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Origin of Life, Phase 2: Biogenesis:
Possibility of Life's Complexity Increasing
Beyond the Simplest Possible Form


by R. Totten (c) 2012

We have discussed abiogenesis on another page. --In that article, we basically defined "abiogenesis" as: "the random assembly of life from lifeless chemicals exclusively through natural, undirected processes." Then we put forward significant reasons to assess the likelihood of whether the simplest life-form might randomly assemble totally without the intervention or management of any intelligent agent, to be a likelihood extremely close to zero. That initial discussion was "Origin of Life, Phase 1: Abiogenesis" in considering the origin of the very first and simplest possible living thing.

But next, moving on to "Phase 2" of the discussion, in this present article we will consider: whether there is a reasonable likelihood of undirected natural processes could add significant amounts of new, functional and coherent DNA information/instructions to the genome of that first and simplest single-celled life-form. -- A "significant amount" of DNA information, would be enough to code for never-before-existant protein machines made from never-before-existant types of functional, folding proteins.

The Starting Point

Let's start out (for discussion's sake) by assuming that this simplest possible life-form exists. Let's call it "Proto-bacterim." --This Proto-bacterium would be simpler than the simplest bacterium alive in nature today, and (per requirements of on-going life) it would have DNA which would code for:
-- the simplest possible protein-manufacturing mechanism (which would use RNA),
-- the most basic cell membrane,
-- the most rudimentary metabolism system, and
-- the simplest possible genetic/replication system

. . . (Just mentioning these cellular functions --however simplified-- raises the massive question again of how they could possibly all come together through unplanned and undirected processes. Merely re-stating the question, again seems to elicit the obvious answer, as explained in the abiogenesis article.)

Now, basically the smallest self-replicating organism on earth today, is the small parasitic bacterium, "Mycoplasma g." -- Its small genome has 582,000 base-pairs in the DNA. (Compare this to the human genome, which has 3 billion base pairs and is thus 5000 times bigger than the Mycoplasma genome.) The DNA of Mycoplasma g. has 482 genes which code for proteins to carry out the above-mentioned cellular functions.
--However, being much simpler than Mycoplasma g., the Proto-bacterium would code for perhaps only 100 proteins. In our "Phase 1 Abiogenesis" article, H. Morowitz said that a living thing with only 100 proteins would be the simplest living thing remotely conceivable within reason. (In fact, other biochemists think that a mere 100 proteins is too few to actually stay alive and also be able to replicate.)

So, this simplest possible Proto-bacterium would just barely be able to live and reproduce on a minimal level, and would have no additional structures or mechanisms at all, for example: there would be no nucleus, no organelles, no cilia and no flagellum (which more complicated bacteria now have, among other things).
-- Quite obviously, in order for "higher" forms of life to come after this Proto-bacterium, there would have to arise immensely more complicated genomes with many times more DNA information involved, which is coherently organized. That is the issue at hand.

For the purposes of this present article, then, let us say that a flagellum is the potential additional bio-machine to be considered. (Though we could actually consider any bio-mechanism comprised of several never-before-existant proteins which are not in the Proto-bacterium.)

--Therefore, initially, the DNA of the Proto-bacterium (since it is minimal) would not code for even one of the 40+ different types of proteins used to build the flagellum, nor would its DNA have any code to direct the proper assembly of those 40+ different proteins into the flagellum (a molecular machine). As a result, a new flagellum must necessarily arise by newly adding all the required DNA to this minimal genome of the Proto-bacterium. These new portions of DNA must include instructions which must code for previously non-existant types of proteins ...as well as previously non-existant DNA instructions to both make and direct the assembly-system for putting these 40+ brand new protein types together into a functional bio-machine.

Increasing DNA Amounts

In order to start with the simplest possible lifeform (the Proto-bacterium), and then develop any totally new and complex machinery, a necessary initial question is: How could that smallest possible genome be expanded in its overall volume; and the second question is: how could the resultant larger amount of DNA be ordered to contain new, complex, specified instructions to make the new machine?

What would first need to occur, is the addition of more DNA to the genome of Proto-bacteria, --and this can reasonably happen by a certain kind of mutations in the DNA called "duplications."
- - Such duplications do happen, and can involve:
1. the doubling of regions in the DNA which have instructions for the making of individual protein-types: This is called a "gene duplication." ...OR...
2. the doubling of the entire DNA of the organism: This is called a "genome duplication."

There is evidence that a "genome duplication" scenario is within reason. --For example, in the genome of today's baker's yeast (Saccharomyces cerevisiae), there are significant stretches of DNA which contain distinctive sequences of various genes, as compared to other streches elsewhere in the yeast's genome which contain almost identical sequences of the same genes. Because of this evidence, different groups of scientists now hypothesize that this situation may well indicate that at some time in the distant past (perhaps 100 million years ago), a yeast offspring underwent a genome duplication, leaving yeast with about twice as much DNA --pretty much as it is today.

So, let's say that a Proto-bacterium underwent a mutation which produced a genome duplication, leaving its offspring with a new genome which was doubled (or --if this happened twice-- quadrupled, etc.) in size. Thus, some of the Proto-bacteria then have twice as much DNA (or more) to work with. -- (In fact, through such duplication occurences, we can also easily say that at any point there is more DNA to work with, so having more DNA volume is never the real issue or problem in this discussion.)

Making the DNA Changes

Next, what are the chances that this newly multiplied amount of DNA could mutate to make the right changes to become code for never-before-existant protein types (which function because they fold properly) along with the new assembly instructions to put those proteins together into a flagellum?

First of all, realize that the genome which has just doubled in size does not initially contain any never-before-seen bio-information. Genome duplication only produces a copy of the very same information that was already there before, ...therefore, no novel types of proteins are coded for right after the genome duplication, and likewise, no new assembly instructions are present to produce any molecular machines that have never existed before. So, the genome-doubled (or quadrupled, etc.) Proto-bacterium would (right at first) look and behave totally the same as before, because there is no new and novel information in the DNA duplication. -- To get new information which codes for novel types of proteins, the DNA will still have to change. --But how could this occur?

If we are limited to exclusively naturalistic changes, the only way that the recently doubled DNA of the Proto-bacterium can aquire never-before-existant information is by random mutations in its DNA ...and therefore, the "search" for novel types of proteins must be an unguided and random search. --This would necessarily mean that changes in the sequential order of the amino acids in the chains which the DNA codes for, would be entirely random changes. --So, for the time being, let's assume (as Darwinism would have us do) that such a naturalistic, random and unguided search for the sequential order of the amino acids is the only method of producing any new information required to make novel types of proteins and new assembly instructions for the flagellar mechanism.

(This is the real issue and problem in this discussion: How can never-before-existant bio-information originate?)

The random mutational changes in the amino acid sequences may be accomplished by:
1. a substitution, or
2. a deletion, or
3. an addition, or
4. an inversion in the order, or
5. duplication of a section.

If natural processes alone were to make random changes in the sequential order of the 20 amino acids which are already properly sequenced to function in the proteins of the Proto-bacterium, then how likely is it that any randomly re-ordered portion would end up being a functional (properly folding) protein?
--Since we are looking for "previously non-existant types of proteins" (which fold properly) out of which to build a previously non-existant nano machine (flagellum), what would we most probably expect from a random search for these totally new/novel protein types?

Experiments Show Functional Proteins To Be Extremely Rare
Among The Possible Combinations

So, what are the chances (probabilities) that a never-before-seen functional (folding) protein-type would result from such a mutation-driven random "search"?

--Experimental work using actual folding proteins from living things, indicates that more than
99.999999999999999999999999999999999999999999999999999999999999 percent of the possible combinations of randomly ordered amino acids would result in non-folding, useless junk chains. So, very nearly 100% would be non-functional for actual proteins which could build and comprise the any new structures in living cells.

--This is explained in the following article: http://www.leaderu.com/orgs/fte/darwinism/chapter6.html

The above article refers to both the work of Dr. Hubert P. Yockey and the laboratory experiments of Dr. R.T. Sauer (MIT), who extensively analyzed the make-up of actual proteins from living cells. The work of these scientists does take into account that there is a small degree of interchangeability of a certain amino acid or two along the sequence of a protein, and the protein still being able to retain some function. ...However, this experimental evidence still indicates that functional classes of proteins are extremely rare among the possible chains of junk sequences that are most likely to assemble by chance. --Despite some amino acid interchangeability, the result of these experiments is that the odds of assembling (by random processes) one new functional protein (which properly folds), are about one chance in 1065. --- (1065 is the number one, with 65 zeros behind it, and is about the number of atoms in all the matter in an average galaxy.) So, the odds of one new functional protein assembling by the random chance processes, would be the equivalent of randomly finding one specific atom out of the galaxy.

This is sort of like saying that if there were a galaxy-sized ocean full of reproducing Proto-bacteria, that galaxy of baceria might produce one functional protein by means of random assembly of amino acids, while at the same time there would also be (on average) 1065 failed attempts or trials, which would be non-functional, junk amino acid chains. -- (A single "attempt" or trial would involve the random assembly of about 200 to 700 hundred amino acids into a chain. It is as if each atom in the galaxy represents "a trial" of randomly putting together a chain of 200 to 700 amino acids.) -- So, the research demonstrates that almost all attempts would be non-functional for life (because they don't fold properly) and useless for the construction and function of living things. If this galaxy-sized mass of trash-sequences of amino acids were to stay assembled for a certain length of time, they would (during that time) clog up all the Proto-bacteria cells and obstruct that one functional protein from getting together with any other new functional protein a galaxy distant away. --Thus, any one functional protein that might hypothetically form would be isolated and lost in galaxy-sized ocean of non-functional, useless amino acid chains.

-- So, if the earth and every other planet in our solar system were filled entirely with reproducing Proto-bacteria, we would expect there to be basically ZERO chance that even one novel and new functional protein would randomly assemble.
...and we would expect basically those same odds even if there were Proto-bacteria reproducing on a hundred billion earth-like planets in the galaxy.
...We might somewhat possibly expect one single functional protein to form in a galaxy if every planet, star and body in it were filled with Proto-bacteria.
--But in one galaxy, we would not expect a second novel functional protein to randomly assemble in order to begin to build something like a flagellum.

--In all the matter in a galaxy, we would not expect the required DNA code for the assembly of even 2 of the 40 new flagellum-construction proteins to occur by random processes in one place ...in one of the Proto-bacteria.

And beyond this, even if 2 new proteins were coded for and built inside a Proto-bacteria cell, this is not close to the 40 required for a flagellum. With only 2 new proteins, there would be no flagellar function. There wouldn't be any flagellar function with even 9 or 10 of the required new proteins. Therefore, the new protein (or two) arising by chance would not give the Proto-bacterium a darwinian "advantage" at all for better survival. In fact, it is more likely that the 2 proteins (having as yet no function, lacking the other 38) would merely clog up the "works" of the cell, and actually confer a disadvantage on the organism.

Much worse: The new DNA flagellar assembly instructions (which cause the cell to assemble those 40 proteins) have not even been considered yet, ...and those instructions would be more complicated than the 40 proteins themselves that go into the flagellum. The new assembly instructions in the DNA would have to develop at the very same time as the new coding for building the 40 proteins.

NOTE: You can try your own hand at intelligently designing a properly folding protein at the following web site:

http://fold.it/portal/info/science

(And if any of your amino acid chains do not properly fold into a discrete shape,
they are then examples of a non-functional chains which cannot be an actual protein.)

Probabilities Spelled Out Further

In this "WorldView Site", I have an article entitled "A Mathematical Proof of Intelligent Design in Nature." It addresses the statistical odds of the random protein-building situation just spoken about. --Please read it, if you have not already.

Conclusions:

Considering the extreme inability of random mutation at coming up with a re-ordering of DNA such that it is turned into new bio-information (in the form of genes which code for new proteins, or in the form of DNA instructions to properly direct the building of functioning protein machines in the cell), it is unlikely in the utmost extreme that random mutation is capable of being the source of new bio-information in living things.

Since there is an abundance of new and novel bio-information in both single-celled organisms (in the form of flagella, etc.) and in higher life-forms, such bio-information must have come from a different source other than random mutation and random re-arrangement of DNA acted on by natural selection.

The only type of source known to be capable of producing large amounts of functional, complex, specified information, is an intelligent source (unless someone can suggest and produce evidence --and demonstrate a feasable probability for-- any other source of information).

Therefore, it seems that the rational and reasonable conclusion is: Every step of incorporating new DNA instructions for the building and assembly of several novel proteins together into a never-before-existant biological machine (such as a flagellum), must have been designed and initially assembled (and incorporated into the organism) by an intelligent designer ...since such a mechanism has no reasonable probability of originating by way of random natural, unguided processes.

And thus, furthermore, it is quite apparent, that the origination of any new species which came about in connection with the inclusion of new proteins (and structures assembled from them), also had to have been designed and initially assembled by an intelligent designer --all along the way, as any new life-forms came into existence during all the history of life.

Since the topic of this discussion has to do with the origin of biological life, the intelligent source required for this consideration would have to be an intelligence which exists prior to all biological life.

The reader is, of course, invited to figure this out from here for themselves. ---However, the present writer and many others down through history feel that such evidence confirms that "In the beginning, God created the heavens and the earth," (Gen.1:1), as well as every living thing on earth.


Prize Offers:

Even though it is well established that micro-evolution is partly true ---I am offering a $2,000 Reward "to the first person delineating experimentally confirmed biochemical mechanism(s) which demonstrate that it is within reasonable statistical probability for biological information and life to have originated from non-living chemicals (abiogenesis) by purely natural processes (...without the agency of any intelligent designer)." This is to stimulate discussion concerning the notion of whether there is a reasonable probability that abiogenesis could have happened. It would appear that there is no such scientifically reasonable probability. This reward is offered, along with two similar challenges for the origin of other complex specified bio-information, through a link in the directory below.

The winning of my reward is contingent upon, and will be awarded to, the person(s) who first win the $1,000,000 "Origin-of-Life Prize". --The "Origin-of-Life Foundation," which offers this "Origin-of-Life Prize," may be trying to coordinate a major effort to substantiate that abiogenesis (a naturalistic materialist origin to life) is within reasonably reachable probabilities.

Relevant Further Reading (links):

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NOTE: You, my friend, are valuable and loved by God, and that's why Jesus Christ came : "For God so loved the world (including you), that he gave his one and only begotten Son, that whoever believes (trusts) in him, should not perish but have eternal life" (John 3:16).

Some Answers : * WHO IS JESUS? *


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