape, according to a report published in the online edition of the journal Nature (Advance Online Publication, August 20, 2003). These findings were the result of a transatlantic collaboration between two teams, one led by Detlef Weigel, Director at the Max Planck Institute for Developmental Biology in Germany, and the other by Jim Carrington, Director of the Center for Gene Research and Biotechnology at Oregon State University. Using the model plant Arabidopsis, the new study shows for the first time how very short RNAs called microRNAs control plant shape by guiding destruction of much larger messenger RNAs. MicroRNAs work like a digital radar to hone in on the messenger RNAs of target genes. The messenger RNA, which is the critical molecule that communicates normal gene function, is either destroyed or inactivated through molecular processes that are directed by the microRNA. Turning off the activity of specific genes is very important to prevent abnormal plant development, just as it is in preventing cancerous growth in animals, according to Weigel, who is also an Adjunct Professor at the Salk Institute in California, where this research was started. The study may be a first step, researchers say, in revolutionizing our understanding of how plants control their shape and growth. A plants ability to grow structures with a specific shape is critical to its ability of capturing energy from the sun and turning it into products such as grain and fiber. As such, these findings could ultimately have profound implications for advances in agriculture and forestry.

Since the DNA double helix was discovered 50 years ago, biologists have focused on the role of DNA in controlling gene activity. Only recently have scientists begun to appreciate the importance of microRNAs in keeping gene activity in check, a discovery that was hailed as the breakthrough of 2002 by Science magazine (Small RNAs make big splash, Vol. 298, page 2296). Just a year ago, several groups, including the one led by Carrington, discovered that plants are full of microRNAs. These tiny RNAs are in turn products of much larger RNAs. "Since plants that do not produce enough microRNAs were quite sick, we knew that we were onto something important, but we couldn't quite trace the exact cause for the many abnormalities we observed," said Carrington.


Fig. : Messenger RNA degradation by microRNAs is essential for normal plant growth. In the plant shown in the foreground, a TCP messenger RNA can no longer be bound by the microRNA, and the plant cannot grow beyond the seedling stage. In the plant shown in the background, there is too much Jaw microRNA, causing excessive cell division in leaves, which gives them a crinkly shape.

Image: Max Planck Institute for Developmental Biology

In their collaborative study, Weigel and Carrington now have pinpointed, for the first time, the precise interplay between a particular microRNA, called "Jaw", and its targets. "For several years, we had a mutant plant that overproduced a large RNA of unknown function. Surprisingly, this RNA did not seem to make a protein, like most other RNAs do. After we read Carringtons publications, we suddenly realized that this RNA was instead chopped up into microRNAs," said Weigel.

With DNA chips, scientists can measure all messenger RNAs in a plant at once. Using such DNA chips, Weigel and Carrington discovered that the Jaw microRNA specifically caused the coordinated destruction of several TCP messenger RNAs. The TCP genes prevent excess cell division in leaves. Without them, there is too much cell division and the leaves buckle instead of staying flat. This was exactly what the mutant plants with too much Jaw microRNA looked like. Next, the researchers changed the TCP genes so that their messenger RNAs could no longer be recognized by microRNAs. Plants harboring the altered TCP genes grew no further than the seedling stage, proving that microRNA targeting of messenger RNAs is very important for normal plant development.

Both the Jaw microRNA and its TCP targets are found in all flowering plants examined, including cereals. "This tells us that this mode of controlling leaf shape is not only used in Arabidopsis, our favorite plant model in the lab, but also in plants of agronomic importance such as corn or soy bean," said Weigel.

As more and more microRNAs are discovered and their role in plant growth becomes clearer, new opportunities may open up to breed more efficient or productive plants. "We will probably discover microRNAs that function in most aspects of plant development, including flowering, root growth and seed production," Carrington said. Weigel agrees: "Indeed, in unpublished work we have found that other microRNAs and their targets seem to have important roles in helping the plant to decide when to produce flowers. The potential impact of this could be quite large, since it provides a new way of adapting plants to their environment."

Also participating in the study were: Javier F. Palatnik, Max Planck Institute for Developmental Biology and The Salk Institute; Edwards Allen, Oregon State University; Xuelin Wu, The Salk Institute; and Carla Schommer and Rebecca Schwab from Max Planck Institute for Developmental Biology.

Experts who can comment on this research:

Prof. Victor Ambros
Dartmouth College, USA
Phone: +1 (603) 650 - 1939
E-mail: victor.ambros@dartmouth.edu

Prof. Kathryn Barton
Carnegie Institution, USA
Phone: +1 (650) 325-1521 x224
E-mail: barton@andrew2.stanford.edu

Prof. Bonnie Bartel
Rice University, USA
Phone: +1 (713) 348-5602
E-mail: bartel@bioc.rice.edu

Prof. David Baulcombe
John Innes Centre, UK
Phone: +44 (0) 1603 450420
E-mail: david.baulcombe@bbsrc.ac.uk


The study, entitled "Control of leaf morphogenesis by microRNAs", was funded by the National Institutes of Health, the National Science Foundation of the US and the Max Planck Society, Germany.
Original work:

Javier F. Palatnik, Edwards Allen, Xuelin Wu, Carla Schommer, Rebecca Schwab, James Carrington & Detlef Weigel
Control of leaf morphogenesis by microRNAs
Nature, Advance Online Publication, 20. August 2003, DOI: 10.1038/nature01958 (http://dx.doi.org/10.1038/nature01958)

[Cyto]

I just got done watching The Science Channel: Planet of Life: Part 1. "The Birth of Earth."

Excellent! They are continuing to improve their Abiogenesis + First Cellular Life presentation to people in a easy to understand way.
Of course they have to since research on both are providing great observations of how this can occur.

I don't know if they will pop it out on DVD or anything since they will make anotherone in about 2-3 months, heh.

[Lazarus Long]

There is a parallel discussion going on in a thread titled "The First Chimpanzee" http://www.imminst.o...3&t=1613&hl=&s=

The focus there is specifically on the evolution of man and I think that we should keep these two threads separate and distinct for a number of reasons but I include the above link because they do overlap.

Here we should stay focused on the larger questions of the origin of life and the general processes for evolution but in that thread we can focus on specific theories involving Human development.

I have also addressed in a recent post some common anti-evolution arguments but in fact the specific arguments presented were not very well organized and are inconsistent to the point that I do not think we should treat it as more than a example of common misunderstanding. In that respect it is useful:
http://www.imminst.o...t=0

But it may also be useful to find some better examples of serious counter argument and post them so as to address them categorically and specifically and clarify the common fallacies that are prevalent in so many of these.

I suggest it is to our benefit to stand this straw-man up and knock him down before at some point becoming inundated by those that suggest repeatedly the same discredited doctrines.

[Lazarus Long]

This article on dyslexia is subtle and subsequent study should be looked for. I have been harboring a suspicion for some time that the human population has been undergoing an "assimilation phase" for a significant mutation effecting cerebral function and potential. I am confident that we are evolving to a more complex level of communication and general competency.

I contend we aren't dumbing down at all but it seems that way at times because many people are getting smarter and by contrast conditions of the status quo appear to be declining. I have been saving these arguments for latter discussion and prefer to only hint at them here but first lets examine this issue of mutations for cerebral function and this one in particular dyslexia. Which may be alternatively be seen as a mutation in the brain effecting many of us. A mutation that I suspect is related to an "advance" in how we "think, perceive, and communicate" as a species.

http://story.news.ya...nce_dyslexia_dc

Finnish Researchers Say Find Dyslexia Gene
Mon Aug 25, 5:09 PM ET Science - Reuters
By Maggie Fox, Health and Science Correspondent

WASHINGTON (Reuters) - Finnish researchers said on Monday they had found a gene they believe could be important in causing dyslexia, the most common learning disorder among children.

Pinpointing the genetic changes that underlie dyslexia could help scientists understand what causes it and perhaps find better ways to help people with dyslexia overcome the handicap.

Dyslexia affects anywhere between 3 percent and 10 percent of the population and is characterized by difficulties recognizing and reading words.

Studies suggest that people with dyslexia process information in a different area of the brain than the average person does, even though they are often of average or above- average intelligence.

Some evidence shows they use the right side of the brain for reading instead of the left side, which is better set up for processing words.

The resulting problems can hold children back in school if they do not get special attention. Dyslexia is known to have a genetic component -- it runs in families -- but it remains poorly understood.

Juha Kere and colleagues at the University of Helsinki in Finland and the Karolinska Institute in Sweden started out with one particular family with several dyslexic members.

"In brief, the father had a history of profound reading and writing difficulties in school but is employed in business," the researchers wrote in their study, published in the Proceedings of the National Academy of Sciences.

His three children also had learning difficulties.

To compare, the team studied 20 unrelated Finnish families, with 58 dyslexic and 61 non-dyslexic members.

In the first family, a gene called DYXC1 was disrupted. In another, DYXC1 has a "stop sign" in the wrong place, which causes cells to produce a shortened version of the DYXC1 protein.

"We conclude that DYXC1 should be regarded as a candidate gene for developmental dyslexia," the researchers wrote.

The gene is expressed, meaning it causes production of a protein, in brain cells. The protein does not resemble any other known proteins.

This gene is unlikely to explain all cases of dyslexia, the researchers said.

"In a complex disorder, even a modest increase in genetic risk may be interesting," they wrote. "There is overwhelming evidence that dyslexia is a genetically complex condition."

The gene may be involved in helping cells handle stress, they added, but said much more study is needed before it becomes clear just what DYXC1 does.

[Cyto]

Laboratory 'Theme Park' Re-Creates RNA World For Study

Bartel, a researcher at Whitehead Institute for Biomedical Research, pursues a theory of early evolution called the "RNA-world hypothesis," which maintains that, in the beginning, long before DNA or protein existed, RNA performed both DNA's job of encoding information and protein's job of catalyzing replication. Because RNA replication is far simpler than protein replication, and because RNA participates in central cellular functions, researchers postulate a primitive, yet elegant, system in which RNA made RNA.

Central to this hypothesis is an RNA enzyme that replicates other RNA molecules. Unfortunately, no such molecule currently exists in nature. To demonstrate the feasibility of this hypothesis, researchers must re-create certain aspects of this RNA world in the lab. Hence Bartel's RNA theme park. According to Bartel, the micro exhibits in his lab are "artificial and fragmented when compared with the real thing, but still well worth a visit."

So far, Bartel has developed some impressive displays. In a paper published in the journal Science in 2001, his lab demonstrated one of the first pieces of hard evidence that such a world is at least possible. But this landmark paper also revealed that Bartel's RNA molecules didn't yet perform to the degree that the RNA world would have required. In a July 2003 follow-up in the journal Biochemistry, Bartel and doctoral student Michael Lawrence published research pinpointing the exact reason for this, findings Bartel claims are "an important step toward figuring out how to improve the efficiency of these RNA replicating molecules."

Re-evolving evolution

Today, cellular machinery coordinates a sophisticated process that involves proteins, DNA, and RNA all working in concert, with proteins typically serving as enzymes to catalyze reactions, and DNA and RNA storing and processing genetic information. If, as the RNA-world hypothesis states, RNA once was in the business of replicating RNA, then enzymes once were composed entirely of RNA and not amino acids - the building blocks of protein. The first step then, in creating an RNA-world theme park, is to create RNA enzymes from scratch. To do this, Bartel employs a process developed with Harvard Medical School's Jack Szostak: in vitro evolution - or evolution in a test tube.

Workers in Bartel's lab fill tubes with anywhere from 1 trillion to 1 quadrillion RNA molecules, selecting for those that can expand by forming chemical bonds with other RNAs. The molecules that can do this are isolated; the rest are discarded. These new, bigger RNAs are multiplied, returned to the tube and tested again for the same ability. Again, losers are removed, and winners multiplied. As this cycle repeats, slight mutations often appear in the RNAs, some of which create molecules superior to the parent molecule. Says Bartel, "Really, we end up selecting for the survival of the best molecules, and then propagating those survivors" - Darwinian natural selection.

So far, Bartel's lab has demonstrated that these new RNA molecules can act as enzymes: In this case, they can bind to an RNA template molecule that serves as the pattern for producing, one nucleotide at a time, another RNA. The Science paper reported both good and cautionary news. The good news was that these RNA enzymes are flexible and robust enough to bind to just about any kind of template regardless of its sequence - findings that eluded earlier experiments. The more sobering news was that these new sequences of RNA are at most 14 nucleotides long, which, while still a major achievement, is far short of the roughly 200-nucleotide goal. As reported in Biochemistry, Bartel and Lawrence have now learned the reason for this: The actual process of assembling the new RNA is fast and efficient once binding occurs, but the binding doesn't last long enough to produce a complete replicate. "What we really need now," says Bartel, "is to work on the binding."
Life was a garbage bag

Less than four decades old, the RNA-world hypothesis has garnered widespread support within the scientific community. However, some researchers subscribe to an alternate view often called the "metabolism first" theory. This idea, in contrast to the RNA world's "information first" thesis, posits that a chaotic soup of small, random molecules led to chance metabolic reactions that evolved into modern cellular life.

Stuart Kauffman, a biologist and RNA-world skeptic affiliated with the nonprofit research center Santa Fe Institute, believes the RNA hypothesis is narrow and fails to take into account the possibility that other polymeric molecules may be able to self-reproduce without making a copy of a template. He theorizes that life originated from a complex mixture of such polymers that eventually yielded autocatalytic reactions.

A similar notion is Freeman Dyson's "garbage bag" hypothesis. Dyson, a physicist at the Institute for Advanced Studies in Princeton, N.J., believes that primordial soup was filled with membranes (garbage bags) that contained random chemicals not nearly as complex as RNA or DNA. These chemicals began catalyzing reactions in each other, some of which eventually caused the cell-like garbage bags to divide and thus evolve.

Proponents of this view claim the key factor in early evolution is the garbage bag rather than the molecule. For University of California, Santa Cruz, chemistry professor David Deamer, it's inconceivable that RNA could have catalyzed and evolved outside the barrier of a cell membrane without just drifting off.

Bartel, rather than countering these critics, takes seriously the need for some kind of cell-like barrier - or garbage bag. "If our lab is able to demonstrate that RNA can replicate RNA, a next step would be to synthesize a self-replicating system that can also evolve," he says. "To do this would require membranes, or some other type of compartmentalization."

Harvard's Szostak, a prominent advocate of the RNA world, counters that he can't imagine a system as complex as cell formation and division not being preceded by some sort of informational transmission, such as RNA creating RNA. However, he adds that the RNA-world hypothesis isn't without its problems. "The big question," he says, "is whether RNA arose as the first genetic polymer from some prebiotic chemistry that we don't understand, or whether there were one or more progenitors of RNA. People are looking at many possible candidates for being a progenitor for RNA."

Szostak looks not to a world of random metabolism, but rather to threose nucleic acid, or TNA, a molecule that, while not existing in nature, has been successfully synthesized in the lab. Szostak believes that TNA's relatively simple composition make it a likely candidate to have spawned RNA in a prebiotic world.

In spite of the various theories, most researchers readily admit that, like the proverbial blind men trying to describe an elephant, each approach may have captured only one angle of life's origins. "We'll never really know the whole story of how life got started," says Bartel, "but every insight that we can discover is important. This is one of the most significant and fundamental questions in science, right up there with 'how does the mind work?' or 'how did the universe begin?'"

Meanwhile, Bartel and his team continue working toward their goal of developing an RNA enzyme that can fully replicate other RNAs. "We're designing these RNAs as well as we can," Bartel says, "and what we can't design, we evolve."

The more successful this re-evolving, the closer he gets to his theme park's grand opening.

[Cyto]

OOOOOOOOOOOOOOTITAN





Spotlight on Saturn's Moon Titan

"The most interesting point about simulations of Titan's hydrocarbon haze is that this smoggy component contains molecules called tholins (from the Greek word, muddy) that can form the foundations of the building blocks of life. For example, amino acids, one of the building blocks of terrestrial life, form when these red-brown smog-like particles are placed in water. When scientists analyze the building blocks of tholins by pyrrolysis, splitting up the tholins using plasma, scientists find a rich array of biomolecular building blocks such as pyrroles, pyrazines, pyridines and pyrimidines. All of these molecules have played an important role in the evolution of life."

Titan - Key to Earth's Evolution?

"It appears that Titan holds abundant and tantalizing clues, its dark organic haze holding the promise of life bearing chemistry. Titan is virtually waterless; however, adding water (i.e. simulating Earth-like conditions) to the macromolecular polymers within its haze yields amino acids. This gives us further evidence that the building blocks of life are ubiquitous and an inevitable result of a broad range of atmospheric chemistry."

Fresh Look at Saturn's Moon Titan Reveals Icy Bedrock

"The new findings are expected to help scientists fine tune their questions and investigation of Titan, which will be studied up close next year. The Cassini spacecraft, due to arrive at Saturn in July 2004, will send the Huygens probe plunging through Titan's atmosphere, collecting data all the way to the surface."

[Lazarus Long]

Agreed and a factor that I see as distinct between Earth and Venus for example. Venus s too hot and never had a stable enough atmosphere to create the molecules in question but Earth and Mars both began with periods that closely resembled what we see on Titan. Combine this with sufficient tectonic activity and you have the crucible of life. You see the accumulation of the molecules in the pools wold then be circulated beneath the body of water to rift zones where pressure and heat would be available to incubate archae.

In the case of Mars the gravitational field is just a little too light to hold the atmosphere secure, water too lacking, and the temperatures too cold to promote the "overall" conditions we find on Earth but what we are beginning to understand is that where we get the right conditions we may start finding life through-out the Universe because what we are looking at may be as much a Natural consequence of normal planetary evolution as an accretion disk.

That such a phenomenon may be normal in my mind does not make it less a "miracle" in what it offers us as opportunity to live but it does make it less "mystical" in why it occurs and this is the problem for all those who fail to understand the subtle beauty of the mundane and think that the sublime is the only residence of the Divine.

Titan has always been on my list of places to visit, now more than ever. )

[Cyto]

New Study of Jupiter's Moon Europa May Explain Mysterious Ice Domes, Places to Search for Evidence of Life



Highlights of...

A new University of Colorado at Boulder study of Jupiter's moon Europa may help explain the origin of the giant ice domes peppering its surface and the implications for discovering evidence of past or present life forms there.

But the scientists now think the dome creation also requires small amounts of impurities, such as sodium chloride or sulfuric acid. Basically the equivalent of table salt or battery acid, these compounds melt ice at low temperatures, allowing warmer, more pristine blobs of ice to force the icy surface up in places, creating the domes

Europa appears to have strong tidal action as it elliptically orbits Jupiter - strong enough "to squeeze the moon" and heat its interior, said Pappalardo. "Warm ice blobs rise upward through the ice shell toward the colder surface, melting out saltier regions in their path. The less dense blobs can continue rising all the way to the surface to create the observed domes."

The domes are huge - some more than four miles in diameter and 300 feet high - and are found in clusters on Europa's surface, said Barr, who did much of the modeling. "We are excited about our research, because we think it now is possible that any present or past life or even just the chemistry of the ocean may be lifted to the surface, forming these domes. It essentially would be like an elevator ride for microbes."

"The surface of Europa is constantly being blasted by radiation from Jupiter, which likely precludes any life on the moon's surface," said Barr. "But a spacecraft might be able to detect signs of microbes just under the surface."

[Cyto]

Biologists Solve Mysteries Of Photosynthesis, Metabolism

"Where we once could see merely the tip of the iceberg, we can now perceive the entire mechanism of photosynthesis," said Cramer, the Henry Koffler Distinguished Professor of Biological Sciences in Purdue's School of Science. "Before we found a way to crystallize the cytochrome, we had a general picture of the photosynthetic process, but possessed only a fraction of a percent of the information we now have. Now that we can examine these proteins closely with X-ray crystallography, it could lead to knowledge about how all cells exchange energy with their environment."

"Plant cell membranes are like the two ends of a battery," said Janet Smith, professor of biological sciences and the team member responsible for much of the structure analysis. "They are positive on the inside and negative on the outside, and they are charged up when solar energy excites electrons from hydrogen within the cell. The electrons travel up into the cell membrane via proteins that conduct them just like wires. Of course, because of their high energy level, the electrons want to 'fall back' like water over a dam, releasing the energy a plant harnesses to stay alive."

While animals do not employ photosynthesis, their cells do make use of similar proteins for respiration. The similarities could lead to a better understanding of our own metabolic processes.

[Cyto]

The Astrobiology Web

[Cyto]

A Very Good (SumUp) Article to add.

Life theories

Scientists usually focus on the destructive nature of asteroids and comets slamming into Earth. But maybe the heavenly bodies were the start of something big. ANNE McILROY delves into research that accentuates the positive

By ANNE McILROY
Saturday, October 4, 2003 - Page F8

The worst aerial bombardment in the history of the world started 3.8 billion years ago, when asteroids began slamming into the planet every 20 years or so. Some were the size of Manhattan, others as large as North America. Each hit with the force of all of the nuclear devices on Earth exploding at once. They spewed up gas and debris, blocking sunlight and creating gigantic craters.

For years, many scientists have focused on the destructive role asteroids have played in the history of life on Earth, possibly wiping out the dinosaurs 65 million years ago and contributing to, if not causing, the mass extinctions found in the fossil record every 26 million to 30 million years or so. Astronomers monitor the heavens, searching for menacing hunks of space rock that may be heading our way.

There is, however, a positive side to asteroids, and one that a handful of researchers has been investigating with renewed vigour in recent years. True, an incoming asteroid the size of Manhattan could be a civilization ender, killing all humans and many other species. But what if asteroids were the source of life on Earth in the first place?

David Kring thinks that is a possibility. A planetary scientist at the University of Arizona, he says the timing is right.

The first traces of life on Earth, found in rocks from Greenland, date to 3.8 million years ago, around the time of the great bombardment. Back then, Earth was a flooded planet, covered by a single shallow sea and lit by the dim fire of a young sun.

It is hard to imagine even one asteroid slamming into our planet, let alone one crashing every 20 to 200 years. To get a sense of the damage, look up at the moon on a clear night. Those ancient pockmarks were made in the same rocky barrage, Dr. Kring says.

Unlike the dusty lunar craters, those on Earth soon bubbled with hot water like primordial Jacuzzis. Their heat source was the molten and shattered rock at the bottom of the crater that absorbed much of the energy of the initial impact. Those rocks were hot enough to heat the water for hundreds of thousands of years. Voilà, Dr. Kring says, a cauldron for the soup of life.

As for the soup ingredients, all the elements needed for life were on board asteroids, which contain hydrogen, oxygen, sulphur, nitrogen and phosphorus. As many as 700 amino acids, the building blocks of proteins, have been detected on space rocks that have landed on Earth.

The general theory about the evolution of life is that these kinds of compounds --whether they came from asteroids or were already here -- eventually gave rise to a single-celled organism such as a bacterium. Exactly how that happened is still a mystery.

Dr. Kring was the first to put forward the idea that asteroid craters were the hydrothermal brew pits for early life. It is a hard theory to prove, however. None of the craters that were formed 3.8 billion years ago remain. They were erased by shifting continents and mountain building. That means Dr. Kring and his colleagues have to glean what they can from the 171 more recent impact sites that have been found on Earth, including 31 in Canada.

The idea of impact sites as "cauldrons of life" has been embraced by scientists investigating the possibility of life on Mars. The red planet is home to many impact craters, and was bombarded with asteroids 3.8 billion years ago when Earth and the moon were regularly hit.

Gordon Osinkski, a researcher at the University of New Brunswick, is part of a team of investigators who have spent the last five summers studying an impact crater on Devon Island in Nunavut. The Haughton Crater is 20 kilometres in diameter, and looks much like the surface of Mars today. But the area would have been much wetter and warmer when an asteroid or comet hit 23 million years ago.

Mr. Osinkski found pipe-like structures around the crater rim, and believes that they acted as vent systems for hot fluid and steam, bringing warm water and chemicals to the surface. "It seems very likely you would have hot springs around the Haughton Crater."

If the same structures are found in Martian craters, it would build the case that life may have evolved there as well. Images from the surface of Mars suggest that water once flowed on its surface.

"Hydrothermal systems represent sites where water, warmth, dissolved chemicals and nutrients may have been available for extended lengths of time. Haughton may therefore provide a valuable case study for understanding how impact-generated hydrothermal systems affected the development of life on early Earth, and possibly other planets such as Mars,'' Mr. Osinkski says.

Others are convinced that life evolved first elsewhere in the universe. In the 1970s, British astronomers Fred Hoyle and Chandra Wickramasinghe argued that bacteria can travel across galaxies on comets. According to their theory, life arrived on Earth riding on a celestial snowball.

While asteroids are composed of metal and rock, comets are made of ice. There is no definitive proof that comets -- or asteroids -- ever arrived on Earth carrying bacteria. But a few weeks ago, in the prestigious U.S. journal Science, Belgian researchers announced new evidence that comets carry large quantities of complex organic compounds. These are the kinds of compounds that could give rise to life.

The problem with comets, in more ways than one, is that they tend to travel faster than asteroids, and so slam into Earth with a greater destructive force. There is still debate over whether the impact crater in Mexico associated with the death of the dinosaurs was caused by a comet or an asteroid.

In any event, the question is whether any living organism -- or the raw chemical material for life -- could survive that kind of cataclysm.

Dr. Kring doesn't think so. But there is evidence they could survive the relatively milder cataclysm of an asteroid impact, says Gordon Southam, a researcher at the University of Western Ontario. He and his American colleague Eileen Ryan tried to simulate the force of an asteroid hitting Earth on a small scale, using small chunks of rock inhabited by bacteria.

"We fire projectiles at two kilometres a second at a rock and basically blow it up," he says. Their results have not yet been published, but he says the bacteria survive.

Surviving the initial impact is one challenge. Temperatures in the "cauldron" formed by the crater would probably have been too high for even heat-loving bacteria to withstand, and might have burned off any carbon or other building blocks of life.

Which brings us to the alternative hydrothermal theory of life. Impact craters may not have been the only hydrothermal environments on Earth 3.8 billion years ago. There were hydrothermal vents at the bottom of the ocean, cracks in the sea floor that are still there today, although the oceans are now much deeper. Hot gas bubbles up through the cracks, along with nitrogen, hydrogen, carbon, methane and sulphate -- the basic ingredients for amino acids.

Kim Juniper is a University of Quebec professor who spends his summers studying the strange creatures that live around the vents, including string-like tube worms, giant clams and spiders, as well as heat-resistant bacteria.

He believes it is more likely that life evolved first in the vents. Dr. Kring agrees that this is a possibility, and says it is impossible to know for sure. There is also a chance that life evolved earlier than 3.8 billion years ago, but was extinguished when the worst asteroid storm in history began. Researchers believe each impact would have been a natural disaster unprecedented in modern times, turning the surface of Earth into a convection oven, and raised enough dust to block out the rays of the sun for years.

"One of the things we still don't understand is whether the bombardment created the conditions necessary for the origin of life, or extinguished pre-existing life forms," Dr. Kring says.

However, both scenarios suggest that humans may owe their existence to heavenly bodies. If asteroids and comets did give rise to life, then we would not have evolved without them.

Some scientists look at asteroid impacts as periodically purging the world of many of its animals, allowing only small, hardy generalists to survive. This regular cleansing, while disastrous for the species that die, regularly clears the decks for the rise of a new world order.

The last major impact was 65 million years ago, when either a comet or an asteroid 10 to 15 kilometres in diameter smashed into the Yucatan Peninsula in Mexico. It may have killed off the dinosaurs and ended the age of the reptile. But it also gave rise to the age of the mammal, which eventually produced Homo sapiens.

Anne McIlroy is The Globe and Mail's science reporter.

[Cyto]

Probability of Abiogenesis FAQs

From TalkOrigins.org

Abiogenesis is the field of science dedicated to studying how life might have arisen for the first time on the primordial young Earth. Despite the enormous progress that has been made since the Miller-Urey experiment, abiogenesis is under constant attack from creationists, who continually claim that the origin of life by random natural processes is so unlikely as to be, for all practical purposes, impossible. Following are some articles that challenge this claim and demonstrate the fundamental misconception at the core of the creationists' arguments.

See Them Here...

[Lazarus Long]

There are actually multiple theories involving extraterrestrial origins for life one that you mention above and another that involves bacterial spores literally drifting onto the planet with cosmic dust clouds as well as the idea that the alteration in the environment could have been precipitated by a comet of planetesimal size impacting the planet to provide sufficient water and a catalytic change in atmosphere. Another is that the impacts spread life and precipitated the great rate of mutation and divergence we see shortly after that time period.

One problem about extraterrestrial origins that I have alway pondered is the idea that it only begs the question of where life began and leaves open the question of evolution on other and multiple planets. An extraterrestrial origin would still in all likelihood be the result of evolution somewhere.

[Cyto]

Parasitism derived
By Cathy Holding

Archaeons are a group of organisms phylogenetically distinct from bacteria and eukaryotes. They inhabit a range of extreme conditions such as hydrothermal vents or anoxic environments that are thought to reflect the conditions that existed on the primordial earth. The recently discovered Nanoarchaeum equitans represents a novel archaeon kingdom and grows in conjunction with the crenarchaeon Ignicoccus. In the October 13 PNAS, Elizabeth Waters and colleagues at Diversa show that N. equitans is parasitic rather than symbiotic and has evolved from a primitive ancestor instead of reductively from a more complex form (PNAS, DOI:10.1073/pnas.1735403100, October 13, 2003).

Waters et al. sequenced what turned out to be the smallest genome to date and observed a circular chromosome only 490 kb long, with 552 coding sequences covering 95% of the genome and containing little noncoding or pseudogene sequence that would have suggested reductive evolution. Function was assigned to two thirds of the genes; 18% had homologues of unknown function, and the remainder represented archaeal-specific sequences. Analysis of gene function, together with the observation that overinfection of the host Ignicoccus impedes its growth, pointed toward the lifestyle of an obligate parasite.

“We suggest that this microbe is a derived, but genomically stable parasite that diverged anciently from the archael lineage. The complexity of its information processing systems and the simplicity of its metabolic apparatus suggests an unanticipated world of organisms to be discovered,” the authors conclude.

Genomic analysis of a parasitic archaeon suggests nonreductive evolution | By Cathy Holding

[Cyto]

I know this isn't a new idea but here is recent research. Overall it is quite interesting. Could RNAs, autocleaving and replicative, find homes in these lipid spheres and further their diversification by division?

More Info Here --> THE RNA WORLD by Brig Klyce
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From Bio.com...
Clays May Have Aided Formation of Primordial Cells

10/24/2003 -- Howard Hughes Medical Institute (HHMI) researchers have discovered that clays may have been the catalysts that spurred the spontaneous assembly of fatty acids into the small sacs that ultimately evolved into the first living cells.

HHMI investigator Jack W. Szostak and colleagues Martin M. Hanczyc and Shelly M. Fujikawa at Massachusetts General Hospital also demonstrated that these vesicles could be induced to grow and to split into separate vesicles under laboratory conditions. They reported their studies in the October 24, 2003, issue of the journal Science.

Szostak and his colleagues were prompted to perform their experiments by the earlier work of other researchers who had found that clays could catalyze the chemical reactions needed to construct RNA from building blocks called nucleotides. They reasoned that if clays could foster the formation of vesicles, it would not be inconceivable that clay particles that had RNA on their surface could end up inside such vesicles. If that were true, the result would offer conditions amenable to the eventual evolution of living cells that could self-reproduce.

"Other researchers had observed that if fatty acid micelles, which are stable at basic conditions, are exposed to more acidic conditions, they spontaneously assemble into vesicles," said Szostak. "This reaction has a long lag period, and some sort of nucleation surface is required to trigger the process. We reasoned that if the right kind of mineral surface was present, this lag phase would be eliminated."

In their experiments, Szostak and his colleagues found that adding small quantities of the clay, montmorillonite, to fatty acid micelles greatly accelerated the formation of vesicles. They also discovered that many other substances with negatively-charged surfaces also catalyzed formation of vesicles.

When the researchers loaded montmorillonite particles with a fluorescently labeled RNA and added those particles to micelles, they detected the RNA-loaded particles inside the resulting vesicles. And, going a step further, Szostak and his colleagues showed that when they encapsulated labeled RNA alone inside vesicles, it did not leak out.

"Thus, we have demonstrated that not only can clay and other mineral surfaces accelerate vesicle assembly, but assuming that the clay ends up inside at least some of the time, this provides a pathway by which RNA could get into vesicles," said Szostak.

However, he said, even primitive, non-living, cell-like structures need a mechanism to grow and divide. Thus, the scientists explored the behavior of vesicles to which micelles had been added - finding that acidic conditions induced the micelles to become unstable and somehow incorporate themselves into a growing vesicle.

"After we showed that efficient growth was possible, the next problem was how to complete the cycle by persuading these vesicles to divide," said Szostak. The scientists discovered that if they extruded larger dye-containing vesicles through smaller pores, the result was a proliferation of smaller vesicles, which still contained dye.

"Exactly how this proliferation happens is not clear, and there are different models for the processes," said Szostak. "The important thing is that it all works. You end up with small vesicles in which the contents stay mostly inside. This is important if the process is to be vaguely analogous to biological cell division," he said.

"Now that we have a proof-of-principle that growth and division is possible in a purely physical-chemical system, we are working on a way to get this cycle to function in a way that is more natural," said Szostak. "Clearly, there are a lot of complicated and interesting processes going on here, and how this pathway leads to biological systems is not at all straightforward."

"We are not claiming that this is how life started," emphasized Szostak. "We are saying that we have demonstrated growth and division without any biochemical machinery. Ultimately, if we can demonstrate more natural ways this might have happened, it may begin to give us clues about how life could have actually gotten started on the primitive Earth."

In particular, said Szostak, further research should aim to demonstrate that the formation of RNA or a related polymer molecule could occur concurrently with vesicle replication. "Ultimately, we'd like to put them together and have replicating RNA inside a replicating vesicle," said Szostak. "If we could demonstrate both processes under arbitrary laboratory conditions, we could begin to work toward making them work under more and more natural conditions."

Source: Howard Hughes Medical Institute