Mental map book

Wednesday, July 11, 2012

Possible start of evolution

This text is a thought experiment to prove it's at least thinkable to think how evolution started. Being a 2 year molecular biology student was enough to give background to achieve this. Its partly dedicated to these creationist that got PhD in biology and still try to prove that if they don't understand it then nobody can. I don't they are as stupid or crazy as they show but just another example of people trying to get famous with faked stupidity so they could advertise their book(s).

DNA evolution affects directly what proteins or peptides (shorter than protein molecules) they produce and work as signal molecules, receptors, structural support and transporters. They also build and break up almost everything cells can build or break up. They are all made out of at least 20 different amino acids (in rare cases bacteria have few extra amino acids) added together in one long chain. Function depends on which pattern were these amino acids assembled. Some amino acids are acidic, some basic and some are mostly non-polar.  

RNA could act as carrier of genome data like the RNA in retroviruses and also cause chemical reactions (ribozyme). RNA is also important in producing proteins in ribosomes.

Ways first amino acids could start

Creating amino acids from nonorganic compounds seems easiest part. Even clay, ice, sulfur, iron and nickel could do it.

Keto acids could turn into amino acids in presence of ammonia, iron and sulfur.
Ammonia and hydrogen cyanide that got frozen for 25 years was rechecked and they found amino acids along with nucleobases that form RNA and DNA.

Amino acids formed larger peptide molecules if they were added to iron, nickel, sulfur, carbon monoxide and hydrogen sulfide.

If nucleotides were added to montmorillonite (crystals common in clay) then they combined and formed RNA molecules up to 50 nucleotides long in 1 day.  

Pre-cellular era

Early proteins and peptides probably existed outside cells and floated around turning larger bodies of water into diluted protein mixture. If any of the randomly forming peptide or protein started to assemble amino acids then it increased likelihood that this body of water gets new proteins faster. About as likely it could form proteins that broke proteins and peptides into amino acids.  

More directed genome formation could start with large protein complexes that could have 1 channel for RNA or DNA and another channel for newly forming protein. Entire complex may change shape depending on what nucleotide was in one part and that can limit what molecule fits on top of the forming protein chain.
As even clay could form 50 nucleotide long RNA molecules then this could sometimes randomly create useful gene data. In case this RNA gave blueprint to build proteins that convert RNA data to protein then this could speed up evolution further. Useless proteins could become raw material for new proteins and as long protein biomass increased it added likelihood of something productive randomly getting created.
Possible that these clay crystals could also connect shorter RNA molecules into larger genomes with several protein plans in one large molecule or some protein may have done it.

RNA and DNA are somewhat similar and some proteins found in retroviruses (reverse transcriptases) can convert RNA into more stable DNA.

After stable DNA genome started evolution could become more stable with previous progress conserving in genome for millions of years.

This could make separate bodies of water evolve in different ways and destructive mistakes in one place (genomes with blueprints for only destructive proteins) would affect other places less likely.

This could also start formation stable metabolism with proteins turning CO2 and other small molecules into heavier nutritious molecules that wouldn't evaporate and start to make older lakes more oily or slimy with extra food accumulating.

Places where this primitive metabolism worked well proteins could have more energy to build more food faster and get more stores for winter or droughts (dry proteins usually don't work (excluding dry proteins in hair, skin and other connective tissue) but water can reactivate their chemical activities). Plus backup also helped to survive times where maybe more was broken up than built.

Start of cells

Cells could form if membrane lipids (mostly fats) happened to surround important proteins and genomes. If early "primordial soup" produced fat then there would probably tons of it around anyway with many tiny fat bubbles floating around thanks to waterfalls or breaking waves. Simple stiff proteins could support the fat bubble from inside.

Fat soluble molecules could get inside and be used by proteins that were there. Possible these early cell could anchor nutrient inside cell by adding phosphate groups to molecules like animals cells do when they let glucose in and keep it there by reducing its solubility in fats by adding polar phosphate group (glucose-6-phosphate). This phosphate group comes from ATP that gives energy to almost all bodily activities and ATP is basically adenosine needed in RNA modified with 3 phosphate groups stuck on it. 
This addition of phosphor groups can make inside of cell much more concentrated with nutrients than ocean so it probably speeded up how fast energy could be used.

After these cells formed they could soon gather much of the nutrient so free proteins and genomes would become increasingly rare due to being used by cells.

Viruses could have formed around the same time as early cells and viruses have less parts that needed to be right. Many viruses can have less than 10 genes (like HIV) with 1 or few protein types covering the virus and its genome with few other proteins inside.

Start of multicellular organism

Development of multicellular organisms depends on which gene at what time gets to be expressed. There are regulatory areas near genes that may wait for some hormone to unlock that gene. Different cell types have somewhat different genes that they express although all cells have same DNA.

Fertilized ovum starts with RNA molecules (DNA is locked through first few cell divisions so it uses premade RNA as replacement for DNA) gathered to one side of cell so when it divides these RNAs separate unevenly and from there on different cells in embryo have different environments and unlocked genes.

Growing cell mass creates increasingly environments for cells inside and on surface of embryo. Different genes expressed at different sides and tips of this mass make those different areas grow in different ways opening bit different new genes to further change it in new directions. Small differences in how long and how fast these proteins work during formation of fetus can have snowballing effect on adult body type.

Simplified hypothetical way to get worm would be for RNA to divide into 2 groups and then have them separate due to all cells between multiply tens of cells long. Those both groups could inhibit formation of structural proteins that let neural axons grow over a meter long but at this stage these proteins are also in other cell types and muscles. So most likely they grow around cell mass avoiding 2 poles of this cell mass. Then motor proteins that make muscles move (like kinesin) can start to pull this ring of long cells tighter to squeeze cell mass longer. If these 2 inhibiting tips get further new constricting rings could form and start elongate it further. During this elongation previously round cells between these rings elongate towards most distant tips of worm due to pressure and they could turn into different muscle groups. One tip of cell mass may have more hormone to start producing sensitive brain and sensory neurons. 

Primitive navigation towards food could start with muscle cells parallel to worms body. If muscle cell on one side of body absorb glucose then they could constrict muscles on one side of body and start to drag worm towards glucose source by turning the body until its straight ahead. Then both sides of body should get equal amount of nutrients and worm could move straight without any side slower.
Negative experiences could have inhibitory effect making creature relax the side of body closest to unwanted substance while moving more actively in other directions.

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