Thursday, June 12, 2014

Darwinism, Creationism and The Seed

The Darwinist contention on life's' origins is diametrically opposed to the Creationist thesis. Creationists proffer that each kind of life was designed separately. Each extant type of life was individually made, in a period of seven days, six thousand years ago. The claim is that no two types are related, and no new types have been made since then. They are adamant the different forms of organisms like Birds, Reptiles, Mammals, etc. are absolutely unrelated and may not form a single common family tree.

Both Darwinist and Creationist agree that Individuals of a given type can be related, forming a single common family tree. For example individuals with the same grandmother are related. First cousins are second generation descendants of the same grandparent. Each cousin's parent is a first generation “copy” of the 1st cousins' grandma. 1st, 2nd, 3rd and 4th cousins are her 2nd, 3rd, 4th and 5th generation descendants. Grandma above is the "mother" of these descendants. 4-great-grandmother, 3-great-grandmother, 2-great-grandmother, great-grandmother, grandmother, mothers, sisters, aunts, first, second, third, fourth and fifth cousins are related by common family roots. When grandparents, parents and aunts (sadly) pass away the generations of cousins may not have been told of their family ties. A Creationist and a Darwinist would concur that all the different kinds of people alive today are literally cousins. We are just unaware of our common genealogy.


Creationist adherents insist, arbitrarily, that different types of family trees are unrelated; family relationships are forbidden beyond the borders of the fixed family types. They insist the different family trees are separated by permanent walls. The Darwinist begs to disagree. We argue that genealogical history may logically extend beyond "permanently fixed" types. We insist that unique types of "family trees" are simply different offshoots from the same tree. We prove this contention by digging deep into the ancient primeval history of life, piecing the jigsaw puzzle of life  together to reveal the family ties that bind all different extinct and extant forms of life into one family tree.
Contrary to the unproven thesis of separate design of types, the Birds and the Bees, Reptiles and Mammals, all Flora and Fauna, and all other currently existing forms of life are descendants of an ancient and long forgotten "lost mother". Birds, reptiles, mammals, monkeys, mice and men are all cousins.


Evolution by Natural Selection contends that, as an organism thrives to sustain its survival, growth and development, by adaptive changes to new environments, it radiates into a myriad of different life forms. In so doing, branches grow on the Tree of Life.


This contention implies that the Tree of life had fewer branches in the past. Taken to its logical conclusion then, eons ago, it must have been a mere seed. How on Earth  did its seed arise? Earth's accumulation of complex chemistry was the basis for a living seed to arise. The tale I am about to tell is based on a true life story; names have been changed to protect the innocent. . .

About three and half to four billion years ago, after hundreds of millions of years of Earth chemistry development, the nucleic acid molecules, ribonucleic acid (RNA), and deoxyribonucleic acid (DNA) molecules emerged. As I started to say, Earth had the potential to bear The Seed of The Tree of Life. This potential laid in DNA and RNA. What makes RNA and DNA especially unique among all other molecules is that they just happen to have the inherent property of replication, or self-cloning. That is, they can copy themselves. Their method of replication is called "complementary base pairing". Let me explain:



RNA and DNA, the two types of nucleic acid molecules, are extremely long chains of four different types of "beads". DNA beads are Guanine (G), Cytosine (C), adenine (A) and Thymine (T); the first three of the DNA beads are also found in RNA but the fourth DNA bead is replaced by Uracil (U) in RNA. In both DNA and RNA, G will only bond with C to make the pair, GC. In RNA, A will only pair up with U (AU). In DNA, A will only pair with T (AT). For example, an RNA strand:


GGGUUUUUUGACCAUGA


Will pair up thus:

The G's will only attach C's; the U's, A's, creating the RNA strand:

              CCCAAAAAACUGGUACU

Then          CCCAAAAAACUGGUACU



Will do the same, creating the RNA strand:



              GGGUUUUUUGACCAUGA

This is an identical copy of the original RNA strand.
In RNA, GC and AU are exclusive twosomes, or they are the complement of each other only. Similarly, in DNA, GC and AT are exclusive twosomes.

 




The chemical nature of G, C, A, U AND T beads is partly alkaline and partly acidic. Another name for alkaline is "base". Complementary base pairing simply means the base portion of G will exclusively pair up only with the base portion of C, and the base portion of A will exclusively pair up only with the base portion of U (or T in DNA). The acid part (phosphoric acid) of each bead (called a nucleotide) has a sugar component. RNA beads have "ribose" sugars; DNA nucleotides have "deoxyribose" sugars. The sugar-phosphate portion of each nucleotide forms the back bone of the RNA and DNA molecules they form when they string together. The details of the backbone is not shown in the above RNA strands. A piece of a DNA backbone made up of deoxyribose sugar and a phosphate, and a piece of RNA backbone made up of ribose sugar and a phosphate attached to their base are illustrated below:




































The RNA nucleotide molecule above is just a tiny portion of a hugely long molecular strand of, at minimum, two thousand beads, consisting of a mix of these four nucleotides.


The backbone is made up of a ribose sugar molecule and a phosphoric acid molecule that attaches either a C, G, A or U. When an RNA strand forms (or DNA double-strand forms) for example with its back bone showing you have:




...SugarAcid-SugarAcid-SugarAcid-SugarAcid...

      |         |         |        |         

      A         U         U        G 






        

But whereas RNA is single-stranded, DNA is double-stranded (double-helix because its two strands are braided together in the shape of a figure "8"):




::dSugarAcid-dSugaracid-dSugarAcid

      |          |         |

      T          T         C                

      A          A         G       
::dSugarAciddSugarAciddSugarAcid   



                

                                 

The back bone of DNA, as you can see, has a slightly different ribose sugar, called deoxyribose sugar (the difference is that ribose has one more oxygen atom than deoxyribose). Threesomes of RNA nucleotides are called triplets, or a CODON. Each codon is the genetic code word for a specific amino acid. For example the genetic code word for the amino acid Serine is UCG, and GCA is the code word for Alanine. There are twenty amino acids; each is paired up with a specific codon. There are sixty-four codons (more than one codon can code for the same amino acid – see the table below). A protein is a specific sequence or string of amino acids. Genes are small portions of the gigantically super long  DNA molecule (by way of comparison, if a gene or RNA strand was an inch in length, a DNA strand would be as tall as the Empire State Building). Each gene is the code for a specific protein. When a DNA molecule copy’s itself this is called replication.


When an RNA copy, called an mRNA (the "m" stands for "messenger"), is made of a gene, which is a small portion of DNA, this is transcription. The mRNA is “read”, or translated from the language of nucleic acid into amino acid language by protein synthesizers called Ribosomes. Specific "Transfer" RNA's (tRNA)transport their specific amino acids to ribosome sites where protein manufacture takes place. A ribosome attaches the specific amino acid to its codon: For example Serine is attached only to the triplet UCG, Alanine only to GCA, Glycine to GGC and so on resulting in a very long amino acid chain. This is a protein.




.... UCG GCA GAG UUC GGC....

      |   |   |   |   |

     Ser-Ala-Glu-Phe-Gly

One of the smallest proteins, hemoglobin, the oxygen-carrying protein in red blood cells, is made up of three amino acid chains, with each chain consisting of at least 144 amino acids.




The DNA molecule is a humongously huge double-stranded molecule consisting of millions of the four different nucleotides per strand.


When DNA replicates the two strands unzip from each other. Each strand acts as a template to manufacture its opposite half. Hence when DNA self copies, each half simultaneously copies its other half to give two identical clones of DNA molecules.

RNA replicates itself in two stages. In the first stage RNA uses itself as a template to create a clone that’s its negative. The original RNA strand is replicated in the second stage when the clone negative acts as its template. In life processes, RNA (mRNA) is made in one step; The mRNA is copied, or transcribed, directly from the gene in a DNA template strand.



As shown in the table above, the genetic code consists of twenty amino acids that are associated with sixty-four nucleic acid codons. Two to up to four nucleotide triplets code for a specific amino acid. For example, you can see from the table above that the triplets UUU and UUC are the only two triplets coding for Phenylanaline, while the four triplets CCU, CCC, CCA, CCG code for Proline. The only four exceptions are Tryptophan (UGG) and Methionine (AUG) with one triplet each, and Leucine (CUU, CUC, CUA, CUG, UUA, UUG) and Arginine (CGU, CGC, CGA, CGG, AGA, AGG) with six triplets each.




The genetic code, consisting OF twenty amino acids and sixty-four nucleotide codons (triplets), is universal. If you examine any protein in any organism you will discover that they are only made up of the amino acids and the Gene codons in the table above. The table shows that Tryptophan for example is only coded for by the triplet UGG. Tryptophan in any protein in any one of the millions of organism is only coded for by that one particular triplet.







It begs the question: if each type of life form, the Bird, the Reptile, the mammal, people, etc., were made uniquely, why is that not even one of them have a unique genetic code? Just as every  ethnic group developed a unique culture due to unique historical experiences, you would expect that, if each species was designed separately they would have their own unique "genetic culture". In other words, there should be different tables of genetic code for each type: one for The Bird,  another for The Reptile and a different one for mammals. What are the chances that thirty million species were lucky enough to have the identical genetic code in the table above? A miracle you say? Why is my tryptophan code, UGG, the same in every single individual organism, from a bacteria, to a whale, to an oak tree? It is no miracle, and it is no longer a mystery; there is a rational Darwinian answer. The best explanation that accounts for all the genetic and fossil record data and the observed family tree pattern of life is that a living cell that evolved the above code by Natural Selection passed it on to its descendants. All organisms share this exact same code because every single one of us is descended from this cell. This primeval cell is our common ancestor.


Life on Earth today is an unbroken chain extending back to this “Mother” of all life.

And the Life-Tale continues . . . Evolution, without its beating heart, Natural Selection, would have remained just a potential. In the absence of replicators Natural Selection would have nothing to do, and would have remained in suspended animation. With an idle Natural Selection, Evolution would not get off the ground. The Seed would not come to be without Evolution and Natural Selection. The happenstance of the molecular replicators, RNA and DNA, Four billion years ago, dramatically changed everything. The natural chemical emergence of these replicators stimulated its heart to start beating with a purpose, and Evolution awakened. The birth of the embryonic Seed of Life, with Natural Selection as midwife, would become a reality.


Self-cloning DNA established a growing colony of DNA replicators. The population was comprised of various types; AlphaDNA, Beta varieties, DNA- Ï€ and DNA~1 forms. The environment was  mainly DNA~1 friendly. These types were preferentially favored. Gradually, over many generations of selective environmental nurturing of DNA~1's and suppression of the growth of the other types, only this form continued to flourish. The others turned out maladaptive and disappeared over time. The once variety-laden DNA colony, thru Natural Selection, transformed and evolved into DNA~1. After several descendant generations, DNA~1 variants appeared due to random copying errors - subgroups DNA~1A, DNA~1H, DNA~1j, DNA~1^f, DNA~1{{5}}and DNA~1red[10]. The colony was largely made up of subgroup DNA~1A. 



A population comprised of the above DNA~1 subgroups became isolated in a new and different land. The sign to its entrance flashed “RED[10]!!. . .RED[10]!!. . .RED[10]!!. . .YOU WILL BE ASSIMILATED INTO RED[10], RESISTANCE IS FUTILE”. This region turned out to be DNA~1red[10] friendly and was not favorable to the other types in "The Lost Colony". Though the other subgroup struggled bravely to survive, slowly but surely, after preferential selection over hundreds of generations, the inevitable happened. All the other groups of "Lost Colony" failed to adapt, save one. Only the descendant lines of DNA~1red[10] were successful.


Another group from the original DNA~1 colony, "The 2nd Lost Tribe", became hopelessly trapped in a whole other country, called Death Valley Country. Except for being DNA~1{{5}} friendly, The Valley proved to be a DNA~1 "killing field". Due to Its unrelenting weeding out of all other variants, only "The Chosen Children of Death Valley", DNA~1{{5}} descendant lines, prospered. "The Tribe" was transformed and evolved into DNA~1{{5} and the land was forever known as "DNA~1{{5} country".



Suddenly an apocalyptic earthquake split the land into four pieces, and creating a deep chasm between the newly formed lands. The original DNA~1 colony was splintered into four population groups that were forever separated from each other. The isolated regions were known as The Southern Steppe, The Northern Prong, The Western FireWall and The Eastern Wings. Only DNA~1A's  were allowed to "sit" on the Steppe; all others were pushed off to their death. After fifteen hundred generations only DNA~1H's could survive the jabbings of The Prong. The FireWall scorched and blocked out all variants except favoring one, DNA~1^f. And only DNA~1j types could soar effortlessly on The Wings. Selection by each environ caused each of the four isolated colony groups to evolve into a type adapted to each specific region, weeding out and suppressing the development of the other forms.


The DNA~1red[10] and the DNA~1{{5}} colonies were more complex compared to DNA~1A. Thus, due to Natural selection, DNA evolved increasing complexity. Also six new branches of DNA evolved from DNA~1: DNA~1red[10],  DNA~1{{5}}, DNA~1A, DNA~1H, DNA~1j and DNA~1^f.







Eventually Natural Selection bred DNA/RNA cooperatives. After hundreds of millions of years of environmental adaptations these cooperatives evolved into DNA/RNA monolithic union blocs. When a bloc cloned itself, it produced a carbon copy monolith.

After a billion years of natural selection, a bloc of DNA gene replicators and RNA replicators, housed in a protective shell, evolved. This first cell was The Seed of The Tree of Life. This cell is the last universal common ancestor, or the LUCA, of all life on the Earth   


As the LUCA thrived to sustain its survival, growth and continued development, by adaptive changes to new environments, its descendants sprouted the first two of the three major branches of life, three and a half billion years ago; ARCHAEA and BACTERIA, the first two different types of prokaryotic cell. The third major branch, EUKARYA, the first animal and plant cell, arose about one billion years ago. Germinating from the LUCA, the tree of life evolved into existence. It continues to grow and branch out through the process of natural selection.


Creationist supporters are adept at designing a Straw Man Model of Darwinism. This model rests on the false premise that evolution's essence is random chance. Then they say how absurd it is to believe that the eye, for example, so complexly exquisite, could organize itself just from shaking up the eye parts until they accidentally connected together perfectly into a complex eye. This, of course, is absolutely absurd nonsense. Evolution by Natural Selection is not premised on such a ridiculous notion; it’s not "Evolution by Random Accident". Natural Selection is nonrandom. The transformation of a species form from one adaptive form to another adaptive species form involves almost imperceptible small adaptive changes over hundreds of thousands to tens of millions of generations of species descendant lines. A variant within the species may develop a light-sensitive patch of skin. If having a light-sensitive patch of skin is a survival tool, and not having any or too little is a survival disadvantage, then a variant so possessed might leave more off springs in the next generation. The genetic trait for light-sensitive skin patch will slowly spread through the breeding population. Natural Selection tends to preferentially nurture and amplify survival traits, or the fittest variants. It also suppresses the development of ill-adapted variants. After many generations the population would be typically dominated by the light patch variant. To continue, the light-sensitive patch gradually, over millions of years, evolved into patches with improved sensitivity. It would not be wrong to say that useful improvements in the sensitivity of the light patch were produced by random accidental mutations. Cloning errors result in accidental mutants. Typically most mutants prove to be maladaptive and may fail to thrive. One or a few mutants might have a larger or more sensitive light-sensitive patch just by accident. If this turns out to be a survival advantage over other variants, perhaps more and more generations will have a larger and larger amount of this variant. The point is that light patch improved variants are preferentially selected and nonrandomly favorably accumulate in the population. Preferential amplification of a variant by selection can be so unrelenting that the population gene pool may not have any individuals left without that advantageous trait. As an aside, the advantages of sight as a survival tool caused many animals to independently nonrandomly evolve several different types of eyes, and it was slow going; the evolution of the eye took on the order of about forty million years to perfect. Insects evolved a variety of compound eyes. The house fly has two compound eyes, with each eye having four thousand lenses! Frogs evolved an eye sensitive to subtle movements (watch a frog grab a moving fly with its tongue). A spider has seven to eight eyes. And the visual acuity of the eagle on the wing is legendary. Owls eyes are so sensitive that they can see prey in almost pitch darkness. Some snakes have eyes that can perceive in the infrared part of the spectrum, and honey bees with their five eyes can see in the ultraviolet.

Picture or Photo of Tree frog with big eyes on branch of a tropical tree in amazon rainforest. Macro of beautiful night animal in rain forest jungle of south america.

Picture or Photo of Head of golden eagle bird isolated on white background
Picture or Photo of Jumping spider on a green leaf, with black backgroundPicture or Photo of A beautiful old rehabilitated Great Horned Owl.Picture or Photo of Venomous green boomslang snake with mouth open and coiled to strike
** Note: Slight blurriness, best at smaller sizes

Let me illustrate that Evolution by Natural Selection is definitely not a purely accidental random process. You are out for a stroll in the woods. You end up in a meadow where you see all kinds of wild flowers and plants. Wild roses catch your fancy. Different varieties of roses are growing randomly all over the meadow. You are a connoisseur of aesthetics, and the Red Rose you find most aesthetically pleasing. You carefully choose a bunch of red roses from among a wide choice of wild varieties. As you walk through the bushy woods you hear baby animals whining. Low and behold it’s a litter of abandoned Gray Wolf pups! They are so irresistibly adorable! And it would be heartless to leave them in that cave where they would surely perish! You bundle the nine little cutie pies and drive home.

What have you done? You made a deliberate selection for various reasons of preference. The deliberate choices you've made from a random variety of wild life is a kind of "nonrandom selection". This could rightly be termed nonrandom Artificial Selection. Plants and animals go through a similar process, naturally. There are all kinds of seeds and animals accidentally entering a region of land by wind, rain, swimming, walking, drifting in from the sea, so on and so forth. Those plants and animals that thrive best in the land will preferentially remain there. Those finding that they are poorly adapting will leave if they are able or become scarce from leaving less and less poorly adapting off springs. The better adapted plants and animals leave more off springs and because they are better adapted like their parents they too grow up and breed more than the other poorly adapting animals and plants. The environment, like you, can said to be deliberately nonrandomly selecting from among various plants and animals randomly entering that particular region ; and this could be rationally termed environmental nonrandom "Natural Selection".



As the pups grow you take an especial liking to a particular individual; she seems to have "personality". You lavish her with special adoration to the point of giving her the most care and attention. She reaches maturity and becomes a mom. As her litter grows there are two or three of her pups who have "personality" but much more than mom. From one generation to the next you consistently select the ones with the best and most personality. This continual selective breeding of personality has been acutely nonrandom on your part.
From accidental randomly occurring pup varieties, you have preferentially selected and bred those Gray Wolf pups with "personality". This Wolf is so different from all other types of wolves you could reasonably say it is no longer any kind of wolf. You seemed to have evolved a new kind of animal whose ancestor was an abandoned Gray Wolf pup. Over thirty thousand years of breeding, in human environmental settings, a Gray Wolf was transformed. Today we call this animal a Chihuahua, a Great Dane, a Poodle, a Shih Tzu, a Rottweiler; in other words, "A DOG".



GRAY WOLF PUPS ABOVE

Chihuahua pup



Great Dane pup






Poodle pup





Shih Tzu pup




Rottweiler_pup_0207



Rottweiler pup




Nonrandom human-environment Artificial Selection evolved The Dog from a Gray Wolf pup. Similarly, a natural stable environment can evolve one kind of animal by naturally selecting from among random accidentally occurring traits, thus transforming one species of animal into a new species by a process of nonrandom Natural Selection.
Evolution depends both on accidentally occurring random traits and nonrandom Natural Selection. Without variety that spontaneously arises, Natural Selection has nothing from which to choose and preferentially nurture. This nonrandom selective nurturing and amplification or augmentation of a chosen trait or traits, from spontaneously arising random characteristics, is responsible for the transformation of one form into another. That is, evolution.

What is our origins, what is your origin, what is my origin? I am a prodigious number of copies of a single cell from my mother. When my mother was a baby she was a growing cooperative of  billions of  copies of a single cell from my grandmother. Grandma is a cache of tens of trillions of copies of a  living cell inherited from her mother. And great-grandma was a . . . All humans are descendant copies  of a  cell from the "mother of all generations". If you walk the time line backwards we eventually reach the first cell. As time moves forward from that seed, it generates more descendant lines. The Seed's cell copies and cell copy collectives, thru natural selection, evolved into the different types of living organisms. Each type of organism is a different branch, twig, bud or leaf of the same family tree.




So, what’s my biological human story? I grew from a twenty-three pair DNA chromosome cell. Half of the genes in my DNA chromosomes came from mom and the other half came from dad; this cell became a zygote which transformed into an embryo. The embryo that was me coming into being grew into a fetus, unfolded into a Homo sapiens baby who grew up in a family of humans to be a dad. You probably have a similar story to tell about your origins.








What about our family tree. How do we figure into the Darwinian scheme of things? No doubt most of us have heard of Eve. According to The Bible, Eve was the first woman and we are all her descendants. Well, there was a real "Eve". She is called "Mitochondrial Eve" and she actually lived on the continent of Africa about one hundred fifty thousand years ago. She is actually one of the last common ancestors of all human beings alive today. The human fossil record shows evidence tracing our roots to Africa; it turns out all of us are Africans: Black, White, Chinese, Indians, all races, all ethnicities can trace their family trees right back to this one woman who actually lived those thousands of years ago! How did we track the real "Eve" down? Through Mitochondrial DNA research; from our sisters' and mothers' mitochondrial DNA. MtEve is the most recent common matrilineal ancestor (MRC-MA), on our mother's side,  with which all humans alive today share the same Mitochondrial DNA  variant. Hers is the only descendant line of her contemporaries that stretch to the present time; all the other descendant lines (her sisters, her aunts, her cousins her neighbors) died out without reaching the present day. Only the descendant generations carrying her mitochondrial DNA variant are alive today. The mitochondrial DNA variants in each and every one of us are from the branching of her mitochondrial DNA. In other words,  The mutation that gave rise to the Mitochondrial DNA variant was passed on to all of us from "Eve". We honest to goodness all belong to the same family! All mitochondrial DNA passes down through the female line only, never from the male line (sperm cannot pass on mitochondrial DNA, only [female] eggs can). But Ahh! There is a "Y-chromosomal Adam". There was an actual living breathing African man, who lived about one sixty-eight thousand years ago, whose Y-chromosome DNA copies passed down through his generations to us male. No, Mitochondrial Eve and Y-Chromosomal Adam never dated. He is called Y-chromosomal Adam because he is the most recent common patrilineal ancestor (MRC-PA), on our father's side, with whom all of us (males) share the same Y-chromosome DNA. The fossils of humans collected over the last one hundred and fifty years were used to trace our human ancestral line right back to Africa. However, conclusive corroborating proof came from female mitochondrial DNA and male Y-Chromosome DNA studies.




There is unanimous consensus within the scientific community that Darwinism is supported by overwhelming scientific peer reviewed evidence. Creationists have provided not one scintilla of scientific evidence to support their thesis. Their "theories" cannot pass muster. Under the withering floodlights of scientific peer review, there’s have been proven to be pseudoscience.

Pieces are still being added to the evolutionary jigsaw. It’s not complete but the outlines of the big picture are clear. Contrary to creationism, we are not strangers to each other with alien natures. We either thrive together as the family that we are or wither in lonely isolation. Thriving as one we develop our growth potential. We are the tree of life evolving in wisdom, with strength renewed through nurturing in the soil of Natural Selection.