Origin of Life Research

Ian Musgrave of the Website Talkorigins (http://www.talkorigins.org/faqs/abioprob/abioprob.html) says creationist scientists are fraudulent when they calculate probabilities for the production of a single functional

Statistics are not quantum physics!

Statistics are not quantum physics!

protein entity by purely materialistic means.  These calculations extrapolate logarithmically as additional biomolecules are considering in the search for a rational explanations for the materialistic origins of life. The statistical analysis of probability events is of course only one response to the absurd notion that life originated by an abiogenic process.  Theistic science is said to be problematic and statistics only mislead the public in order to favor a design alternative to the problem of life’s origin.  Ian cites his objections, suggesting a number of problems and then expands upon his understanding of each problem.

Problems with the creationists’ “it’s so improbable” calculations:

They calculate the probability of the formation of a “modern” protein, or even a complete bacterium with all “modern” proteins, by random events. This is not the abiogenesis theory at all.

SURE IT IS!  Probability considerations are only one of the simplest considerations when dealing with highly unlikely events.  Since no one knows the chemistry of the early earth or its temperature, or if there was water or if there was an early earth for that matter, when speculation is taken as fact by experts in materialistic mysticism, one simple way to determine fact from fiction is probability determinations and these lead to

 

me2

 

possibility determinations.

Every origins researcher must start somewhere and, to keep it very simple, the consideration of the formation of a single protein is a good starting point.  It is a fair starting point.

Any sensible attempt at calculating probabilities for random events has specific parameters that must be established before the math is calculated.  Intelligent agencies like humans understand that imagining an improbable chemical event is just that; imagining.  It is not science, it is philosophical and antithetical to known chemistry since we know that biomolecules don’t just happen.  But chemistry, being founded on laws, and biochemistry, being built on those laws as well as advanced algorithms and theoretical postulates that help to explain the extremely fine tuned protein-protein interactions that promote life functions, never seem to get in the way of evolutionary speculations.  The integrated network of biochemical interactions that drive reactions in directions favorable to create metabolic pathways found in cellular life are bewildering and today, require sophisticated computer software to understand and to keep track of the metabolic matrix resulting from our understanding of cell physiology.  Theistic scientists know these details long before they care to simplify the questions surrounding the abiogenic idea of the formation of life using simple probability calculations. In addition, and more importantly we ignore them since biochemical systems did not exist in the imagined

Lab experiment testing the primordial soup theory.

Lab experiment testing the primordial soup theory.

primordial world.  This is in favor of a materialistic probability assumption.  We first throw out everything we know about biochemistry and then pretend that biosynthetic chemistry could occur in the absence of biology.

So, in calculating the very minimal criteria for random events to form a linear arrangement of some 300 amino acid residues we do not assume the natural conditions or speculate on considerations that would have had to exist for any sort of chemical synthesis to occur in a natural prebiotic world of any kind. Instead, the fundamental requirements for conditions conducive for a purely natural synthetic approach to biosynthesis are assumed in favor of a materialistic, non-intelligent formation of just one single molecule of a particular protein that has at least one known function.

The fundamental natural conditions conducive to protein formation are given so that only the probability estimates become relevant to the argument.  In this way, speculations of earth conditions, availability of water, the source of complex monomers, and a hundred other conditions that we know would only interfere with the synthesis of a functional p2737828-256-ke26ce6a6rotein are ignored.  They would only add to the speculation and increase the improbability calculation to numbers far in excess of any reasonable consideration; approaching the miraculous.  So, given the benefit of the doubt about life’s early events and ignoring what we know of biochemical reactions, we keep it simple and assume all these are in favor of making the stuff of life.

So for calculations of the probability of something as fundamental as a single enzyme that digests a single molecular bond of, for instance a fat molecule, the assumptions go something like this:

  1.  Given that the oceans are full of amino acids only; no bases, no alcohols, no toxins, no interfering compounds, oils, ketones, aromatics, aliphatics,  nitrogenous bases, sugars etc…,
  2. Given that these amino acids are found in concentrations favorable to collisions that would allow some form of covalent bond formation from some source of energy; typically heat,
  3. And given ideal conditions of the aqueous medium (water in which the reactions will occur) such as the proper pH, osmolality (salt), turbulence, heat, or lightening or any one of hundreds of environmental conditions favorable to the formation of the peptide bond (the covalent bond between amino acid residues),
  4. And given that none of the assumed favorable environmental conditions are at all detrimental to the formation of such peptide bonds (another completely ridiculous consideration),
  5. And given all the Hubble Time (the life of a universe is one Hubble Time or about 30 billion years) in multiple universes to be unrestricted,
  6. And given that the only chemical reactions that will occur will be between the primary amino group of one amino acid and the primary carboxy-terminal group of the next amino acid (literally thousands of other chemical bonds could form between the 20 essential amino acids even in an sublime chemical soup as described here),
  7. And given that all and only the 20 essential amino acids are available to participate in the chemical reactions under consideration,
  8. And given that all the amino acids available are only left handed residues; the only kind that are chemically made by biological systems (in a world where such chemicals are created synthetically or theoretically by materialistic means this is and would be impossible to control for)

Then and only then, can we ask the question, “what is the statistical probability of a single polypeptide chain

Amino acid chain via polymerization chemistry.

being randomly formed in the correct linear sequence of amino acids that would form say the lipase enzyme?”  It turns out that it is somewhere in the neighborhood of 1 chance in 2.04 x 10390.  This can be spread over as much time as you want with as many conceivable worlds all simultaneously undergoing prebiotic synthesis concurrently.  This number is ridiculously large and no amount of story telling helps to improve the chances of this occurring.  The visible universe is not sufficiently large or old enough to improve the statistically probability number.  Add as many more universes as you like and the probability does not improve by very much.  The conclusion is clearly that a materialistic means for the formation of a biological molecule literally requires a miracle; or the programming of cellular chemistry as is found in living cells.  Neither of these ideas help the materialistic method of chemical evolution. Theoretical abiogenic processes do not contribute to an answer for life.  The answer becomes a metaphysical one.  Science supports a metaphysical reality since even the simplest form of biochemistry requires a complex program (DNA) and complete decoding system (the cell) to manufacture specified proteins.  It is proven that this is what is required to make a single protein. No molecular stories aid the abiogenic hypothesis.

Ian asserts that: Firstly, the formation of biological polymers from monomers is a function of the laws of chemistry and biochemistry, and these are decidedly not random.

This statement is patently false.  Ian may not know chemistry of any kind or he may be deliberate in this deception. Any chemist or biochemist knows that polymerization of any monomeric unit requires highly controlled and near pristine conditions and sometimes a catalyst must be available to create a thermodynamically favorable direction for the polymeric reaction to take place. There are only two sources that are currently known for polymer formation: synthetic polymers that are man made and biopolymers made by biology.

Many polymers used in DNA or Protein research such as the formation of polyacrylamides require extremely pure acrylamide subunits and a catalyst that drives the reaction to the formation of polymerization.  In this

The Peptide Bond

The Peptide Bond

case, the polyacrylamide formed is a random network of strands that create a gelatinous mesh. This gel is used to strain or sieve other molecules when an electric field is generated through the mesh by a power supply.  The effect is to separate molecules or fractionate them based upon there size.

However, in the formation of DNA, RNA or protein molecules, which are all polymers, many types of monomeric units are involved in the synthesis of each type of molecule.  Random networks are not made in the polymerization of biomolecules, but a linear arrangement of monomers is required.  Large multimeric enzymatic catalysts called polymerases or transcriptase’s or ribosomes are involved in polymer formation and this, at the expense of enormous amounts of cellular energy.  The formation of the DNA polymer requires not just a random string of monomers but also a template of DNA to begin the polymerization.  The code of information for DNA polymerization is found in the specified linear arrangement of data on the template.  The catalysts duplicate the information, which results in the functional double stranded genetic code replicated for the purpose of directing protein synthesis.

In the case of proteins, each sequence of say 300 residues (monomers) is the result of highly ordered linearly alignment of molecules based upon a transcript (dictated information) to create a highly specific three

Monomers liked like beads on a string.

Monomers linked like beads on a string.

dimensional bio molecular machine.  Such an protein (molecular machine) possesses a catalytic site favorable to perform a single, well-defined enzymatic reaction using the free energy of the universe to drive a reaction to a point of equilibrium… a minimum requirement for any enzyme.   There are typically many other important and well defined regions of the protein other than the catalytic site that form other domains. These carryout specific biophysical jobs in the activity, control, longevity, and structural integrity of the protein.

As stated, there are no known chemical reactions that result in the linear polymerization of amino acids to form a polypeptide chain (protein) under any natural conditions other than living systems.  This type of polymerization does not take place outside the living cell unless an intelligently designed machine such as a peptide synthesizer is constructed.  Such a device comes with a highly refined and specifically designed resin from which single residues are automatically added using well known organic chemistry that is favorable to a single, highly reactive covalent bonding event between an amino terminal of one amino acid and a carboxyterminal of another amino acid residue. This process is repeated by computer control until a polypeptide chain is made.  After the first

Different levels or structural order.

Different levels or structural order of a protein molecule.

addition event the resin must be washed free of the excess unreacted residue and prepared for the second addition by a computer controlled system so that the next defined monomer can be added to the growing linear chain of residues.  The result is a polypeptide chain of some 80 residues, which is the best we have been able to do to produce to protein synthetically. Otherwise, genetic engineers like myself use biological systems like living bacteria or plants to produce kilogram quantities of a single, valuable protein.

One of the simplest lipase molecules comes from a bacterium.  It digests lipid, fats and oils and has around 306 amino acids residues in fairly exact linear sequence in order to be useful to a living system like the bacterium.  There are many forms of the same protein but their fundamental structures provide the key elements to both recognize and digest lipids.  Below is the number 1, written 306 times (Figure 1).

 

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111111111111

1111111111111111111111111111111111111111111111111111111111

Figure 1:  Linear arrangement of single type of unit.  A graphic example of polymerization.

Under the most pristine conditions in nature you will not find polymerization of a single organic monomer to take place such that the monomer will be chemically attached to form a linear (a straight line) of polymeric structure; like beads on a string.  It must be under the direction of a biological process. There are some theories in regards to the origin of petroleum that suggest this oil may not be of biological origin but rather the result of collections of a methane gas molecules that have undergone polymerization in the depths of the earth.  Not many petrochemical engineers really care how the oil got there though such a polymerization reaction can be performed in the laboratory.

Now consider Figure 2 where 20 amino acids are placed in a specified order to give rise to a recognizable and functional entity, a lipase protein from a bacterium.

GADNIDVSFQ TILQQERNWA GLQSKSLKVG DITWSYSEGG SSTKPTLLLI HGLAGSRDNW NRVAHYLTTN YHVIIPDLPG SGETIVSQDF DYSVPNLAEK LRRFVEAANL KGPIHIAGHSLGGSIALLYA GQYPFETKSL FLVDSGGIFR SANTIYLKDP TYLKQLLVSK KGDFNYLLKQ TGFNPPFIPK EFLQAQEKLX INQAPQTQKL DQLIALNKVYTPDSFAVLT KTIDAPTLILWGKQDKIINV EVANELKRLL KNAQPPVILE NVGHXPILEA EQLVIQQYVP FLLKVETNQS SKTTTP

Figure two: A linear arrangement of a protein that has been determined to be a lipase, a protein that aids in the digestion of lipids (fats) from a bacteria called Acinetobacter.  It is able to digest fats because of the linear arrangement of amino acids.  This arrangement results in protein that folds to create the globular protein having the specified function of digesting lipids.

This protein has specified arrangements of amino acids that then fold and twist to form a globular protein having the ability to recognize and digest lipids (oils and fats) (Figure 3).  The linear arrangement of amino acids is called the primary structure of the protein.  Depending on the linear arrangement, portions of the protein may form higher ordered structures called secondary structures.  The protein may coil creating alpha helical structures.  One or more amino acids may allow a bend in the protein; the severity of the bend is determined by the particular amino acid or acids placed at that particular position.  Other structures form sheets where the residues alternate the angle of their peptide bonds to form features much like this:  VVVVVVVVV.  These are called beta sheets.  Other alignments of the amino acids give rise to finger domains, hand loops, and catalytic sites and there are many other well defined structural features or “motifs” (meaning image, pattern or theme).  Some of these motifs have the function of holding the protein in three-dimensional space such that its molecular form allows highly specified interactions with a very limited number of other molecules.  For the enzyme lipase, there is a specified site of the molecule that recognizes fats and oils and binds to that site, breaking the bonds of the molecule.  This is the catalytic site and it reduces the lipid to smaller compounds that can be absorbed or transported into the bacterium. 

Lipase

Figure 3: The 3-D folds of the lipase molecule as shown using ribbons and arrows for specific secondary structural configurations… this is a model of the functional protein.  The smaller molecules in black and red represent the glycerol solution used to crystallize the purified protein. 

To put this in a linguistic metaphor, the monomers are the alphabet, the motifs or domains become the words and the protein makes up the sentence “go digest lipid molecules”.  For comparative analysis and to understand the complexity of producing a single useful protein from 20 amino acids let’s consider the metaphor of the human language.  There are 26 letters in the English alphabet. There are 20 encoded essential amino acids.  When they are aligned correctly they form words or in the case of the amino acids, domains.  When words are aligned correctly they form sentences.

For the sake of simplicity, let’s use several sentences of a well-known Bible passage that is 304 letters long (Figure 4).  Pretend that each letter or space is a monomer or residue. We will ignore punctuation for now. The sentences contain highly specified information from the orderly and linear arrangement of the words, which result from the linear placement of letters and spaces.  This is just like a polypeptide chain. There are three lines and one paragraph shown in this illustration, though it may be incomplete. The arrangement of the letters and the spaces create words or in chemical terms, domains, within the sentence structure.  Just as proteins have motifs that define a shape in the overall structure of the protein, resulting in a molecule of highly specified complexity, words contribute conceptual meaning and when arranged correctly result in a higher order conceptual meaning that we recognize as a sentence.  How could the linear arrangement of letters that produce the content of this information have come into existence under any other circumstances given any amount of time or any natural mechanisms other than by intelligence? 

In the beginning God created the heavens and the earth Now the earth was formless and empty, darkness was over the surface of the deep and the Spirit of God was hovering over the waters  And God said Let there be light and there was light. God saw that the light was good, and he separated the light from

 Figure 4: The first few sentences of Genesis 1.  Even without punctuation the meaning of the passage is clear. 

 

Now, if I use a random order generator to align the 304 words of the Genesis record what kind of information is obtained (Figure 5)?

Said the in saw the God deep hovering that over and the the darkness formless over light God and was and empty good now spirit beginning was the the the be and let  face separated of light the waters God was light God of and  earth was  the there heavens earth the the created there and  was

Figure 5: A random order generator that aligns the first 304 words of the genesis account in a linear fashion.

 

Let’s try this again:

 

light        in              over        light        and         light        was         let            and         the          God         and empty           there     the          deep      hovering                spirit      the          the                   separated            be            of              there     beginning             of              the          earth     was         and         good       the          God         formless                said        the          saw                   that        God         earth     darkness               heavens                god          the          waters  was         was         and         over        created                  the          and         now        face                   was         he            the

And again:

let            the          of              was         the          saw         deep      was         face        in              God         there     and         god          light        light        and         was         be            over        and empty   formless                God         earth     and         waters  the          good       heavens                the          was         now        and         beginning             created                  the          light                  the          that        God         separated            he            earth     the          and         hovering                there     over        the          the          spirit      of              the          said                  darkness               was

If we take this down one step, to the level of the alphabet and try to align the letters to produce just 10 words of the beginning of the book of Genesis in the order it was written, what kind of information content is obtained from such a naturally random selection process?

For instance let’s take this sentence: In the beginning God created the heavens and the earth.  Since there are 26 alphabets to choose from and one spacer, each position in this sentence has a 1 in 27 chance of being the correct letter or space.  We need 54 slots into which 1 of 27 possible characters or spaces must go to produce a meaningful sentence.  In regards to biochemistry we will not deal with the complexity of the chemical conditions that must be established for reactions to take place for the formation of the peptide bonds between amino acids. This example is much simpler for the benefit of a materialistic synthesis of proteins, which is argued led simple organic chemicals to form into prebiotic biochemicals. What we do know is that for the first 54 letters (amino acids) to align in a proper sequence to form the first portion of the Genesis account (a protein sequence) there is a certain probability of the event occurring.  In the situation outlined so far, with 27 possible alternatives for each of 54 slots the probability of getting the first 10 words of the Genesis account created is 54 to the 27th power.  This calculates out a number that is 2.0 x 1077 or in terms of a ratio, 1 chance in 2.0 x 1077 tries.   Below are 10 iterations of randomly placing one of 27 possibilities into each of 54 slots in order to reproduce the sentence composed of 10 words.

itertions

 

 

 

 

 

 

Figure 5:  Ten iterations of alignments of the letters and spaces that make up the first 10 words of the first sentence of the Book of Genesis.   We may have to repeat this process up to 2.0 x 1077  time to get the 10 words spelled and aligned correctly

One might argue that not all the letters of the alphabet are found in the 10 words used in that sentence so that the statistics look slanted. They are, but not significantly.   However, this is in favor of the materialistic argument that such polymer chemistry can occur in the ancient past under any conditions.  And this is the point.  In the fantasy world of origins, not only are there 20 left-handed amino acids floating in the oceans but there must be 20 right-handed amino acids.  This is 40 amino acids.  Furthermore, if these exist by some unknown means, many other molecules must also exist by some means as well – complicating the abiogenic hypothesis.  Whatever process created the primordial soup of amino acids (meteorites?) also created a thousand non-essential amino acids.  Also present in the soup there must have been alcohols, a thousand different nitrogenous bases, alkenes, aromatics, aliphatics, esters, sulfates, acids, and a limitless number of other organic and inorganic compounds that would overwhelm the synthesis of anything that today we find familiar and abundant in living systems.

Let’s say the lipase did form.  Let’s say even the DNA polymerase, RNA polymerase, and the ribosome formed.  Let’s say there was a biological membrane of perfect modern molecular structure that formed as well.  And let’s go so far as to say that the entire 2000 proteins needed for all the functions of life formed and were abundantly available to make a universe full of bacteria.   We still have to explain how the DNA molecule came to encode all of those 2000 proteins and possess the ability to control when, where and how many proteins are crack the codegoing to be produced for cellular life to continue?

No amount of evolutionary story telling helps us account for this relationship between the existence of proteins and the means by which those proteins came to be genetically encoded to be heritable; that is, passed onto the next generation of cells.  What we are asking mother nature to do is provide an unnatural means by which the information content in DNA comes into being such that it just happens to have a language for the construction of at least hundreds if not thousands of protein molecules that formed independent of the code.    We have, through good scientific observation and analysis, arrived at a metaphysical crossroad.  Either we throw up our hands and say the words “slowly evolved” or we appeal to a higher intelligence.  Either way, we enter religion and not science… but it was hard science that forced us to this conundrum, not religioin.

Ian says there is a secondary problem for theistic scientists who claim that probability calculations mean something to the argument for an intelligence to the origin of life. He says:

Secondly, the entire premise of statistics is incorrect to start off with, because in modern abiogenesis theories the first “living things” would be much simpler, not even a protobacteria, or a preprotobacteria (what Oparin called a protobiont [8] and Woese calls a progenote [4]), but one or more simple molecules probably not more than 30-40 subunits long. These simple molecules then slowly evolved into more cooperative self-replicating systems, then finally into simple organisms [2, 5, 10, 15, 28]. An illustration comparing a hypothetical protobiont and a modern bacteria (sic) is given below.

Does this explain anything?

Ian cannot rely on any empirical evidence and resorts to the use of storytelling to argue his bias.  Statistical assessment of the abiogenesis theory cannot be correct because the first living things would be simpler.  Simpler than what?  A protein is about as simple as one can get in the discussion of how life could have originated without intelligence; and we have seen that this is not reasonable.  Ian goes to molecules much less than 300 residues long

Bacterial cells.

Bacterial cells.

and suggests that a molecule of 30-40 subunits would slowly evolved into more cooperative self-replicating systems.  His references to articles would seem to support that abiogenic processes can work in the lab. But, in fact those references note the difficulties in making such a subunit as well as pointing to conditions that resemble the solid state substrates used in modern biosynthetic mechanization used today to make short peptides.  These papers do not support abiogenic prebiotic chemistry; even if the authors of these papers do support these atheistic concepts.

First, where did these 30-40 subunit molecules come from in a primordial soup? Ian does not say. Then, how does the 30-40-subunit molecule evolve?  Ian does not say.  What selects the peptide’s existence in a chemical soup of acids, bases, alcohols, lighting, heat, and whatever other special evo goo is in the mix?  Ian does not mention this as a problem. Then, this evolution proceeds along the lines of “slowly evolving” a cooperating self-replicating systems!  This is convenient, but what does he mean?  This sentence has no meaning in chemistry or biology or physics or engineering.  It is a purely metaphysical description of an event that is not known to occur by the laws of nature.  Nevertheless, simply

Blue-green algae.

Blue-green algae.

enough, the self-replicating system finally turns into a “simple organism”.   What? How? Where is the explanation for why probability statistics and fundamental chemical requirements are insufficient to explain away evolution from soup?  Ian does give us an illustration of an entity he calls the protobiont.  This cartoon is of an entity that exists nowhere but in the imagination of evolutionists.  He does not explain what it does or how it got there or how it “slowly evolves” into bacteria.  Moreover, using the worlds “it evolved slowly” explains nothing.  Why not use the classical incantation used to explain such events: “hocus pocus.”

Ian proceeds with his criticism:

Where the creationist idea that modern organisms form spontaneously comes from is not certain. The first modern abiogenesis formulation, the Oparin/Haldane hypothesis from the 20’s, starts with simple proteins/proteinoids developing slowly into cells. Even the ideas circulating in the 1850’s were not “spontaneous” theories. The nearest I can come to is Lamarck’s original ideas from 1803!

So, in response to the creationist proof that proteins cannot form from soup, Ian simply starts with proteins that then develop slowly into cells.  Is this an explanation?  Ian seems to believe that if you simply assume some things exist and then add the words “slowly evolved” that somehow this has explanatory power.  It does not.

A third objection to the use of modern statistical methods and information theory in the assessment of the origins by evolution story is what he calls “The myth of the “life sequence””.  He says that he has heard creationist say that  “… there is a “life sequence” of 400 proteins, and that the amino acid sequences of these

Single celled animals

Single celled animals

proteins cannot be changed, for organisms to be alive.  This happens to be a claim of origin of life scientists.  I have never heard that this saying originated from creationist.  The argument is relatively useful in that the simplest living bacterial cell type is the mycoplasma bacterium and it does survive with the smallest of genomes encoding some 400 proteins.

But, Ian is not happy with 400 proteins being the simplest of cellular requirements. His inspection of the genome suggests that only 256 genes are needed for life to exist.  The myth of life sequence of 400 proteins is actually the myth of life sequence of 256 proteins for Ian.  What he fails to mention is that there is no cellular life form of 256 genes nor is there a mythical probiont or preprobiont, except in the minds of those who are desperate to rationalize the failure of an abiotic origin to life. In fact, scrutiny of the mycoplasma finds that it survives by the manufacture and control of around 400 protein molecules only because it is, in fact, parasitic or saprophytic.  These last two life styles indicate that the organism is a evolutionary degenerate and has lost the ability to synthesize key

Paramecium - single celled animals.

Paramecium – single celled animals.

metabolites, or even a cell wall. It is dependent on premade biomolecules from other living things or it requires premade compounds from once living beings.  The creationist is willing to suggest a minimal requirement for biological molecules to support a life form, recognizing that this is most likely not sufficient since such forms of life require other forms of life from which to procure the things it cannot make.  This puts much greater scrutiny on the claims of evolutionists who would believe that even simpler life forms must have existed in the great primordial past.

Ian has a few more arguments against the use of statistical probabilities but he has not thought out the real problem of abiogenesis or life from non-life very well, even as most other evolutionary scientists fail to point out the extremely great differences between life and non-life.  Ian like others, places great faith that given only one molecule that could self-replicate, evolution would be off to a grand start.  Though even this simple wish is fraught with phony confidence the evidence given is that there are some small proteins and RNA molecules that do seem to have some enzymatic function either to build up or tear down other molecules but non of them are truly “self replicators”.  All that is ever cited in the literature are molecules that recognize other premade molecules and through some interaction with those molecules will increase the rate of a synthetic reaction; some a 100 fold, some 10000 fold, not a million fold as required by life.  The resulting molecule may have some strong identities to the “enzyme replicator” molecule but even this is not self-replication.  Self-replication is only known at the cellular level.

True self-replicators have always required multiple components or entire systems to work in order to duplicate

Volvox - single celled plants.

Volvox – single celled plants.

themselves.  For instance the ribosome is composed of 3 or in some cells 4 RNA molecules and up to 70 protein molecules as well as some 200 supporting molecules to replicate itself.  No one molecule, is known that can replicate itself from building blocks like amino acids or nucleotides and this is what is so often ignored by the origin of life researchers.  What we are told is that if a self-replicator was formed then natural selection took hold and evolution ensued.  This is not true in reality.  This is a metaphysical statement that relies on unknown, unknowable and, as of yet, undiscoverable forces of nature.  What origin of lifers need to show is the chemistry that caused molecules to come into being that were capable of storing and replicating genetic information.  Even DNA is not a self-replicating molecule in the truest sense of the word.  It needs an entire cellular world in order to be replicated.

Like many of “origin of lifers”, Ian thinks that by adding many steps to the countless steps required to build the first cell, that evolution from chemicals becomes more reasonable.  The claim that theistic scientist jump from nothing to the first cell is a bogus criticism and cannot be found in the creationist literature.  However, the evolutionist believes that production of the first cell is more sound if time and many steps of less than cellular-like entities are put in between the soup and the first cell.  Though no one can explain from a chemical point of view what would sustain the existence of these many intermediate steps, to evolution it is irrelevant so long as you add the worlds, “it then slowly evolved”.  For instance Ian says, “Note that the real theory has a number of small steps, and in fact I’ve left out some steps (especially between the hypercycle-protobiont stage) for simplicity. Each step is associated with a small increase in organisation and complexity, and the chemicals slowly climb towards organism-hood, rather than making one big leap [4, 10, 15, 28].”  Neither Ian nor anyone else in the origins of life research have ever given us any “number of small steps” leading to life.  It is always speculative and at odds with known chemical science.

Is any of this really an explanation of how cellular life developed?  A hypercycle-protobiont (what is this?)

Diatoms - single celled animals.

Diatoms – single celled animals.

increases in organization (how?) and complexity (how?) and chemicals slowly climb towards organism-hood (what?).  There is very little difference in this story and the story of the three bears.  The embarrassing description of the origin of life by “slow and small increases that climb“ explains nothing.   It is a tale told by simpletons, full of sound and fury, signifying nothing.   And somehow this is better than using the proven tool of statistical probabilities to deduce the unlikely hood of naturally rare chemical reactions leading to anything useful like a protein?

Ian is willing to believe the likelihood of just about anything that keeps sentient beings out of involvement in the origins debate.   As for me I don’t believe that life originated from soup.  As for me I have studied protein technology and molecular biology for over 20 years and have yet to find any reason to believe that life just happens.  Sentient beings discover the genius of information technology condensed into microscopic entities that have been described in cellular biology.  This means something to me.  Dreaming dreams is fine for fairy tales but progress in knowledge and understanding is not promoted when

Was there a primordial Earth?

Was there a primordial Earth?

one considers things antithetical to realty and then depend on on those kinds of dreams to explain reality.  It is not only madness.  These kinds of dreams are nightmares.   It might be a good episode in the Twilight Zone but adds nothing to the history of science except great embarrassment.

 

 

 

 

[

19 Responses to “Origin of Life Research”

  1. Mody Nader

    Dear Sir :
    Thanks for your valueble posts , allow me a question :
    Re. Dr. Covert whole cell simulation of Mycoplasma Genitalium , and the huge hype of materialistic media , what do you think concerning the evaluation of that project as anti-faith propaganda? And what is its scientific merit in comparison to real cell of M. G. ?
    Regards
    M.N. With respect

    Reply
    • Dr. Daniel Moran, Ph.D.

      This is a great question. I am glad you are keeping up with the hard science of cell biology. computational modeling of cellular physiology is a great tool for understanding what is nearly impossible in single cell studies and mycoplasma, being the smallest of genomes afford a much more manageable experimental system to start with before more complex biology is worked on. The work of Covert in his most recent publication, Cell. 2012 July 20; 150(2): 389–401, is pure science. It offers no anti-faith propaganda and has real merit in the studies of cell physiology; adding to our knowledge of protein-DNA associations and the kinetics of replication versus cell division (which is a particular problem with mycoplasmas since they are cripple organisms and degenerate from their original design, depending on parasitism for successful reproduction.
      This work will never replace single cell biology experiments but it will allow many questions to be asked and answered and then tested at the single cell level pushing us to a better understanding of the incredible complexity and beauty of life. There are many that will use this technology to further the origins issue but every study done will always leave room for an alternate interpretation within the theistic model.
      Regards,
      Dan

      Reply
  2. Mody Nader

    I wrote my comment after I found many media comments concentrating on one point : life is chemistry and that was proven by covert , my firm belief is that life is more than chemistry which cannot explain morphology , behavior and awareness ….
    For me , I find that covert,s work proves that we can never start with biochemistry as input then end with Form / morphology as output , in his great work ;form was introduced as a cylinder and two hemi- spheres input and every thing depended on cell increase in volume ….
    I wrote to him that ignoring the division of attachement organelle and migration of one of them to the opposite pole may require two or three more modules rendering the whole present simulation irrelevent , in addition ; the termination of the simulation by cell division produced a cylinder plus semi-sphere instead of full sphere rendering the second round of cell cycle outside the simulation scope ….
    I write this to show the reader that even in the most “” simple “” cell , Divine creation cannot be avoided ..,, remember that the M.G. Sim. Required 128 processors plus the intelligent efforts of highly sophisticated labs and ascientists ….I read a paper that Sim . Of E-Coli would require 24 houres of super computer processing ……
    In The Begining GOD Created …..
    No scape from this ultimate Fact.
    Thanks
    Mody with respect
    Retired professor of structural analysis.
    .

    Reply
    • Dr. Daniel Moran, Ph.D.

      I hear you Dr. Mody,

      No simulation will ever capture the biochemistry of cellular life. In fact, the need to use computers to understand the complexity of chemical networking is proof positive that intelligence is the foundation of living systems. Thanks for all you comments.

      Reply
    • Dr. Daniel Moran, Ph.D.

      I agree with your statements here in regards to simplicity with which modeling programs handle cell biology when the reality is much more complex and dynamic. It is hard to believe that any program will ever duplicate this complexity as we have learned that most proteins have multiple functions besides any particular catalytic activity they may possess. Networks have been drawn for the biosynthesis of a single particular nucleotide and these show several dozen proteins are recruited to build the nucleotide from carbon compounds and the cross-talk, feedback and feedforward domains associated with these many enzymes are voluminous; so precisely controlled are the intermediate states of product formation. And, while we know that most scientists working in this virtual world of programming are indeed developing such tools in order to peak behind the veil of life’s secret complexity for both curiosity, and to add to our knowledge, many of these tools are freeware, though supported by government grants and other resources. While you and I see the magnificence of engineering involved in cellular physiology, most secular scientists do not care or know who to thank for this beauty and quality of craftsmanship. nevertheless, the strides we all make to understand biology will add to our understanding of the grandeur nature of the created order and add to the argument for His praise.

      Reply
  3. Mody Nader

    Dear Dr. :
    For many times I sent them a suggestion with negative response every time …. Instead of starting from imaginary simple molecules , we as creationists give them the previlige of having an E-Coli cell in the most super-suitable solution then just make a hole in its wall/membrane ..the cell is dead ..here they have every single molecule in a living cell ready made and available but dead ..OK , atheists just bring it bavk to life ….it is that simple and clear cut proof that life is MERE chemistry ..Do it or permanently shut-up .
    What more proof they need ?
    No Sir ; it is money , prestige , fame and position are the motivation not science and truth .. It is the publish or perish fight to stay on the surface of an ugly ocean of deception, arrogance and prejudice … Never before was
    the goal of science opposing the evidence wherever it leads !!!!!!
    MN

    Reply
    • Dr. Daniel Moran, Ph.D.

      please send me some other references of Cover’s
      Thanks
      Dan

      Reply
  4. Mody Nader

    Dear Dr. Nader,

    Thank you for the emails and your interest. With regard to your questions about the shape, you have a good point – the shape of the organism, particularly the characteristic flask shape of M. genitalium, did not arise spontaneously from the interactions of the molecules in the model. This is largely because the shape is not currently well-enough understood to capture based on physical principles – although progress is definitely being made in this area, and I would refer you to scientists such as my colleague KC Huang at Stanford, or Ned Wingreen at Princeton, both of whom are theoretical physicists studying cell shape. On a related note, you might know that the attachment organelle is also thought to provide motility, in the form of what some consider to be a screw-type motor. We didn’t consider motility explicitly here, as the model is of a single cell in a rich, well-mixed culture environment – however, multi-cellular simulations are in the works.

    FInally, with regard to your question of the “spark” that starts the model, we simply intialize the cell as a collection of molecules and states, and the model updates that. Probably the aspect of the model that drives growth is the linear optimization scheme we employ to simulate growth, which uses an objective function that maximizes the production of biomass components. There is an extensive literature in this area, I can refer you to http://www.pubmed.gov where you could search for “flux balance analysis”.

    I hope that’s helpful.

    Regards,
    markus

    Reply
  5. Mody Nader

    Dear Dr . Dan :
    My principle point is : chemistry is unable to generate morphology /form , behavior or awareness ,
    I challenged many of high caliber researchers to state just one whatever network they chose that starts as input with biochemistry and ends as output with form or sensation or purposeful behaviour
    That is the main attributes of Life , not chemistry but purpose driven behaviour ….
    I will send you a paper in which a formal proof was provided that biochemistry is unable in principle to generate form.
    Mody

    Reply
  6. Mody Nader

    As you can see , the paper is titled “”…….. Predicts phenotype from genotype “” which is not the case
    the simulation DID NOT predict form from molecules ….it only doubled the Biomass volume .
    …..inprinciple no phenotype can be predicted from genotype , and as carl sagan said : where is the Catness in the Cat DNA ? THAT IS THE QUESTION ….period.
    Mody

    Reply
  7. Mody Nader

    You can see that 1900 chemical parameters were needed to just simulate the doubling of cell mass , as such ; any simulation to output the cell form is impossible since the algorithm must include in the input parameters the same form that is required as output …..this is a formal proof that no natural means can generate Form from physics and chemistry ,,,,,that is the importance of Dr. Covert,s
    Simulation.
    Mody

    Reply
    • Dr. Daniel Moran, Ph.D.

      Yes I must agree. This technology is in its infancy and even now it is fascinating to learn what we can with such technology as, for you and, I it reflectd the creativity of the intelligence behind it. I don’t suppose too many secular scientists ever experience that moment of realization that something greater is watching. The crystallization of a realization that awakens the soul, dulled by materialistic training, through a shudder of thought that reveals the fingerprint of the Divine orchestration of all things, whether visible or invisible. The majesty in the created order is often overwhelming and the pleasure found in discovering the ingenious material devices that make life possible is a great blessing.

      Reply
  8. Addictedshield646.Webs.Com

    Hey! Do you know if they make any plugins to assist with
    SEO? I’m trying to get my blog to rank for some targeted keywords but I’m not seeing very good results.

    If you know of any please share. Kudos!

    Reply
    • Dr. Daniel Moran, Ph.D.

      Follow the rules for SEO. Before you wright, plan to use a catch phrase over and over. Use it in the title. Blend it into the story. The best scoring will increase your hits in searches and push you to the top. WordPress helps you by scoring your choice of SEO phrases but you have to blend it into the story for high score.

      Reply

Leave a Reply

Your email address will not be published. Required fields are marked *