SUPPORT DOCUMENT #42 Viruses are a tough protein coat in a crystallized state, plus DNA or in some cases RNA inside. They, like bacterial endospores, can survive for years unchanged until they are wetted and placed into contact with their particular hosts. At first I guessed that viruses may have evolved as a type of bacterial endospore - they both become dormant until the proper energy is available, they both have a hard shell, etc. But viruses also act much like bacterial plasmids, those small circles of DNA that contain additional genes in the cells of bacteria. Though plasmids do not have the crystallized shell that viruses have, they may be transferred from one bacteria into another (which seems similar to viruses), and it's not hard to conceive that plasmids once had, or could evolve to have a shell like viruses have now. (Here is a 2nd opinion from J. from sci.bio.evolution newsgroup) It is not inconceivable that plasmids evolved into viruses. Another method bacteria can become transformed is by direct uptake of DNA from the surrounding environment. It is also possible that these fragments, which usually come from lysed cells evolved into viruses. SUPPORT DOCUMENT #43 I have suggested in my Hendricks Health Theory that all life moderates/reacts to energy: IN LOW ENERGY life becomes dormant IN HIGH ENERGY life becomes active, reproduces. Lets look at bacteria for an example: IN LOW ENERGY: Endospores are bacteria in their dormant stage "They form in response to environmental signals that indicate a limiting factor for vegetative growth such as loss of essential nutrients. (Some bacteria were on a camera left on the Moon. When the next group of astronauts retrieved the camera the bacteria had survived) Endospores germinate and become vegetative cells when the environmental stress is released". Endospores formation is a mechanism of survival rather than a mechanism of reproduction. Endospore shell is the most durable shell produced in nature. (Another bacteria story: Some bacteria were revived and cultured after some 25 MILLION years of encapsilation in the guts of a bee trapped in resin - NASA) IN HIGH ENERGY: Growth rate and energy: "There is a steady increase in growth rate between the minimum and optimum temperature, but slightly past the optimum a critical thermolabile cellular even occurs, the growth rate plunges rapidly as the maximum temperature approaches" (K. Todar) Example methancoccus jannaschil grows from 60 - 90 C. It increase from 60 - 85, then plunges quickly from 85-90. SUPPORT DOCUMENT #44 In my Hendricks Health Theory (all life is energy reactor/ moderators) I suggested 3 things: 1. That a scale of the heat tolerances of different organisms seems to suggest that the earlier the life form the more tolerant it is to heat - therefore first life was probably a thermophile. 2. That methanogens may have proceeded photosynthesis (getting H2 from the atmosphere instead of getting it from water) 3. That perhaps the G-C bond preceded the A-U bond, and that the A-U bond was at first no more than a stopping mechanism for the pre-RNA G-C string. Evidence that supports this shows that "thermophiles have a high G and C content in their DNA such that the melting point of the DNA (temperature at which the strands of the double helix separate) is as least as high as the organisms maximum temperature for growth" Here's some added comment on point #1 by Stanley Friesen from sci.bio.evolution newsgroup Not necessarily. As more efficient life forms evolved they could well > have out-competed the older forms in moderate habitats, restricting the > archaic lineages to marginal habitats. > > A more recent example of this is the replacement of conifers in tropical > and temperate forests with angiosperms, largely restricting conifers to > subarctic and swamp habitats. By your reasoning above one would > conclude that conifers evolved in cold habitats. The fossil record > shows this to be false. > > Also, one should not forget the effect of the Oxygen Revolution - the > cause of first great mass extinction. Somewhere around 2 to 2.5 BYA > free oxygen started to accumulate in the atmosphere, killing almost all > life forms not tolerant of oxygen, except in marginal habitats where > oxygen levels remained low. Most of the "early" life forms still > surviving are also more or less anaerobic, thus making them relictual > groups. This means their current distribution is, of necessity, > specialized. SUPPORT DOCUMENT #45 In my Hendricks Health Theory I have suggested that the key to all life is energy reaction which evolved to energy moderations, and that all life becomes dormant in times of low energy, and becomes active AND reproduces in times of high energy. Here are 2 more examples: 1 " In the arid Australian outback, the appearance of temporary ponds stimulates amphibians known as water-holding frogs to mate and lay eggs. The fast-growing tadpoles mature into adult frogs in as little as two weeks. Then, as the ponds begin to shrink, the frogs store water inside their bodies. After becoming round and bloated, they burrow deep into the mud beneath the disappearing ponds, coat themselves with mucus, and await the return of rain to reproduce once more." 2 " Tiny tadpole shrimp of the American Southwest survive in a somewhat similar way. Their eggs, lying dormant in the soil, hatch as soon as a temporary pool forms. Within a matter of weeks, the little crustaceans mature and produce a new generation of eggs. The adults die when the ponds dry up. But the eggs can endure many years of drought before hatching when it rains once again." (both from ABC's of Nature) SUPPORT DOCUMENT #46 In my Hendricks Health Theory, I've stated that all life reacts/ moderates energy, therefore life should be most active and plentiful in the tropics of the earth where conditions are wet and warm, etc. I have given examples for life on land that support this. Now for the seas: 1. Coral reefs belt around the mid section of the globe only in shallow seas that are warmer than 70 F and exposed to direct sunlight. Except for mammals and insects almost every major group of animals is represented in the coral reef habitat. 2. On a smaller scale: life is amazingly rich in the bromeliad of the tropical rain forests. The cuplike leaf bases of bromeliads, epiphytic plants of the pineapple family, etc. collect water. These mini ponds serve as homes for an amazing variety of life: insect larvae, midget crustaceans, aquatic worms, and even tadpoles of certain types of tree frogs - all this while perched high on the branches of giant forest trees. (both ABC's of Nature) SUPPORT DOCUMENT #47 In my Hendricks Health Theory, I have stated that all life becomes dormant in low energy. Most of the time this corresponds to low temperature, but not always. Here is an example: ESTIVATION: "It is the hot weather equivalent of hibernation. In African marshes and elsewhere tortoises, frogs, lungfish, and catfish burrow into the mud before it dries up and cakes, and remain there until released by the wet season rains." (ABC's of Nature) In estivation then the low energy is loss of water, and the dormant stage ends when water returns in the form of rain. SUPPORT DOCUMENT #48 Where did life begin? Here are some possible clues: 1. It needed water. So look to the seas. Today the most abundant form of life is plankton, the uncountable hordes of tiny drifters that swim only feebly or float passively with the currents in the SURFACE LAYERS OF THE SEA. Besides the plankton, the algae, on which all other ocean life depends, thrives best IN COASTAL SEAS. There the water is richest in dissolved mineral nutrients, the natural fertilizers that support vigorous plant growth ... the minerals are washed down to the sea by rivers flowing off the land. Also vertical currents, called upwellings, carry minerals from ocean depths to the surface. (ABC's of Nature) Also note that Archaens are quite abundant in the plankton of the open sea. (Note the top of the sea is best for receiving sunlight for photosynthesis) 2. Tides turn rocks into sand, (as well as throw nutrients onto a beach) and microscopic creatures spend their lives in the thin film of seawater filling the spaces between grains of sand. Animals in the tidal zone, alternately washed and exposed by the sea, are most active when water covers their homes. The inshore area, always wet is the most hospitable to life. 3. Tide Pools. A surprising variety of plants and animals manage to cope with the changing conditions in tide pools. On summer days these pools can become as warm as bathwater, and in winter freezing cold. Evaporation can make it briny, sudden downpours rain can sometimes freshen it too much for sea creatures. (These tide pools may have acted as cauldrons stirring up first life chemical processes like a pot on a stove. With the tides bringing in new 'soup' and carrying out the 'waste' as it leaves - thus the tide pool becomes the 'skin' of first life). Also this more extreme heat change from high tide and low - day and night, may have supplied the necessary energy to jump start life processes. 4. Near the high-water mark on rocky coasts there is usually a stripe of blue-green algae (the oldest fossil known is cyanobacteria, blue-green algae at 3.5 billion) 5. Thermophiles live in hot springs or even smokers at the bottom of the sea (though they may have been pushed into these corners due to the build up of oxygen in the atmosphere) (note: while we are on tide pools - further evidence that life becomes dormant in low energy, and active and reproduces in high: "Animals in the tidal zone, alternately washed and exposed by the sea, are most active when water covers their homes ... When the food-laden waters recede, most burrowers shut down operations." (most facts from ABC's of Nature) So in summary, first life probably began at the top of the sea AND/OR at the top of the sea near the shore AND/OR at the top of the sea in tide pools. SUPPORT DOCUMENT #49 Let's look at the makeup of a procaryotic Cell and see if there might be some clues to how life began: The cell has 3 basic parts: appendages, cell envelope, and cytoplasmic region. APPENDAGES: flagella / (predominant chemical composition:) protein pili / protein CELL ENVELOPE: capsules / polypeptide (?) cell wall / murein plasma membrane / phospholipid and protein CYTOPLASMIC REGION: ribosomes / RNA and protein inclusions / highly variable chromosome / DNA plasmid / DNA (www.bact.wisc.edu/bact303/structure) Now look at the GROWTH FACTORS for bacteria 1. purines and pyrimidines for synthesis of nucleic acids DNA & RNA 2. amino acids for synthesis of proteins 3. vitamins needed as coenzymes and functional groups of certain enzymes (enzymes being protein and/or RNA in some cases) Now look at Viruses: protein coat (capsid) (sometimes enclosed within a membrane) and DNA or RNA What stands out is that just about everything is either protein or RNA! (The DNA probably evolved out of the RNA) Matter of fact the molecular composition of E. Coli , under conditions of balanced growth = PROTEIN 55% RNA 20% Those 2 together add up to 75.5% or 3/4ths of the total. The clue for first life then is PROTEIN & RNA. In all life there are 2 groups the genotype - the information center that directs the growth and activities of the other side, the protein-based phenotype. That suggests that RNA (or more likely pre-RNA G-C bonds) is the genotype, PROTEIN ( or more likely amino acids) is the phenotype. SUPPORT DOCUMENT #50 In a previous post I showed how bacteria is 75% Protein and RNA, and suggested that that was a clue to first life. Let's start from Protein and RNA (actually DNA/RNA) and evolve backwards and see what happens: 1. Protein and DNA/RNA. It is likely that the RNA came before DNA. 2. Protein and RNA. RNA has some catalytic properties so it may have acted as an enzyme to create the protein. 3. (Before protein is peptide bonds, and before peptide bonds is amino acids so:) Amino Acids and RNA 4. But I have suggested that RNA evolved out of G-C bonds and that the A-U bonds came later, and at first were only stop and start codons. So Amino Acids and G-C strings. Now for some wild speculation: How could amino acids and G-C only-RNA do anything to start life? Perhaps amino acids were the first 'food', and G-C the first enzyme that ate the first 'food'. Then G-C = RNA 'ate' amino acids and linked them up into peptide and protein strands. And somehow all this string began to act like a long string of wire that curves on itself (like RNA does) and produces an empty ball shape with one of the enzymes (protein and RNA could both act like enzymes supporting each other) at the end of the wire inside the ball shape (bacteria have a protein shell with the chromosome inside, attached to the plasma membrane ). Now our enzyme in the center of a protein shell is protected somewhat yet still the water outside flows in and through. Somehow tides make this cell hot and dry during the day (?) and wet and cool during the night (?) and this changing of daily temperature and energy pushes the 'whatever we got' forward, (replicating by either the fragile strand/ball breaking into 2 segments, or the high heat of day melting the bond into 2 strands and in the cool of night re- bonding both single strands into 2 new strands that curve into cell like balls), then amino acid food is gone so 'whatever we got' survives by eating H2 and Co2 or ... SUPPORT DOCUMENT #51 Here are some ideas that may have been factors as to why dinosaurs died out and mammals survived. First of all when we speak of mammals we probably are more accurate to say rodents which account for about half of the species of mammals and may well outnumber all the rest of mammals. They are small and thanks to their size each individual needs little food to survive when larger animals might starve. They can hid just about anywhere. They reproduce quickly: a house mouse may begin breeding five weeks after birth and have more than 50 young a year. They can adopt to diverse conditions and eat almost anything - seeds, buds, shoots, fruits, nuts, insects, etc. Rodents also store food for the winter. They also have all the advantages of being warm-blooded. They live from the arctic to tropics, desert to rain forest, mountains to lowlands; underground (thus escaping any drastic atmospheric changes - some mammals in family groups occupy the same burrows for generations - ex. American Gophers) in trees, in water, etc. Often on island environments - giantism occurs (this is dinosaurs on a vastly smaller scale). Species with no known predators evolve to very large sizes: elephant birds of Madagascar and moas of New Zealand stood more than 10 feet tall. Giant tortoises still live on the Galapagos and on certain islands in the Indian Ocean. Certain plants from sunflower relatives to cacti may grow to tree size. Stowaway rats who jump ship onto such an island - with no known mammal predators can quickly overrun the island. And finally some mammals eat reptile eggs: raccoons and foxes - ex. crab-eating fox of S.America enjoys turtle eggs. The dinosaurs also may have had to compete with rodents for the foods they ate. All this suggests that a. the smaller more versatile rodents had many more ways to adopt to changes than the dinosaurs, and in the toughest of times the rodents may have eaten not only the foods that the dinosaurs needed to live but the dinosaur eggs thus further reducing the number of dinosaurs. (ABC's of Nature) Here are some related comments by Arne, from 'sci.bio.evolution' newsgroup. > A cigar to you, Tom ! > Yes, the dinosaurs were literally eaten up. > Whether they were rodents "per se" is not really known. > What DID exist were placental mammals and in these we can see a > couple of traits which made them into such formidable enemies of the > large reptiles. > First, placental mammals are such because their pelvis is a closed > ring. This means that they can't lay an egg big enough to support the > development of their young; it would not fit through the birth canal. So > we allow our young to mature internally until such time as they can > leave the fetal position, "uncoil", and be extruded. Marsupials did not > quite reach the point of a joined pelvis so they give birth to what are > essentially embryos. > The BIG benefit of the closed pelvic ring is as a stable platform > for the rear legs. Look at the way that birds or marsupials ambulate. > The swinging leg twists the entire 2-part pelvis with each step. > kangaroos get around this by launching with both feet at once. > But "us" eutherians can push off with one rear leg and still walk ( > or RUN ! ) in a straight line. A duck waddles because of their pelvis. > Compare that to the smooth walk or run of a cat. > The big ostrich has a sort of "windmill" gait, very like what is > shown in cartoons. > Placental mammals can jump, walk, stalk, leap, and run in straight > lines. Our closed pelvis is mechanically a better platform than the > 2-part pelvis. > And having the babies inside of us for so much of their development > means that we are not so dependent on a stationary nest. > Most birds which nest in trees lay fewer eggs than the > ground-nesters. > The ground-dwelling dinosaur, no matter how fierce, still had to > defend it's eggs and young during the day AND during the night. > Night is when most mammals hunt and scavenge. > If the last dinosaur had a flashlight, clicking it on at midnight > would have shown the relections of hundreds of red eyes. These hungry > little mammals loved nothing better than a nice omelet. > Screw the asteroid. We ATE UP the dinosaurs. > Why do you think most birds nest in trees??? > Arne SUPPORT DOCUMENT #52 When protein is actively being manufactured in the cell, there always seems to be a good deal of RNA in the vicinity. Here's some more possible clues to first life: 1. Strips of RNA made primarily of G-C combinations are stronger than A-U combinations. This would suggest that RNA should be made entirely of the stronger G-C bond. That isn't so. Somehow each bond must be stronger in certain conditions. Dr. Manfred Eigen found that in a particular soup (primordial soup) a particular sequence of nucleotides would tend to emerge. And though not always the identical sequence they are almost identical. What this suggests is that EITHER/OR the mixture of the soup determines the sequence OR the temperature of the mixture OR wet or dry determines the sequence OR any combination of these 3. (Also note that the charges holding the G-C and the A-T bonds are slightly different and a weak electrical current will separate the 2.) MIXTURE: adding lead to the mix and RNA chains can form up to 40-50 units. Adding zinc helps hold together chains of up to 150 units. TEMPERATURE may be a key. When it's hotter all chemical processes speed up. Perhaps the G-C bond binds strongest at a certain temp. and the A-U bond binds strongest at another temp. Perhaps sequence of amino acids is determined by temperature. Ex. G-C bonds best as temperature increases and A-U as it decreases. Thus in daytime Sun the G-C bonds best, when night comes the A-U bonds best. WET OR DRY may be a key. Sydney Fox got proteinoids by heating and drying amino acids. 2. Let's say one way or another we now have short strands of RNA. At 150 nucleotides there exists enough information in the sequence to code for very simple protoenzymes. Yet this RNA is seldom stable. Eigen suggests that 2 strands of RNA act as co-enzymes one helping to feed the other. This could work if each acted under different conditions. Example: enzyme "A" works at soup mixture AA, temp AA, and/or wet dry conditions AA, while enzyme "B" works at soup mixture BB, temp. BB and/or wet/dry conditions BB. That would suggest that while A works the other, B stabilizes/rests, then they switch as the conditions switch. (Info from BluePrints, Solving the Mystery of Evolution) SUPPORT DOCUMENT #53 This is a first draft of a possible explanation for the beginning of life. Specifically 1. raw material into RNA and 2. RNA replication. Key Clue: To have life you DON'T need a mechanism for energy. You DO need a mechanism to stop energy. A. The first life metabolism is outside of the chemical soup. It is the sun and/or the heat of the earth and/or ?. At first the chemicals in our soup can only react to energy. And they can react to it in only 2 ways 1. become less chemically active when energy/heat is low. 2. become more chemically active when energy/heat is high (all chemical reactions speed up as temperature increases - up to a point). Earth is hot during the day. Perhaps water boils in the late afternoon at the hottest point of the day. But at night it cools back to the range of temperature of water in liquid form. We have a tide pool - a basin in rock. In high tide the basin fills up with water. In low tide some or much of the water boils away. Then high tide replenishes it. We have chemicals in our soup kettle. (If radiation is a problem, it's shielded by a rock ledge or foam on the sea or ? . The chemicals include run-off minerals from the rock and/or sea streams that take nutrients from the bottom of the sea and bring them to the shore. The basin acts as the first cell wall and loosely protects the pre-life chemicals within it. In our kettle is 1. amino acids, 2. purines and pyrimidines (all possible)... (to be continued in post 2) SUPPORT DOCUMENT #54 Please read the post, First Life, a very rough draft, part one first (Support Document #53). Let's continue: Step 1 raw material into RNA Step 2 RNA replicates. Step 1. Day breaks and soon our soup kettle begins to boil. There is one bond that stands out from the rest, the G-C bond (G=Guanine nucleotide, C= Cytosine nucleotide. Its noted as a very strong bond) The G-C bases are one of the pair of bases of RNA (the other being A=Adenine nucleotide, and U=Uracil nucleotide). During the day they connect up and form strings of G-C bonds. They are sturdy chemical bonds, but not sturdy enough. Each afternoon, the hottest time of the day, the G-C bonds melt from the heat and whatever was forged together is broken apart. Evolution enters the equation. One day the G-C bond has an interloper, one or more A's replaces a G (both purines), and/or U replaces a C (both pyrimidines). And something miraculous happens. This slows down the melting process and the G-C bonds do NOT melt at the hottest time of the day. They survive the day - with a bond that is longer and stronger and more 'fit' to survive. This retardation of the melting point of the G-C bond is enough to keep our 2 bases G and C, plus the 2 stop bases A and U progressing. (and the stop codons are mostly A's and U's - also see my post on why there are duplicate codons for many amino acids). They progress in 2 directions: RNA - as enzyme and as protein maker (then evolve into other properties) and PROTEINS (synthesized by the RNA) Replication comes about whenever the heat DOES melt/divide the 2 strings of G-C and A-U bases - much like DNA divides now. Though each day the strings that survive become longer and longer before they melt/divide from the heat. Over time the pre-life that survives evolves to more and more control when this division takes place. HOW TO TEST: We should be able to test this theory and see if any of this works. CLUE First note that there are wide variations in the ratio of A-U to G-C in various organisms and this must be explained somehow. This aspect should be studied. Take a kettle of purines, pyrimides (mostly G and C), minerals, etc. Begin to heat (sun radiation? earth heat? both?). The G-C bond should 1st bind together. Then as the heat continues to rise, it should break apart at its melting point. Then cool the mixture down and repeat (This experiment is similar to that of Sydney Fox who made proteinoids) Add more A and U. The A-U bond should act as a catalyst and slow down or inhibit this melting point. (Also the water in the kettle may have to be boiled away so that the contents that are left, are dry, then re-wet as they cool.) If any of this produces results, use the results as clues on how to proceed. What is important here is that now we may now have the basics of energy reaction/moderation that I've outlined as the key to life: In LOW ENERGY the chemical processes slow down in HIGH ENERGY the chemical processes speed up BUT NOW we have a 'stop' mechanism that keeps the pre-life from melting. In it's place is a type of controlled melting that evolved to replication. We now have metabolism and replication (plus a mechanism for RNA and PROEINS, plus the beginning of energy moderation) ... maybe.