human origin

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““You must not lose faith ”

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#280
Jan 22, 2014
 

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Another conference
http://www.nature.com/natureevents/science/ev...

The Physics of Soft and Biological Matter

This conference will bring together the broad and diverse community interested in the physics of soft and biological matter, which includes liquids, liquid crystals, polymers, colloids, membranes, interfaces, cellular biophysics, and biological macromolecules. The programme will span a number of key cross-cutting themes, including self-assembly and patterning, rheology, biomimetics, non-equilibrium phenomena, as well as molecular imaging, optical methods and spectroscopies, which are all relevant to the wide range of length- and time-scales present in these fascinating systems.

http://www.nature.com/nature/journal/v441/n70...
new insights mantle-seawater-noble gasses 2006

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#281
Jan 22, 2014
 

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http://www.ncbi.nlm.nih.gov/pubmed/2194124

1990 May;40(2):269-78.

Water and urea transport in human erythrocytes infected with the malaria parasite Plasmodium falciparum.

Zanner MA, Galey WR, Scaletti JV, Brahm J, Vander Jagt DL.

http://www.ncbi.nlm.nih.gov/pubmed/7475094

1995 Aug 21;175(4):583-94.

Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?

Kondrashov AS.

Malaria and osmotic effects.

Includes recent papers.

“I have upset the hand of god”

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#282
Jan 22, 2014
 

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MAAT wrote:
http://www.ncbi.nlm.nih.gov/pu bmed/2194124
1990 May;40(2):269-78.
Water and urea transport in human erythrocytes infected with the malaria parasite Plasmodium falciparum.
Zanner MA, Galey WR, Scaletti JV, Brahm J, Vander Jagt DL.
http://www.ncbi.nlm.nih.gov/pubmed/7475094
1995 Aug 21;175(4):583-94.
Contamination of the genome by very slightly deleterious mutations: why have we not died 100 times over?
Kondrashov AS.
Malaria and osmotic effects.
Includes recent papers.
Maat, the paper below is one I found recently on the deleterious mutations and extinction.

Lynch, Michael, John Conery & Reinhard Burger. 1995. Mutation accumulation and the extinction of small populations. The American Naturalist. 146(4): 489-518.

I don't know how easy it will be for anyone to get, so I am posting the Abstract below.

Abstract.-Although extensive work has been done on the relationship between population size and the risk of extinction due to demographic and environmental stochasticity, the role of genetic deterioration in the extinction process is poorly understood. We develop a general
theoretical approach for evaluating the risk of small populations to extinction via the accumulation of mildly deleterious mutations, and we support this with extensive computer simulations.

Unlike previous attempts to model the genetic consequences of small population size, our
approach is genetically explicit and fully accounts for the mutations inherited by a founder
population as well as those introduced by subsequent mutation. Application of empirical estimates of the properties of spontaneous deleterious mutations leads to the conclusion that populations with effective sizes smaller than 100 (and actual sizes smaller than 1,000) are highly vulnerable to extinction via a mutational meltdown on timescales of approximately 100 generations.

We point out a number of reasons why this is likely to be an overly optimistic view. Thus,
from a purely genetic perspective, current management policies that provide formal protection to species only after they have dwindled to 100-1,000 individuals are inadequate. A doubling of the deleterious mutation rate, as can result from the release of mutagenic pollutants by human activity, is expected to reduce the longevity of a population by about 50%. As some investigators have previously suggested, the genetic load of a population can be readily purged by intentional inbreeding. However, this effect is at best transient, as intentional inbreeding can only enhance the probability of fixation of deleterious alleles, and those alleles that are purged are rapidly replaced with new mutations.

““You must not lose faith ”

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#283
Jan 22, 2014
 

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Interesting, especially when put beside the newest studies.

I was busy looking at platelet derived growth-factors.(aka cytokines.
A cytokine storm is a nasty thing)

The humane least risk method (not allowed in America, since the prefer distilling drugs i.e. pill sized cures, which can however gring out the negative effects) is extracting blood fro the patient, extract the platelets and reinject. 12 inch needle!! Roight , ths is where i started my search as distraction.

The post did not appear, so quick:
http://www.biomet.com.tr/tr-medical/tr-biolog...
www.mdpi.com/1424-8247/3/3/572/pdf&#8206 ;
M Raica - ‎2010
http://en.wikipedia.org/wiki/Cytokine
http://en.wikipedia.org/wiki/Transforming_gro...
http://en.wikipedia.org/wiki/Insulin-like_gro...
signal pathways also interesting
http://www.ncbi.nlm.nih.gov/gene/7422
VEGFA
http://genesdev.cshlp.org/content/22/10/1276....
Role of platelet-derived growth factors in physiology and medicine

Johanna Andrae1,2,
Radiosa Gallini1, and
Christer Betsholtz
The Dude

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#284
Jan 23, 2014
 

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replaytime wrote:
<quoted text>
It is so funny how you all dislike the term "Man from Monkey" but that is what evolution teaches.
You misunderstand. It's not that I don't like the term. We did not come from "monkeys" (as you understand the term) but go back far enough and our ancestry leads from Simiiforms which likely similar to old-world monkeys.

The only "problem" I was pointing out is that the extent of YOUR biological knowledge which amounts to "monkey-man". And that's it. Like I said, that's not evolution's problem. It's your problem.
The Dude

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#285
Jan 23, 2014
 

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replaytime wrote:
<quoted text>
The most obvious difference between monkeys and chimpanzees is that monkeys have tails, some of which are prehensile, and chimpanzees do not have tails. Funny we humans are supposed to have had tails at one point. Isn't that what they say about the human coccyx bone that it is remnants of a tail? Chimpanzees share 93-99 percent of their DNA with humans(depending on what you read for some say 93%, some say 95%, some say 97%, some say 98%, some say 99%),
Depending on how they're measuring the genome, whether it be bases, genes, chromosomes, ERV's, whatever, those sound about right. A base for base comparison is about 98%.
replaytime wrote:
while monkeys share about 93 percent with humans so monkeys are just a little further back down the evolution line.
Uhuh. Their lineage separated from ours perhaps over 16 million years ago.

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#286
Jan 23, 2014
 

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http://imgpublic.mci-group.com/ie/PCO/AllAbst...

Koonin suggests that genome wide evolution is directed at preventing malfunction and not at gaining function.

And at that we would have to adapt as fast as virussus evolve, or loose.

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#287
Jan 23, 2014
 

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page 42 genome-wide gene-tree and species connected in new approach.

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#288
Jan 23, 2014
 

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Regards to Fear is not real and Dude:

http://www.topix.com/forum/news/evolution/TG1...
The Dude

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#289
Jan 23, 2014
 

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Much less technical, but a brief overview of how the Descent Of Man eventually led to the revolutionary view of humanity's origins:

http://www.dailykos.com/story/2014/01/16/1250...

“I'm Your Huckleberry ”

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#290
Jan 23, 2014
 
The Dude wrote:
<quoted text>
You misunderstand. It's not that I don't like the term. We did not come from "monkeys" (as you understand the term) but go back far enough and our ancestry leads from Simiiforms which likely similar to old-world monkeys.
The only "problem" I was pointing out is that the extent of YOUR biological knowledge which amounts to "monkey-man". And that's it. Like I said, that's not evolution's problem. It's your problem.
Monkeys evolved before the split between monkeys and apes. So I say again; The most obvious difference between monkeys and chimpanzees is that monkeys have tails, some of which are prehensile, and chimpanzees do not have tails. We humans are supposed to have had tails at one point. Isn't that what they say about the human coccyx bone that it is remnants of a tail?
The Dude

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#291
Jan 24, 2014
 

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replaytime wrote:
Monkeys evolved before the split between monkeys and apes.
New world monkeys split from the simians 40MY ago. Old world monkeys split 25MY ago. So yes, monkeys are more distantly related to us than apes are.

http://en.wikipedia.org/wiki/Simian#Classific...
replaytime wrote:
So I say again; The most obvious difference between monkeys and chimpanzees is that monkeys have tails, some of which are prehensile, and chimpanzees do not have tails.
Yes, that is one difference. New world monkeys often have prehensile tails, while old world monkeys often have non-prehensile tails. As we get to more closely related species like apes they tend not to have tails at all.
replaytime wrote:
We humans are supposed to have had tails at one point. Isn't that what they say about the human coccyx bone that it is remnants of a tail?
Yes, the ancestors of both modern monkeys and humans had tails, hence the coccyx. Remember these ancestors would not have been monkeys, but monkey-like.

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#292
Jan 24, 2014
 

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replaytime wrote:
<quoted text>
Monkeys evolved before the split between monkeys and apes. So I say again; The most obvious difference between monkeys and chimpanzees is that monkeys have tails, some of which are prehensile, and chimpanzees do not have tails. We humans are supposed to have had tails at one point. Isn't that what they say about the human coccyx bone that it is remnants of a tail?
Technically and scientifically this is right. It all depends on how far you want to go back. With all regards one can say we cam from a single celled jello organisms with no brain or vital organs or bones as we now have. The difference is that you are looking at evolution as a whole where as your conversers are looking at evolution back to MRCA/LUCA. So technically and scientifically you all are right with the exception that one converser looks back farther than the other conversers.

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#293
Jan 24, 2014
 

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Best AnswerVoter's Choice
DNAunion answered 2 years ago


a. Activated pyrimidine ribonucleosides were produced under prebiotically plausible conditions (1).

b. Activated ribonucleotides can polymerize on montmorillonite (2)(3).
In addition, cyclic nucleotides can link up into long chains, up to 100 units long, with the proper bonding, in water, without catalysts (4).

c. Multiple ribozymes (catalytic RNA molecules) that performed biologically relevant reactions (RNA ligases) were found in a large pool of RANDOM SEQUENCE RNA molecules (5).

d. Scientists have evolved a general purpose, RNA-dependent, RNA polymerase ribozyme, capable of copying up to 14 nucleotides of just about any primer-template RNA sequence thrown at it.(6)

A variant (called B6.61) of the above RNA-dependent, RNA-polymerase ribozyme was able to copy up to at least 20 nucleotides of a particular primer-template, and was faster and more accurate.(7)

e. Jack Szostak has made good progress showing the plausibility of a single-gene protocell. He works with fatty-acid vesicles, which are prebiotically plausible. The vesicles also contain montmorillonite, which, as mentioned above, catalyzes the linkage of nucleotides into chains.

f. Szostak has also shown that activated nucleotides can enter the vesicles, but once they are linked together they cannot exit. This provides a means of concentrating nucleotides from the surroundings.

G. Further, Szostak showed that vesicles with more RNA in them "steal" fatty acids from their neighbors, resulting in both competition and growth.

H. In addition, it has been found that ribose preferentially passes through the fatty-acid membrane of the protocell, helping to explain how ribose could be concentrated from a complex mix of sugars.

Is it all worked out, from A to Z? Nope, but a lot of progress has been made in the past 10 years.

(1) Matthew W. Powner, Beatrice Gerland, & John D. Sutherland,Synthesis of Activated Pyrimidine Ribonucleotides in Prebiotically Plausible Conditions, Nature, Vol. 459, 14 May 2009, p239

(2) Martin M. Hanczyc, Shelly M. Fujikawa, & Jack W. Szostak; Experimental Models of Primitive Cellular Compartments: Encapsulation, Growth, and Division; Science 24 October 2003: Vol. 302. no. 5645, pp. 618 622

(3) M. G. Sacerdote and J. W. Szostak, Semipermeable lipid bilayers exhibit diastereoselectivity favoring ribose, PNAS April 26, 2005 vol. 102 no. 17 6004-6008

(4) Generation of Long RNA Chains in Water, Giovanna Costanzo, Samanta Pino, Fabiana Ciciriello, and Ernesto Di Mauro, November 27, 2009 The Journal of Biological Chemistry, 284, 33206-33216

(5) James P. Ferris, Catalyzed RNA Synthesis for the RNA World, p285 of the book The Molecular Origins of Life, edited by Andre Brack, Cambridge University Press, 1998

(6) W.K Johnston, P.J Unrau, M.S Lawrence, M.E Glasner and D.P Bartel, RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension, Science 292 (2001), pp. 13191325

(7) Selection of an improved RNA polymerase ribozyme with superior extension and fidelity, Hani S. Zaher and Peter J. Unrau, RNA 2007. 13: 1017-1026

Source:

BS in biology; university biology tutor

““You must not lose faith ”

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#294
Jan 24, 2014
 

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To qualify as "empirical science" means only that the question can be approached through the examination of evidence ... both observation and experiment.

The fact that the question of abiogenesis (the origins of the first life forms from non-living organic materials) is as of yet not solved ... does NOT mean that there is no empirical approach to the question!

The question IS approachable through evidence ... both observation (of the existing composition of the available elements in the earth, oceans, and atmosphere), and experimentation (on the types of compounds these elements can produce, and what kind of energy conditions can produce more complex molecules). This allows us to make progress separating plausible hypotheses from dead ends.

That is what makes it more than just "conjecture", even though some clearly don't understand the process.

That makes it "empirical science", whether one understands what that means or not.

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#295
Jan 24, 2014
 

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Furthermore on this aspect of the discussion:

>"Evolution could not happen without a beginning to life. "

Yes, but that does not mean that we should conclude that evolution does not exist until we have solved how life started.

That would be like concluding that gravity does not exist until we have solved how gravity started!

Or are you saying that gravity is also just "conjecture"?

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#296
Jan 24, 2014
 

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Consider a population which is changing from one generation to the next as per the equation N(t)= R*N(t-1), where N(t) represents the size of the population at time t and R is a constant growth parameter. Under what condition is the population likely to go extinct?
(A) R=2
(B) R<1
(C) R=1
(D) R>1

N E answered 13 hrs ago


I think the formula is probably supposed to be exponential? So, rather than:
N(t)= R x N x (t-1)
the formula should be
N(t)= R^(N(t-1))

In this case, also assuming that N is the initial population size, then we can just plug in some numbers and see what happens. If we let N=2 and t=2, then if R=2, N(2)=2^(2(2-1))=4, as time, t, increases, then N(3)=2^(2(3-1))=2^(4)=16, so the population size increases, so answer A is wrong. If R=1, then as t increases, the population size will increase, but at a slower rate than if R=2. If R>1, then this is a similar condition to R=1 or R=2, the population size will increase. So, the answer we are left with is B, R<1. Let's let R=0.5, N=2, t=2, then t=3, then t=4 and see what happens:

N(t)= 0.5^(2(2-1))
N(2)=0.5^2=0.25
N(3)=0.5^(2(3-1))=0.5^4=0.0625
N(4)=0.5^(2(4-1))=0.5^6=0.0156 25

So, the population size gets smaller and smaller as time goes on (t increases), so answer B, if R<1, the population size will decrease and the likelihood of extinction is increasing with the passage of time.

Asker's rating & comment
thank u.. it was given N(t)= R*N(t-1), in the question.. may be they typed it by mistake..

The above as well as a contribution by Subduction Zone (Avogrado) included in this thread might clarify some discussions.

Schoolng: since this is what this thread is meant for. Background from a evolutionary perspective. Not discussion or summary judgements. And contribution only if a valuable contribution.

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#298
Jan 25, 2014
 
FREE SERVANT wrote:
<quoted text>Cycling is the way nature produces. Repetition produces things and systems are patterned with structural components which are driven be a clock-like rhythm which is built in and self sustained and adjusted to local environments. The intelligent approach to problems is managed through repeating cycles.
This article might interest you.

I'll quote what interested me:
The observation of a specific organic chemical in any quantity (even as part of a complex mixture) in one of the above sources would justify its classification as "prebiotic," a substance that supposedly had been proved to be present on the early Earth. Once awarded this distinction, the chemical could then be used in pure form, in any quantity, in another prebiotic reaction. The products of such a reaction would also be considered "prebiotic" and employed in the next step in the sequence.

The use of reaction sequences of this type (without any reference to the origin of life) has long been an honored practice in the traditional field of synthetic organic chemistry. My own PhD thesis advisor, Robert B. Woodward, was awarded the Nobel Prize for his brilliant syntheses of quinine, cholesterol, chlorophyll and many other substances. It mattered little if kilograms of starting material were required to produce milligrams of product. The point was the demonstration that humans could produce, however inefficiently, substances found in nature. Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA.

Fortunately, an alternative group of theories that can employ these materials has existed for decades. The theories employ a thermodynamic rather than a genetic definition of life, under a scheme put forth by Carl Sagan in the Encyclopedia Britannica: A localized region which increases in order (decreases in entropy) through cycles driven by an energy flow would be considered alive. This small-molecule approach is rooted in the ideas of the Soviet biologist Alexander Oparin, and current notable spokesmen include de Duve, Freeman Dyson of the Institute for Advanced Study, Stuart Kauffman of the Santa Fe Institute, Doron Lancet of the Weizmann Institute, Harold Morowitz of George Mason University and the independent researcher Gnter Wchtershuser. I estimate that about a third of the chemists involved in the study of the origin of life subscribe to theories based on this idea. Origin-of-life proposals of this type differ in specific details; here I will try to list five common requirements (and add some ideas of my own).
(1) A boundary is needed to separate life from non-life
(2) An energy source is needed to drive the organization process.
(3) A coupling mechanism must link the release of energy to the organization process that produces and sustains life.
(4) A chemical network must be formed, to permit adaptation and evolution.
Here enters the cycle.
(5) The network must grow and reproduce.

http://www.scientificamerican.com/article/a-s...

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#299
Jan 26, 2014
 
http://www.hindawi.com/journals/ijg/2012/4245...
Comparative and Functional Genomics
Volume 2012 (2012), Article ID 424526, 4 pages
http://dx.doi.org/10.1155/2012/424526
Review Article

Pseudogenes

Yusuf Tutar1,2,3

http://books.google.nl/books...

Origin and Evolution of New Gene Functions
bundled by Manyuan Long

Kluwer Academic publishers
http://www.springer.com/biomed/human+genetics...
( and i guess the / any introduction in statistics would also not come amiss. Though the above book offers very clear insight in that too.)

Also
http://faculty.washington.edu/wjs18/Newgenes....
THE ORIGIN OF NEW GENES:
GLIMPSES FROM THE YOUNG
AND OLD
Manyuan Long*, Esther Betrn, Kevin Thornton and Wen Wang||

Genome data have revealed great variation in the numbers of genes in different organisms,
which indicates that there is a fundamental process of genome evolution: the origin of
new genes. However, there has been little opportunity to explore how genes with new
functions originate and evolve. The study of ancient genes has highlighted the antiquity and
general importance of some mechanisms of gene origination, and recent observations
of young genes at early stages in their evolution have unveiled unexpected molecular
and evolutionary processes.

Any other articles in the book can be googled i found.

http://pondside.uchicago.edu/ecol-evol/people...
Long:
Molecular and evolutionary studies have provided powerful analytical tools for the detection of the processes and mechanisms that underlie the origin of new genes.

Three levels of questions about this process can be defined. First, at the level of individual new genes, what are the initial molecular mechanisms that generate new gene structures? Once a new gene arises in an individual genome in a natural population, how does it spread throughout an entire species to become fixed? And, how does the young gene subsequently evolve? Second, at the level of the genome, how often do new genes originate? If new gene formation is not a rare event, are there any patterns that underlie the process? And, what evolutionary and genetic mechanisms govern any such patterns? Third, what are functions and phenotypic effects of new genes? How are the detected patterns impacting the phenotypic evolution, e.g. e.g. the environmental adaptation and evolution of development?

end quote.

http://longlab.uchicago.edu/sites/default/fil...
New genes in humans and our
primate relatives add a new component to the understanding
of genetic divergence between humans and non-humans.

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#302
Jan 27, 2014
 


http://en.wikipedia.org/wiki/Montmorillonite

Montmorillonite is also known to cause micelles (lipid spheres) to assemble together into vesicles. These are structures that resemble cell membranes on many cells. It can also help nucleotides to assemble into RNA which will end up inside the vesicles. It has been demonstrated that this could have generated highly complex RNA polymers that could reproduce the RNA trapped within the vesicles.[8] This process may have led to the origin of life on Earth.[9]

Similar to many other clays, montmorillonite swells with the addition of water. However, some montmorillonites expand considerably more than other clays due to water penetrating the interlayer molecular spaces and concomitant adsorption. The amount of expansion is due largely to the type of exchangeable cation contained in the sample. The presence of sodium as the predominant exchangeable cation can result in the clay swelling to several times its original volume. Hence, sodium montmorillonite has come to be used as the major constituent in non-explosive agents for splitting rock in natural stone quarries in order to limit the amount of waste, or for the demolition of concrete structures where the use of explosive charges is unacceptable.

Use in medicine and pharmacology[edit]

Montmorillonite is effective as an adsorptive of heavy metals.[6]

http://www.newscientist.com/article/dn4307
Clay's matchmaking could have sparked life
19:00 23 October 2003 by Philip Cohen

The study of montmorillonite clay, by Martin Hanczyc, Shelly Fujikawa and Jack Szostak at the Massachusetts General Hospital in Boston, revealed it can sharply accelerate the formation of membranous fluid-filled sacs.

These vesicles also grow and undergo a simple form of division, giving them the properties of primitive cells. Previous work has shown that the same simple mineral can help assemble the genetic material RNA from simpler chemicals. "Interestingly, the clay also gets internalised in the vesicles," says Leslie Orgel, an origin of life expert at the Salk Institute for Biological Sciences in San Diego, California. "So this work is quite nice in that it finds a connection between the mechanism that creates RNA and encloses it in a membrane."

Szostak wondered whether montmorillonite could also help the assembly of vesicles from simple fatty acid precursors. He remembers the day his colleagues Hanczyc and Fujikawa ran into his office to show him their first results: the clay caused a 100-fold acceleration of vesicle formation.

"It was pretty amazing," he says. Once formed, the vesicles often incorporated bit of clay and were able to grow by absorbing more fatty acid subunits.

His team also showed the clay could hold RNA and form vesicles at the same time. Fluorescently-labelled RNA attached to the clay ended up assembled into vesicles after the reaction. And the researchers were able to get these "protocells" to divide by forcing them through small holes. This caused them to split into smaller vesicles, with minimal loss of their contents.

Szostak admits that in a natural setting the vesicles would rarely be forced to divide in this way. So now his group is searching for different mixtures of membrane-forming molecules that might divide spontaneously when they reach a certain size.

Journal reference: Science (vol 302, p 618 )

http://en.wikipedia.org/wiki/Abiogenesis
cyano bacteria

I see... they expanded the article. lol
Gunther Wchterhuser is also mentioned.

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