3.2+The+origin+of+Life

The origin of life

cience shows us that the universe evolved by self-organization of matter towards more and more complex structures. Atoms, stars and galaxies self-assembled out of the fundamental particles produced by the [|Big Bang]. In first-generation stars, heavier elements like carbon, nitrogen and oxygen were formed. Aging first-generation stars then expelled them out into space – we, who consist of these elements, are thus literally born from stardust. The heaviest elements were born in the explosions of supernovae. The forces of gravity subsequently allowed for the formation of newer stars and of planets. Finally, in the process of biological evolution from bacteria-like tiny cells (the last universal common ancestor) to all life on earth, including us humans, complex life forms arose from simpler ones. Upon considering this self-organization of material structures in the realm of philosophy, one may conclude that it happens either because the underlying laws of nature simply are the way they are, or because they were designed by God for this purpose. Since we know that the laws of nature are so self-sufficient that, based on them, the complexity of the entire physical universe evolved from fundamental particles, and further, complex life forms from simpler ones during biological evolution, we can reasonably extrapolate that they would also allow life itself to originate spontaneously, by evolution of complex structures – regardless if we believe these laws are designed or undesigned. Therefore, we should expect an origin of life by natural causes from both theistic and atheistic philosophical perspectives



taken from: http://www.talkorigins.org/faqs/abioprob/originoflife.html

=Origin of Life – Theories and Genetics = Revised May 2002 ** ||  || **For more extensive and recent information on Genetics, Theories of Aging, and Evolution Theories see: [] ** ||
 * || **T.C. Goldsmith May, 2001


 * Recent rapid advances in the study of genetics and molecular biology have produced additional insight into fundamental questions such as the origin of life on Earth. This paper provides an overview of Genetics from an engineering perspective as well as discussions of these questions. **
 *  As a computer engineer, I became interested in genetics because of the striking similarities between genetics processes and computer science. There is a digital genetic code. There is digital logic with “and” functions and logic matrices. There is even “error correcting” in digital copying of genetic code. **

 Genetics

 *  All living organisms have a genetic code generally represented by the sequence of //nucleotides// in their DNA. Since there are four possible bases used in construction of the code (denoted A, G, C, and T), each letter in the code carries two bits of information. The DNA is normally in the form of a double strand (the famous “double helix”) where the second strand is complementary to the first strand. That is, in the second strand a sequence such as “AGCTTT” is replaced by “TCGAAA” which carries the same information. So the terminology “base pair” refers to one letter of genetic code represented by the base and its complement and equivalent to two bits of information in computer parlance. **
 *  Humans have a genetic code (the “genome”) of about 3.3 billion base pairs (6.6 gigabits or 825 megabytes). Yes, the human genome would easily fit on a typical laptop hard drive. Each human has two copies of the genome in virtually every cell of his or her body because of inheritance of one set each from both father and mother. Actually males have about 2 percent less code in one of their genomes because they only have one “X” chromosome. During growth and normal life processes cells endlessly read, and interpret the genetic codes, copy various snippets of the code, and use the copies as templates in the manufacture of proteins. **
 *  Early naturalists thought that genetic traits were inherited in more or less “analog” fashion in which offspring had an average of their parent’s characteristics. Gregor Mendel was the first to realize through extensive experiments with breeding of peas that at the lowest level, inheritance is binary, and that there is a minimum unit of inheritance now known as a “gene”. Mendel found that some traits are “recessive” and can appear in progeny even if neither parent has the trait. He also found that inheritance of a trait is independent of inheritance of other traits. **
 *  Genes are now known to be implemented as sequences of genetic code that direct specific cells to produce a particular protein at a particular time. An essentially infinite number of possible different protein molecules can be produced depending on the particular order of amino acid molecules used in their construction. The code for protein production has been “broken” so that we now know that a three-letter sequence (a //codon//) is used to specify a particular amino acid (there are 20 amino acids). For instance, the sequence GGC specifies that the amino acid glycine is to be added to a protein molecule. Start and stop codons mark the beginning and end of a protein coding sequence in a manner startlingly like modern data communications schemes. There are 64 possible codons and only 20 possible amino acids so some redundancy and error correction exists. The //regulatory// code sequences in genes that specify in which parts of the body and/or at which times a protein will be produced are much more complex and less well understood. **
 *  For humans, approximately 45,000 genes are contained in 23 separate strands of DNA known as chromosomes (46 if both sets of code are counted). The number of chromosomes is not indicative of complexity. Dogs have 78; Horses have 64. Ferns have 512. **
 * The international Human Genome Project (HGP) has completed a preliminary “draft” sequencing of the entire human genome genetic code. Sequences of a small number of other organisms such as the mouse, fruit fly, and //e coli// are completed or in work. Having the sequence is very different from understanding what it means. **
 * Mendelian Genetics is somewhat like Newtonian Physics. Eventually scientists noticed subtle deviations from the inheritance model predicted by Mendel. Specifically, inheritance of certain traits was not completely independent of other traits. We now know that inheritance of traits will be independent only if they are carried by different chromosomes and that the probability of jointly inheriting traits carried by the same chromosome is proportional to the physical distance between the two genes on the chromosome. Extensive inheritance studies have resulted in maps of the genome showing the approximate location of some trait genes and human genetic disease genes on specific chromosomes. This information can eventually be combined with the detailed sequence data to disclose the genes which (when incorrect) are responsible for genetic diseases. There are an estimated 3000 different human genetic diseases. **

 Gene Logic
= Origin of Life on Earth = =Theory 1 - Life Appeared Spontaneously = = Life Evolved from Simpler Organisms = = Its Unknowable = = It Came from Outer Space =
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> The genetic code has been compared to a blueprint specifying the design of an organism. In fact the genetic code specifies not only the design of the organism but provides for the mechanisms needed to “read” the code and manufacture the components of the organism as well as specifying the procedures needed for the life processes of the finished organism. Simple organisms are completely defined genetically. Each tiny nematode worm has exactly 958 cells. Humans, on the other hand, have trillions of cells and less than 100,000 genes so the genetic code is more of a general plan. For example, major blood vessels are genetically specified. Everybody has an aorta. But minor blood vessels grow where needed according to genetically defined rules. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> Although all the somatic cells in an organism contain the complete genetic code, in any given cell only a relatively few genes are active. The difference in the genes that are active determines the difference between, say, liver and brain cells. A complex gene logic determines //when// and //where// a particular gene will be “turned on”. The gene logic can accommodate varying amounts of //positional// detail. The eye, which has a complex structure in which adjacent cells can be very different, presumably requires many genes to implement a relatively small structure. The femur is much larger but much less complex and requires less genetic information. The gene logic also controls //when// various activities will take place. Cells divide rapidly in growing organisms but do not divide in adults unless needed to replace dead or discarded cells. (Cancer involves a major breakdown in the gene logic in which cells grow in both an inappropriate position and at an inappropriate time. Cancer is thought to require multiple mutations, some of which can be inherited.) **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> The gene logic is implemented using //signaling proteins//. That is, genes can control the production of proteins which are actually the building blocks to produce muscle and other structural components in growing cells but can also control production of other proteins which are logic signals. These logic signals can then be received by other genes and determine whether those genes are activated. Some logic proteins are long range in that they can travel through essentially the entire organism (think insulin). Other shorter range signals appear only near their point of origin, possibly only immediately around the cell in which they are generated. Since genes can both generate and detect signaling proteins, many genes can implement a very complex logic. The positional logic framework which governs where in the body specific types of cells are found is an example of a “boot-strap” problem. The logic framework itself has to be constructed as the organism grows from a one-cell fertilized egg to an adult. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">A mutation occurs when the genetic code in a cell is altered such that descendent cells formed by division of the altered cell also have the altered DNA. If the mutation occurs in the chain of cell division between the original fertilized egg and reproductive (sperm or egg) cells (the //germ line//), then the mutation can be passed to progeny. Many other mutations presumably have no effect because they occur in genes that are never activated in the descendents of the affected cells. (A mutation in a gene that was only active in the brain would have no effect if it occurred in the line of cells that were to form a leg, etc) **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> Evolution takes place by means of mutations which affect the germ line. Often a mutation results in loss of some essential function and is therefore fatal to progeny and not passed on to living descendants. Sometimes the mutation results in an evolutionary advantage and therefore may eventually become universal in descendants. Sometimes mutation results in characteristics which are different (such as a red eye color in a species that previously had only brown eyes) but confers no particular advantage or disadvantage and so becomes common but not universal in descendants. Higher organisms also have extensive non-functional sections in their genetic code. Mutations in the non-functional parts of the code would have no observable effect on the organism and therefore would be passed to descendents. Since the rate at which mutations occur should be relatively constant, differences in non-functional code can be used to determine the time since two individuals shared a common ancestor. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> The HGP indicates that the human genome contains about 50 percent apparently non-functional code much of which consists of many repetitions of simple sequences such as ..ATATATATATAT…which clearly have little or no information content. Some of the repeat sequences are known to be necessary synchronization patterns such as the sequences at the beginnings and ends of chromosomes. The purpose, if any, of other repeat sequences is unknown. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">So, what does all this have to do with the origin of life? **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">The genetic code represents an historical record of the development of the organism with an extraordinary amount of detail (825 megabytes is a lot of detail!). An organism which shares significant code sequences with another organism very likely has a common ancestor. By looking at changes in non-functional DNA we can estimate the time since that ancestor lived. By comparing genomes we can construct a “family tree” of life on Earth. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Based on data from the HGP and other sources we can say things like the following: **
 * **<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">All humans are descended from a single individual who lived about 270,000 years ago. **
 * **<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Humans and New World monkeys share an ancestor which lived about 7 million years ago. **
 * **<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Humans and mice share a common ancestor which lived about 50 million years ago. **
 * **<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">All life on earth is thought to be descended from an original primordial single cell organism which lived about 3.5 billion years ago. **
 * **<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">The Earth was formed about 4.5 billion years ago but was probably incompatible with life until perhaps 3.8 billion years ago so life apparently appeared relatively quickly. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> As more genetic code data is available on various other organisms and as analysis of differences and similarities of codes progresses the entire family tree of life on earth will eventually be developed and more will be known about the characteristics of the primordial organism. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> SO, where did that original primordial organism come from? **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">There seem to be several schools of thought. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Some scientists believe that life arose spontaneously from available materials present on the early Earth. In fact, experiments have been conducted in which air, water, carbon dioxide, methane, and common minerals were “cooked” in the presence of energy sources such as heat, sunlight, and simulated lightning to see if life or precursors of life would appear. Indeed, organic “building blocks” such as amino acids did appear. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">But it is a very, very long way from amino acids to a life form. The genetic work indicates that the complexity of genetic codes doesn’t track that well with the apparent complexity of the organism and that even very simple organisms have quite complex genomes. The simplest known living thing is the microbe mycoplasma genitalium which causes human non-gonococcal urethritus. This microbe has a genetic code of about 570,000 base pairs. Viruses are simpler but aren’t really “alive” in the sense that they cannot reproduce or grow without using the mechanisms in a living cell to do so. The bacteria //e coli// has a genetic code of about 5.7 million base pairs. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> But e coli and mycoplasma can’t live in the absence of other more complex organisms (e coli lives in animal gut, mycoplasma lives in … well you get the idea). In fact the primordial organism must have been at the bottom of the food chain, capable of synthesizing its own food from non-living material, and living without assistance from any other living organism. It could have possibly been something on the order of blue-green algae which has 3.6 million base pairs in its genetic code and is thought to be about 3.5 billion years old. Mycoplasma, bacteria, and viruses all must have “devolved” from more complex organisms in response to the availability of more complex forms to act as hosts or links in the food chain. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> The original organism had mechanisms (ability to grow, reproduce, and evolve) which led to the evolution of the diverse life forms which now exist on Earth and as indicated above this evolution is documented in the genetic codes of organisms now alive as well as in fossil evidence. But under this scenario the original organism would have had to appear by random happenstance aggregation of materials. This is somewhat like believing that because while digging you found a rock that looked like a brick, if you dug long and hard enough you would eventually find something that looked like the Sistine Chapel complete with Michelangelo’s //Creation// on the ceiling. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Some scientists feel that life originated spontaneously as a much simpler organism than any now found. A difficulty with this idea is the absence of any current examples of the simpler organism. In general, appearance of more complex organisms has not resulted in disappearance of simpler forms. We still have cockroaches. We still have fruit flies. Indeed, there is evidence of devolution. Eventually, back tracking of many living genetic codes should enable some insight into the probability of this theory. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Some scientists take the view that the origin of the primordial organism is “unknowable” meaning that not only do we not know but we are unlikely to ever know and that the subject is therefore more appropriate for philosophy or religion than science. The origin of the primordial organism is therefore the biological equivalent of the “Big Bang Theory” in Astrophysics in which astrophysicists think the entire universe was once the size of a golf ball which then exploded to create the observed universe. They can trace observed cosmic phenomena such as galaxies, red shift, and background radiation back to the golf ball but they admit that it is “unknowable” as to how the golf ball got there. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;">Some believe that life originated elsewhere in the universe and was then somehow distributed. This doesn’t have to mean biological contamination of the early Earth by space travelers flushing their ballast tanks. It could be that life was distributed via simple frozen or sporelated organisms carried by fragments of a destroyed planet or ejecta blasted into space by meteorite impact. Comets are known to contain water and ice and NASA thinks it has found evidence of fossilized bacteria in meteorites. DNA has been recovered from material 20 million years old. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> The possibility that life originated somewhere else in the universe (it is a Very large universe) and then came here seems to many more likely than the idea that life originated on Earth. The space theory is also less egocentric. Keep in mind that all previous “Earth is the center of the universe” theories have been disproved. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> A consequence of the space theory is that life might be widely distributed. Life might appear relatively rapidly on any planet that has appropriate conditions, at least in regions which were in a position to be seeded from the source – a sort of “universe as Petri dish” concept. In other words, if there is life on Earth, then there is likely to be life in any nearby system that has planets with appropriate conditions. **
 * <span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: left;"> Noted astronomer Fred Hoyle supports the space theory. **

taken from:http://www.azinet.com/originoflife.html

<span style="font-family: Arial,Helvetica,sans-serif;">To account for the origin of life on our earth requires solving several problems: <span style="font-family: Arial,Helvetica,sans-serif;"> A number of theories address each of these problems.
 * <span style="font-family: Arial,Helvetica,sans-serif;">How the organic molecules that define life, e.g. amino acids, nucleotides, were created;
 * <span style="font-family: Arial,Helvetica,sans-serif;">How these were assembled into macromolecules, e.g. proteins and nucleic acids, — a process requiring catalysts;
 * <span style="font-family: Arial,Helvetica,sans-serif;">How these were able to reproduce themselves;
 * <span style="font-family: Arial,Helvetica,sans-serif;">How these were assembled into a system delimited from its surroundings (i.e., a cell).

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> As for the first, three scenarios have been proposed: organic molecules
 * 1) <span style="font-family: Arial,Helvetica,sans-serif;">were synthesized from inorganic compounds in the atmosphere
 * 2) <span style="font-family: Arial,Helvetica,sans-serif;">rained down on earth from outer space
 * 3) <span style="font-family: Arial,Helvetica,sans-serif;">were synthesized at hydrothermal vents on the ocean floor

<span style="font-family: Arial,Helvetica,sans-serif;">1.
<span style="font-family: Arial,Helvetica,sans-serif;"> Stanley Miller, a graduate student in biochemistry, built the apparatus shown here. He filled it with <span style="font-family: Arial,Helvetica,sans-serif;"> He hypothesized that this mixture resembled the atmosphere of the early earth. (Some are not so sure.) The mixture was kept circulating by continuously boiling and then condensing the water. <span style="font-family: Arial,Helvetica,sans-serif;"> The gases passed through a chamber containing two electrodes with a spark passing between them. <span style="font-family: Arial,Helvetica,sans-serif;"> At the end of a week, Miller used [|paper chromatography] to show that the flask now contained several amino acids as well as some other organic molecules. <span style="font-family: Arial,Helvetica,sans-serif;"> In the years since Miller's work, many variants of his procedure have been tried. Virtually all the small molecules that are associated with life have been formed: <span style="font-family: Arial,Helvetica,sans-serif;"> One difficulty with the primeval soup theory is that it is now thought that the atmosphere of the early earth was **not** rich in methane and ammonia — essential ingredients in Miller's experiments.
 * <span style="font-family: Arial,Helvetica,sans-serif;">water (H 2 O
 * <span style="font-family: Arial,Helvetica,sans-serif;">methane (CH 4 )
 * <span style="font-family: Arial,Helvetica,sans-serif;">ammonia (NH 3 ) and
 * <span style="font-family: Arial,Helvetica,sans-serif;">hydrogen (H 2 )
 * <span style="font-family: Arial,Helvetica,sans-serif;">but no oxygen
 * <span style="font-family: Arial,Helvetica,sans-serif;">17 of the 20 [|amino acids] used in protein synthesis, and
 * <span style="font-family: Arial,Helvetica,sans-serif;">all the [|purines and pyrimidines] used in nucleic acid synthesis.
 * <span style="font-family: Arial,Helvetica,sans-serif;">But abiotic synthesis of **ribose** — and thus of **nucleotides** — has been much more difficult. However, success in synthesizing pyrimidine ribonucleotides under conditions that might have existed in the early earth has recently (**Nature** 14 May 2009) been reported.

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> This meteorite, that fell near Murchison, Australia on 28 September 1969, turned out to contain a variety of organic molecules including: <span style="font-family: Arial,Helvetica,sans-serif;"> The question is: were these molecules simply terrestrial contaminants that got into the meteorite after it fell to earth. <span style="font-family: Arial,Helvetica,sans-serif;"> Probably not:
 * ~ <span style="font-family: Arial,Helvetica,sans-serif;">Representative amino acids found in the Murchison meteorite. Six of the amino acids (blue) are found in all living things, but the others (yellow) are not normally found in living matter here on earth. The same amino acids are produced in discharge experiments like Miller's. ||
 * <span style="font-family: Arial,Helvetica,sans-serif;">Glycine || <span style="font-family: Arial,Helvetica,sans-serif;">Glutamic acid ||
 * <span style="font-family: Arial,Helvetica,sans-serif;">Alanine || <span style="font-family: Arial,Helvetica,sans-serif;">Isovaline ||
 * <span style="font-family: Arial,Helvetica,sans-serif;">Valine || <span style="font-family: Arial,Helvetica,sans-serif;">Norvaline ||
 * <span style="font-family: Arial,Helvetica,sans-serif;">Proline || <span style="font-family: Arial,Helvetica,sans-serif;">N-methylalanine ||
 * <span style="font-family: Arial,Helvetica,sans-serif;">Aspartic acid || <span style="font-family: Arial,Helvetica,sans-serif;">N-ethylglycine ||
 * <span style="font-family: Arial,Helvetica,sans-serif;">purines and pyrimidines
 * <span style="font-family: Arial,Helvetica,sans-serif;">**polyols** — compounds with hydroxyl groups on a backbone of 3 to 6 carbons such as [|glycerol] and [|glyceric acid]. Sugars are polyols.
 * <span style="font-family: Arial,Helvetica,sans-serif;">the amino acids listed here. The amino acids and their relative proportions were quite similar to the products formed in Miller's experiments.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Some of the samples were collected on the same day it fell and subsequently handled with great care to avoid contamination.
 * <span style="font-family: Arial,Helvetica,sans-serif;">The polyols contained the [|isotopes] carbon-13 and hydrogen-2 (deuterium) in greater amounts than found here on earth.
 * <span style="font-family: Arial,Helvetica,sans-serif;">The samples lacked certain amino acids that are found in all earthly proteins.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Only **L** amino acids occur in earthly proteins, but the amino acids in the meteorite contain both ** D ** and **L** forms (although ** L ** forms were slightly more prevalent).

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> This meteorite arrived here from Mars. It contained not only a variety of organic molecules, including polycyclic aromatic hydrocarbons, but — some claim — evidence of microorganisms as well. <span style="font-family: Arial,Helvetica,sans-serif;">Furthermore, there is evidence that its interior never rose about 40° C during its fiery trip through the earth's atmosphere. Live bacteria could easily survive such a trip.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Link to a discussion of the possibility of [|life on Mars] and more on the [|ALH84001] meteorite. ||

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> Astronomers, using infrared spectroscopy, have identified a variety of organic molecules in interstellar space, including
 * <span style="font-family: Arial,Helvetica,sans-serif;">methane (CH 4 ),
 * <span style="font-family: Arial,Helvetica,sans-serif;">methanol (CH 3 OH),
 * <span style="font-family: Arial,Helvetica,sans-serif;">formaldehyde (HCHO),
 * <span style="font-family: Arial,Helvetica,sans-serif;">cyanoacetylene (HC 3 N) (which in spark-discharge experiments is a precursor to the pyrimidine **cytosine**).
 * <span style="font-family: Arial,Helvetica,sans-serif;">polycyclic aromatic hydrocarbons
 * <span style="font-family: Arial,Helvetica,sans-serif;">as well as such inorganic building blocks as carbon dioxide (CO 2 ), carbon monoxide (CO), ammonia (NH 3 ), hydrogen sulfide (H 2 S), and hydrogen cyanide (HCN).

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;">There have been several reports of producing amino acids and other organic molecules by taking a mixture of molecules known to be present in interstellar space such as: <span style="font-family: Arial,Helvetica,sans-serif;"> and exposing it to <span style="font-family: Arial,Helvetica,sans-serif;"> Whether or not the molecules that formed terrestrial life arrived here from space, there is little doubt that **organic matter** continuously rains down on the earth (estimated at 30 tons per day).
 * <span style="font-family: Arial,Helvetica,sans-serif;">ammonia (NH 3 )
 * <span style="font-family: Arial,Helvetica,sans-serif;">carbon monoxide (CO)
 * <span style="font-family: Arial,Helvetica,sans-serif;">methanol (CH 3 OH) and
 * <span style="font-family: Arial,Helvetica,sans-serif;">water (H 2 O)
 * <span style="font-family: Arial,Helvetica,sans-serif;">hydrogen cyanide (HCN)
 * <span style="font-family: Arial,Helvetica,sans-serif;">a temperature close to that of space (near absolute zero)
 * <span style="font-family: Arial,Helvetica,sans-serif;">intense [|ultraviolet] (uv) radiation.

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> Some [|deep-sea hydrothermal vents] discharge copious amounts of hydrogen, hydrogen sulfide, and carbon dioxide at temperatures around 100°C. (These are not "black smokers".) These gases bubble up through chambers rich in iron sulfides (FeS, FeS 2 ). These can catalyze the formation of simple organic molecules like acetate. (And life today depends on enzymes that have Fe and S atoms in their active sites.)

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> Another problem is how **polymers** — the basis of life itself — could be assembled. <span style="font-family: Arial,Helvetica,sans-serif;">This has led to a theory that early polymers were assembled on solid, mineral surfaces that protected them from degradation, and in the laboratory polypeptides and polynucleotides (RNA molecules) containing about ~50 units have been synthesized on mineral (e.g., clay) surfaces.
 * <span style="font-family: Arial,Helvetica,sans-serif;">In solution, [|hydrolysis] of a growing polymer would soon limit the size it could reach.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Abiotic synthesis produces a mixture of ** L ** and ** D ** enantiomers. Each inhibits the polymerization of the other. (So, for example, the presence of ** D ** amino acids inhibits the polymerization of ** L ** amino acids (the ones that make up proteins here on earth).
 * <span style="font-family: Arial,Helvetica,sans-serif;">[|Link to a discussion of enantiomers.] ||

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> All metabolism depends on enzymes and, until recently, every enzyme has turned out to be a protein. But proteins are synthesized from information encoded in DNA and translated into mRNA. So here is a chicken-and-egg dilemma. The synthesis of DNA and RNA requires proteins. So <span style="font-family: Arial,Helvetica,sans-serif;"> The discovery that certain RNA molecules have enzymatic activity provides a possible solution. These RNA molecules — called ribozymes — incorporate both the features required of life: <span style="font-family: Arial,Helvetica,sans-serif;"> <span style="font-family: Arial,Helvetica,sans-serif;">While no ribozyme in nature has yet been found that can replicate itself, ribozymes have been synthesized in the laboratory that can catalyze the assembly of short oligonucleotides into exact complements of themselves. The ribozyme serves as both <span style="font-family: Arial,Helvetica,sans-serif;">(The figure is based on the work of Green and Szostak, **Science** **258:**1910, 1992.) <span style="font-family: Arial,Helvetica,sans-serif;"> In principal, the minimal functions of life might have begun with RNA and only later did <span style="font-family: Arial,Helvetica,sans-serif;"> Several other bits of evidence support this notion of an original "RNA world":
 * <span style="font-family: Arial,Helvetica,sans-serif;">proteins cannot be made without nucleic acids and
 * <span style="font-family: Arial,Helvetica,sans-serif;">nucleic acids cannot be made without proteins.
 * <span style="font-family: Arial,Helvetica,sans-serif;">storage of information
 * <span style="font-family: Arial,Helvetica,sans-serif;">the ability to act as catalysts
 * <span style="font-family: Arial,Helvetica,sans-serif;">[|Link to a discussion of **ribozymes**.] ||
 * <span style="font-family: Arial,Helvetica,sans-serif;">the template on which short lengths of RNA ("oligonucleotides" are assembled following the rules of base pairing and
 * <span style="font-family: Arial,Helvetica,sans-serif;">the catalyst for covalently linking these oligonucleotides.
 * <span style="font-family: Arial,Helvetica,sans-serif;">proteins take over the catalytic machinery of metabolism and
 * <span style="font-family: Arial,Helvetica,sans-serif;">DNA take over as the repository of the genetic code.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Many of the cofactors that play so many roles in life are based on ribose; for example:
 * <span style="font-family: Arial,Helvetica,sans-serif;">[|ATP]
 * <span style="font-family: Arial,Helvetica,sans-serif;">[|NAD]
 * <span style="font-family: Arial,Helvetica,sans-serif;">FAD
 * <span style="font-family: Arial,Helvetica,sans-serif;">coenzyme A
 * <span style="font-family: Arial,Helvetica,sans-serif;">[|cyclic AMP]
 * <span style="font-family: Arial,Helvetica,sans-serif;">GTP
 * <span style="font-family: Arial,Helvetica,sans-serif;">In the cell, all deoxyribonucleotides are synthesized from ribonucleotide precursors.
 * <span style="font-family: Arial,Helvetica,sans-serif;">Many bacteria control the [|transcription] and/or translation of certain genes with RNA molecules (Link to "[|riboswitches]"), not protein molecules.

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> Perhaps the earliest form of reproduction was a simple fission of the growing aggregate into two parts — each with identical metabolic and genetic systems intact.

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> To function, the machinery of life must be separated from its surroundings — some form of [|extracellular fluid] (ECF). This function is provided by the [|plasma membrane]. <span style="font-family: Arial,Helvetica,sans-serif;"> Today's plasma membranes are made of a double layer of [|phospholipids]. They are only permeable to small, uncharged molecules like H2O, CO2, and O2. Specialized [|transmembrane transporters] are needed for ions, hydrophilic, and charged organic molecules (e.g., [|amino acids] and nucleotides) to pass into and out of the cell. <span style="font-family: Arial,Helvetica,sans-serif;"> However, the same Szostak lab that produced the finding [|described above] reported in the 3 July 2008 issue of **Nature** that [|fatty acids], fatty [|alcohols], and <span style="font-family: Arial,Helvetica,sans-serif;">[|monoglycerides] — all molecules that can be synthesized under prebiotic conditions — can also form lipid bilayers and these can spontaneously assemble into enclosed vesicles. <span style="font-family: Arial,Helvetica,sans-serif;"> Unlike phospholipid vesicles, these <span style="font-family: Arial,Helvetica,sans-serif;">These workers loaded their synthetic vesicles with a short single strand of deoxyguanosine (dC) structured to provide a template for its replication. When the vesicles were placed in a medium containing (chemically modified) dG, these nucleotides entered the vesicles and assembled into a strand of Gs [|complementary] to the template strand of Cs. <span style="font-family: Arial,Helvetica,sans-serif;"> Here, then, is a simple system that is a plausible model for the creation of the first cells from the primeval "soup" of organic molecules.
 * <span style="font-family: Arial,Helvetica,sans-serif;">admit from the external medium charged molecules like [|nucleotides]
 * <span style="font-family: Arial,Helvetica,sans-serif;">admit from the external medium hydrophilic molecules like [|ribose]
 * <span style="font-family: Arial,Helvetica,sans-serif;">grow by self-assembly
 * <span style="font-family: Arial,Helvetica,sans-serif;">are impermeable to, and thus retain, polymers like oligonucleotides.

<span style="font-family: Arial,Helvetica,sans-serif;">From Unicellular to Multicellular Organisms
<span style="font-family: Arial,Helvetica,sans-serif;"> This transition is probably the easiest to understand. <span style="font-family: Arial,Helvetica,sans-serif;"> <span style="font-family: Arial,Helvetica,sans-serif;"> Several colonial flagellated [|green algae] provide a clue. These species are called colonial because they are made up simply of clusters of independent cells. If a single cell of **Gonium**, **Pandorina**, or **Eudorina****Chlamydomonas** cell. Then, as it undergoes mitosis, it will form a new colony with the characteristic number of cells in that colony. is isolated from the rest of the colony, it will swim away looking quite like a <span style="font-family: Arial,Helvetica,sans-serif;"> The situation in **Pleodorina** and **Volvox** is different. In these organisms, some of the cells of the colony (most in Volvox) are not able to live independently. If a nonreproductive cell is isolated from a Volvox colony, it will fail to reproduce itself by mitosis and eventually will die. What has happened? In some way, as yet unclear, Volvox has crossed the line separating simple colonial organisms from truly multicellular ones. Unlike Gonium, Volvox cannot be considered simply a colony of individual cells. It is a single **organism** whose cells have lost their ability to live independently. If a sufficient number of them become damaged, the entire sphere of cells will die. <span style="font-family: Arial,Helvetica,sans-serif;">What has Volvox gained? In giving up their independence, the cells of Volvox have become specialists. No longer does every cell carry out all of life's functions (as in colonial forms); instead certain cells specialize to carry out certain functions while leaving other functions to other specialists. In Volvox this process goes no further than having certain cells specialize for reproduction while others, unable to reproduce themselves, fulfill the needs for photosynthesis and locomotion. <span style="font-family: Arial,Helvetica,sans-serif;"> In more complex multicellular organisms, the degree of specialization is carried much further. Each cell has one or two precise functions to carry out. It depends on other cells to carry out all the other functions needed to maintain the life of the organism and thus its own. <span style="font-family: Arial,Helvetica,sans-serif;"> The specialization and division of labor among cells is the outcome of their history of [|differentiation]. One of the great problems in biology is how differentiation arises among cells, all of which having arisen by mitosis, share the same genes. [|Link to a discussion of the solution.] <span style="font-family: Arial,Helvetica,sans-serif;"> We are not certain that Gonium, Pandorina, Eudorina, and Pleodorina represent stages in the evolution of multicellular Volvox from unicellular Chlamydomonas. However, these organisms illustrate how colonial forms may have arisen from unicellular ones and multicellular forms from colonial ones. They also illustrate the subtle shift in cell relationships that occurs as one crosses the uncertain boundary between colonies of independent cells and organisms constructed of many interdependent, differentiated cells.

<span style="font-family: Arial,Helvetica,sans-serif;">
<span style="font-family: Arial,Helvetica,sans-serif;"> The 3 kingdoms of contemporary life — [|archaea], [|bacteria], and [|eukaryotes] — all share many similarities of their metabolic and genetic systems [[|Link]]. Presumably these were present in an organism (or organisms) that were ancestral to these groups: the "LUCA". Although there are not enough data at present to describe LUCA, comparative genomics and [|proteomics] reveal a closer relationship between archaea and eukaryotes than either shares with the bacteria. (Except, of course, for the mitochondria and chloroplasts that eukaryotes gained later from bacterial endosymbionts [[|Link]].)

<span style="font-family: Arial,Helvetica,sans-serif;">Creating Life?
<span style="font-family: Arial,Helvetica,sans-serif;"> When I headed off to college (in 1949), I wrote an essay speculating on the possibility that some day we would be able to create a living organism from nonliving ingredients. By the time I finished my formal studies in biology — having learned of the incredible complexity of even the simplest organism — I concluded that such a feat could never be accomplished. <span style="font-family: Arial,Helvetica,sans-serif;"> Now I'm not so sure. <span style="font-family: Arial,Helvetica,sans-serif;">Several recent advances suggest that we may be getting close to creating life. (But note that these examples represent laboratory manipulations that do not necessarily reflect what may have happened when life first appeared.) <span style="font-family: Arial,Helvetica,sans-serif;"> Examples: <span style="font-family: Arial,Helvetica,sans-serif;"> In 2008, scientists at the J. Craig Venter Institute (JCVI) reported (in **Science** 29 February 2008) that they had succeeded in synthesizing a complete bacterial chromosome — containing 582,970 base pairs — starting from single deoxynucleotides. The entire sequence of the genome of Mycoplasma genitalium was already known [[|Link]]. Using this information, they synthesized some 10,000 short oligonucleotides (each about 50 bp long) representing the entire genitalium genome and then — step by step — assembled these into longer and longer fragments until finally they had made the entire circular DNA molecule that is the genome. <span style="font-family: Arial,Helvetica,sans-serif;"> Could this be placed in the cytoplasm of a living cell and run it? <span style="font-family: Arial,Helvetica,sans-serif;"> The same team showed in the previous year (see **Science** 3 August 2007) that they could insert an entire chromosome from one species of mycoplasma into the cytoplasm of a related species and, in due course, the recipient lost its own chromosome (perhaps destroyed by [|restriction enzymes] encoded by the donor chromosome) and began expressing the phenotype of the donor. In short, they had changed one species into another. But the donor chromosome was made by the donor bacterium, not synthesized in the laboratory. However, there should be no serious obstacle to achieving the same genome transplantation with a chemically-synthesized chromosome and we may hear about this soon. <span style="font-family: Arial,Helvetica,sans-serif;"> So stay tuned!
 * <span style="font-family: Arial,Helvetica,sans-serif;">The ability to created membrane-enclosed vesicles that can take in small molecules and assemble them into polymers which remain within the "cell" (as [|described above]).
 * <span style="font-family: Arial,Helvetica,sans-serif;">The ability to assemble functional ribosomes — the structures that convert the information encoded in the genome into the proteins that run life — from their components.
 * <span style="font-family: Arial,Helvetica,sans-serif;">**Assembling and Swapping Genomes.**

<span style="display: block; font-family: Arial,Helvetica,sans-serif; text-align: right;"> //taken from:http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/AbioticSynthesis.html#Panspermia:_The_Murchison_Meteorite//