Jason Machalicky

Writer’s comment: After putting off the mandatory English requirement for as long as possible, I finally decided to take English 20, Computer-Aided Intermediate Composition. When my professor, Pamela Major, assigned the research paper on a topic of our choice, however, I decided that the class wasn’t going to be all bad. I had been wanting to write a paper on creation versus evolution for some time, and I was thankful for this chance. Inspired by the Microbiology 102 and Evolution 100 classes I was taking that same quarter, I narrowed down my topic to the origin of life.
        After choosing my topic, I had to figure out how to write the paper so that I could include upper-division science concepts and still reach a general audience. I believe that the origin of life is a topic that all people need to think about, and I do not like scientists, armed with technical jargon and knowledge, to force a reader into submission to their views. (It is so easy for a reader to say, “I don’t understand what he is saying, but he sounds scientific, so he must be correct.”) In describing some of the difficulties with current theories about the origin of life, I have tried to both explain technical concepts without overwhelming the reader and dispel the idea that science has disproven the existence of God. Though it was difficult to bring all the information together, it was well worth the effort to try to do so.
—Jason Machalicky

Instructor’s comment: I’ve always loved a good footnote! An explanatory footnote at the right moment can add tantalizing layers to a piece, often both furthering and commenting on the writer’s argument. But the footnotes are just one example of the care with which Jason has crafted this truly impressive essay. With enthusiasm, good humor, and imagination, he undertook the general directive I gave each student in my English 20 class—to develop over the quarter a well-researched, well-written paper on a topic that captures your interest.
        To say that Jason chose a difficult topic is, of course, an understatement. Nevertheless, from journals to proposal to literature review to numerous drafts, I watched with delight as his project evolved (no pun intended) into an exceptional essay. In “Spaghetti-O . . .” Jason has made incredibly complex material tangible, creating a clear and intriguing argument, whatever one’s views in the controversy.
—Pamela Major, English Department



How life arose is a question that is fundamental to both philosophy and science. Responses to it enable one, in turn, to answer such questions as, “Who am I?”, “Why am I here?”, and “How do I make sense of this world?” This secondary set of questions can be answered in a myriad of ways for a variety of reasons, but the answer to the first question has only two responses. As Douglas Futuyuma says, “Creation and evolution, between them, exhaust the possible explanations for the origin of living things” (197). Either we are the product of the chemical and physical laws of nature operating over time, or we have been formed, at least in part, by some supernatural Force or Deity. The acceptance of one of these options as a foundation will determine how one will establish a belief system to determine his place in the world. This is a matter of crucial importance, yet in most biology classes offered at U.C. Davis, we learn that life came from nonlife by strictly natural (as opposed to supernatural) processes. The possibility that perhaps the origin of life cannot be explained by a natural mechanism is ignored, and this is disturbing. For if we limit what explanations we are willing to accept for the origin of life, we could be closing our eyes to reality.
         Francis Crick, co-discoverer of DNA, has said that “the origin of life appears to be almost a miracle, so many are the conditions which would have to be satisfied to get it going” (Horgan 27).2 Noted evolutionary astronomer Frederick Hoyle has described the chances of life having evolved from nonlife to be about as likely as the chances that “a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein” (Johnson 106). Why do respected scientists doubt what textbooks teach as fact? It would appear that these scientists know something that current theories describing the origin of life fail to explain. While current theories describe scenarios in which genetic material such as RNA becomes entrapped in a protective cell membrane as a likely recipe for the formation of life, they generally do not focus on the difficulties of forming and concentrating all of these components in the first place.3 To clarify, current theories suffer from what I call the “cookbook mentality.” They say something like, “Combine brownie mix, eggs, and oil in a bowl. Stir.” But in general, the theories fail to describe both how those ingredients were actually made and what agent moved those ingredients from their respective locations in the kitchen to the mixing bowl. Though experiments that simulate pre-biotic (before life) conditions have demonstrated the possibility of forming the building blocks for life, they fail to accurately represent all that would have happened in the early atmosphere, especially in regard to the effect of ultraviolet (UV) light from the sun. In addition, there is reason to doubt whether the various components produced could have been close enough together, sufficiently concentrated, to have reacted in meaningful ways.4 These difficulties are serious enough to lend credence to the idea that life could not have originated without some form of supernatural intervention.
         To discuss the origin of life, one must first understand the atmosphere of early Earth. Some four-and-a-half billion years ago, the Earth was formed. After a period of cooling, the Earth theoretically formed an atmosphere consisting mainly of hydrogen, methane, carbon monoxide, carbon dioxide, ammonia, and nitrogen. It is important to note that this atmosphere lacked oxygen gas, which would have destroyed the components necessary for life. While this oxygen-less atmosphere, called a “reducing atmosphere,” would have been toxic to humans, it would have been hospitable to the formation of organic intermediates, the precursors to the building blocks of life. Energy sources such as lightning, heat, shock waves, and UV light from the sun could have caused the molecules of the primitive atmosphere to form these organic intermediates and building blocks, which would subsequently have fallen into the ocean, the famed primordial soup. Further reactions and thickening of the soup are supposed to eventually have led to the formation of the main ingredients of life.5
         Probably the strongest evidence in support of this scenario has come from experiments that try to simulate conditions of the early Earth. Researchers have placed the proposed first molecules in an apparatus that pushes them through a spark (which represents the energy sources of the Earth) to make them react, and then collects the newly formed compounds in a water trap. Through variations on this setup using different quantities of early atmospheric molecules, scientists have been able to synthesize most, if not all of the building blocks of life.6 These building blocks include amino acids, which can combine to form proteins; lipids, which can form the cell membrane; and various sugars that can either serve as a food source or combine with other molecules to form nucleotides, the building blocks of genetic material (e.g., RNA or DNA). After a further set of chemical reactions, it is theorized that the proteins and genetic material could aggregate inside a cell membrane, eventually forming a living entity (Zimmer 78).
         Though experimental evidence demonstrates that organic intermediates and some building blocks could have formed in a pre-biotic atmosphere, two questions remain: Could sufficient quantities of these molecules have been produced to participate in reactions that would promote the formation of life? And, if so, would they have been close enough together to have reacted with one another? After all, the ocean is a pretty big place. One can’t just plunk an amino acid into water and expect it to react with another amino acid fifty feet away. Either there has to be an abundance of amino acids in the ocean or there has to be some way of concentrating them—in a tide pool or lake, for example. Can we really demonstrate that on the early Earth enough molecules could have congregated and subsequently carried on reactions that they eventually would have led to the production of life? Not without a leap of faith that is more blind than rational. Here is why.
         First, one of the assumptions behind experiments that simulate pre-biotic conditions is that energy forms present in those times caused reactions between the first molecules of the atmosphere. These first molecules interacted to form intermediate organic compounds that, with enough energy, could have formed the building blocks of life (biomonomers); in other words, direct absorption of energy organized simple molecules into more complex arrangements. Energy alone, however, is not necessarily sufficient to increase the complexity or organization of a bunch of molecules (Thaxton 43). To illustrate, one might expect a bull in a china shop to have either destructive effects or no effect at all (if it just walked out). We certainly wouldn’t expect the bull to mold a saucer into a salt shaker! In the same way, energy sources most likely destroyed, rather than shaped, the components of the early atmosphere into more complex structures.
         Ultraviolet light from the sun is a good example of this proverbial bull. In a primitive atmosphere without the oxygen-formed ozone layer, UV light would have destroyed most of the molecules and intermediates suspected of composing the Earth’s early atmosphere. For instance, it would have destroyed methane’s chances of meaningful activity by causing methane (and other hydrocarbons) to disassociate and form either a very complicated mixture (a tar) or such simple, rather stable molecules as carbon dioxide and water (Cairns-Smith 42). In other words, it would have produced road pavement, not life. UV light also would have degraded 99% of the atmospheric formaldehyde into carbon monoxide and hydrogen gas. (Formaldehyde is a key intermediate in origin-of-life experiments because it can participate in further reactions to yield building blocks such as amino acids and sugars.) Last, solar UV radiation would have degraded another important atmospheric component, ammonia, into nitrogen and hydrogen, reducing the concentration of ammonia to “so small a value that it could have played no important role in chemical evolution” (Thaxton 43).
         As we’ve seen, UV light would have destroyed several of the key components of the early atmosphere. Without these molecules, crucial intermediates could not have formed, and without the intermediates, the building blocks of life would be in very short supply. Even if the building blocks of life had somehow formed, however, they too would have been subject to UV destruction. For amino acids, the building blocks of proteins, “it has been estimated that perhaps no more than 3% of the amino acids produced in the upper atmosphere could have survived passage to the ocean” (De Hull, qtd. in Thaxton 45). It is also well known that UV light destroys the replicative properties of nucleic acids, the building blocks of genetic material (Lehninger 345). Current theories are beginning to acknowledge these problems and to propose instead that meteorites and cosmic dust could have delivered the various building blocks straight to the ocean. Yet the ocean would not have been a safe haven either, since UV light penetrates tens of meters below the ocean surface (Sagan 198). Even those building blocks that did escape to deep enough water would still have been at risk since ocean currents would periodically have surfaced even deeper waters.
         Obviously, the destructive force of UV light in the primitive atmosphere would have been formidable—so formidable that contemporary organisms would have acquired a mean lethal dose of UV radiation in 0.3 seconds (Sagan 197). But not all molecules are subject to UV degradation. For example, hydrogen cyanide, perhaps “the most important intermediate leading to the origin of life” (Thaxton 48) because of its role in forming nucleic acids and some amino acids, resists degradation by UV light. In sufficiently concentrated solutions (0.27 grams per liter) it could have led to the formation of life’s building blocks. Unfortunately, the highest average concentration of hydrogen cyanide in the early ocean is given to be 2.75 X 10-5 grams per liter. In such a low concentration, hydrogen cyanide would preferentially react with water and get ruined. Thus “it is very unlikely that HCN [hydrogen cyanide] could have played a significant role in the synthesis of biologically meaningful molecules in an oceanic chemical soup” (Thaxton 49).7 It is hard to envision any way in which hydrogen cyanide could have accumulated in some little pool without first being ruined.
         At this point, we have seen that components of the early atmosphere would have had little chance to combine and form organic molecules because UV radiation would have destroyed both them and the organic building blocks they would have produced. We have also noted that the important molecule hydrogen cyanide could not have played a significant role in forming organic building blocks. Scientists acknowledge these difficulties and instead propose that organic molecules and building blocks could have aggregated in little pools on the land, in bubbles, or on clay particles. Of course, by whatever method they were concentrated, any organic molecules could not have been exposed to UV light.
         Suppose that these organic molecules could have formed and collected in some protected region. So now we have a pool or a bubble or a clay aggregate containing significant quantities of aldehydes, ketones, sugars, amino acids, and even nucleotides.8 Now we’re well on the road to producing proteins, DNA, and all the other components for life, right? Wrong. Though our goal is to have each component react only with other components of the same type (e.g., amino acids reacting with each other to form proteins and nucleotides reacting with each other to form genetic material), in reality, they all would have reacted with one another to form useless conglomerations of organic garbage. For example, both individual and chains of nucleotides and amino acids would have reacted with formaldehyde, an important intermediate molecule, and subsequently would have lost their use as building blocks to protein and genetic material, respectively.9,10 The only way to reverse this attachment is to boil the complex in acid—an unlikely option on early Earth. This means that we would end up with useless organic material that could be restored to its original useful components only with great difficulty (Thaxton 50).
         The significance of all of these useless chemical interactions might be described in terms of an analogy. Let’s say we have a bowl of randomly mixed Legos and some of them, the blue ones, are coated with super-glue. Each color of Lego will represent one specific organic intermediate or building block. (The red ones are amino acids, the white ones are nucleotides, etc.) By just shaking the bowl of Legos, we need to maneuver all the same-colored Legos together without getting any other Legos stuck between. Now, shaking the bowl isn’t going to attach any Legos for us; to do that we are allowed to reach into the bowl with our eyes closed every couple of seconds and attach a few Legos that are next to each other. This attaching event will represent the random combination of compounds due to energy input from the primitive atmosphere. Though we would like to connect only same-colored Legos, it is much more likely that we will generate a useless rainbow stack, especially considering that shaking a bowl will not do much to segregate the Legos by color. And even if we did manage to push together a stack of, say, all white blocks, a super-glue-covered, blue Lego could still come and attach to it (without our intervention) and destroy any functional potential of the stack. Of course, this analogy is a vast simplification of a pre-biotic scenario, but it is this sort of problem that current origin theories fail to solve.
         Actually, the chances of forming a viable protein from a concentrated pre-biotic soup are far worse than I have described them. First, remember that amino acids are the building blocks of proteins. There are more than 500 kinds of naturally occurring amino acids, and all species use only about 20 of those kinds to form proteins (Vollhardt 1024). Presumably, in a pre-biotic environment, hundreds of nonproteinaceous amino acids could have formed and could have combined with a proteinaceous amino acid chain. So not only do we have to figure out how amino acids could have conglomerated; we also have to figure out how the proteinaceous amino acids avoided bonding with the non-proteinaceous ones. Though it is possible that (had things worked out differently in the formation of life) those amino acids we call “nonproteinaceous” could have been proteinaceous, this point still should be kept in mind, especially considering that no one to my knowledge has ever demonstrated that functional proteins can be formed from nonproteinaceous amino acids.
         Yet another difficulty in the formation of proteins has to do with the shape of the amino acids that form them. Nineteen of the twenty proteinaceous amino acids come in two forms, a left-handed version and a right-handed version.11 In most species, proteins are made up solely of the left-handed version, called L-amino acids. This fact amazes scientists and, as far as I know, there are no known species that contain proteins with a mixture of the two amino acid versions (Lehninger 114). The reason this is so amazing to scientists is that on the pre-biotic Earth, equal quantities of both versions of amino acids would have been present. How could proteins containing only one version of the amino acid have been formed? In a primordial pool, a growing polypeptide would have incorporated both amino acid versions and formed a useless molecule. Yet, inexplicably, it didn’t happen that way. No theories that I know of even attempt to explain this mystery.
         As we have seen, it would have been exceedingly difficult to have assembled a protein that contained all the same version of proteinaceous amino acids. Let’s just say, however, that we managed to string together a sequence of amino acids that met all the requirements. Not only that, but let’s say that the sequence of amino acids just happened to code for a functional protein.12 Does this mean we would actually have obtained a functional protein? Unfortunately, no. Proteins are more than just a string of amino acids. In order to form a functional protein, the string of amino acids must fold and twist into a specific three-dimensional shape (conformation). And the vast majority of proteins cannot fold into their proper conformation on their own; they need help from specialized proteins called chaperones or hsp’s (Alberts 214). Okay, what if we happened to form a string of amino acids that coded for a chaperone protein?13 Couldn’t that sequence fold up on its own and subsequently help other amino acid sequences to fold properly? No, chaperones cannot fold up on their own either. They need help from another specific type of protein to fold properly. Scientists don’t know how far back this need for “helper proteins” goes (Crow, personal communication), but the requirement dashes the hopes of those who believe that proteins were the first step in the formation of life.
         Leslie Orgel and David Deamer have proposed alternatives to the protein-first theories. Instead of forming proteins, Orgel proposes that genetic material such as RNA could have formed first when random nucleotides combined.14 Enzymatic RNA (called ribozymes), along with inorganic catalysts (certain minerals), could have done some sort of primitive RNA replication without the need for proteins.15 If this possibility for RNA replication is correct, Orgel reasons, then the main problem left for scientists would be to determine how the RNA came into being.16 If some form of self-replicating genetic material could have formed, biophysicist David Deamer theorizes that the genetic material could have been protected from destructive chemical reactions in stable lipid bilayers. (Lipid bilayers form the outer boundary of some cells). Further experimentation has demonstrated that a “quasi-cell” made up of genetic material in a lipid bilayer could have taken in inorganic ions, nucleotides, and amino acids. With the addition of a complex enzyme called RNA polymerase, it could have been possible to make strands of RNA in the cell.17 This is still far from a real cell, Deamer acknowledges, but it is a step in the right direction. Unfortunately, even these current theories suffer from the “cookbook mentality” and fail to adequately resolve the crucial problems I have raised.
         It is reasonably safe to say that life could not have originated on this planet as a result of strictly natural physical and chemical processes operating over time. We have seen that these processes would most likely have led to the destruction of key components of the pre-biotic Earth and, on the off chance that organic compounds could safely have concentrated, to the nearly irreversible formation of useless organic garbage. Scientists who wish to perpetuate the view that life could have originated by strictly natural processes need to find a mechanism that would both concentrate and segregate specific organic compounds. Then each type of building block could react only with other blocks of the same type, without any side reactions. I have not come across any model that proposes a way to accomplish this. Until scientists can come up with a way to demonstrate the possibility of this phenomenon, it is not logical to claim that, with enough time, “the improbable became inevitable” (Lehninger 77). Time alone is not a sufficient explanation for such an amazing feat of organization to have occurred. In fact, time will only make the situation worse as more Legos get added and contribute to the growing rainbow mess.
         Instead of perpetuating the dogma that life must have arisen from nonlife through strictly naturalistic processes, textbooks should leave open the possibility that supernatural intervention was essential in the formation of life. We have seen that textbooks hold on to a naturalistic explanation for the origin of life by blind faith. At its worst, the belief in supernatural intervention is on this same level of blind faith. Though it is frustrating to leave the origin of life to supernatural forces, it is time for all scientists to acknowledge that natural forces alone do not appear to be capable of generating the intricate and immense conglomeration of molecules called life.


Notes

1 Okay, so Spaghetti-O’s are really made by Franco-American.

2 Based on his disbelief in a naturalistic origin of life on Earth, Crick has theorized that life must have arisen from organic garbage left here by aliens. (This is called “directed panspermia.”)

3 We’re going to have to establish some terms for these “components of life.” I use the terms “molecules,” “organic intermediates,” “building blocks,” and “ingredients” in this paper. Molecules refers to the original components of the early atmosphere such as methane, ammonia, and hydrogen gas. Intermediates are formed when the molecules react together. Examples of these are hydrogen cyanide and formaldehyde. Intermediates react to form building blocks (e.g., amino acids and nucleotides), and building blocks stack together to form the ingredients necessary for life (e.g., proteins and genetic material such as DNA or RNA). I use “compounds” or “components” in situations in which I want to keep things general.

4 A low concentration means that the compounds are far apart, while a high concentration means that they are close together. It is important to have a high concentration because compounds only react if they are close to one another.

5 Changes in the soup would involve raising the concentration of the compounds, either by producing lots of them or by isolating them—in little pools, for example.

6 As evolutionist Cairns-Smith notes, however, “all such ‘molecules of life’ are always minority products and usually are no more than trace products. Their detection often owes more to the skill of the experimenter than to any powerful tendency for the ‘molecules of life’ to form” (44).

7 Since I have used Thaxton’s book extensively, let me mention that evolutionists Sidney Fox, David Deamer, and Robert Shapiro, among others, have given the book favorable reviews.

8 Don’t worry if you don’t know what all these things are; they are just products of some of the origin-of-life experiments.

9 For the organic chemists out there, carbonyl-containing molecules (ketones, aldehydes, and reducing sugars) react with free amino groups (of purines, pyrimidines, and amino acids) to form imines, which are useless for the formation of life.

10 Formaldehyde attaches to three of the five important nucleotides and ruins base pairing between them. Base pairing is necessary for replicating genetic material.

11 Molecules that display this “handedness” are called chiral. L and D amino acids are practically identical, though still different, just as our right hand appears to be the mirror image of our left, though it is still different.

12 This is a rather huge assumption. Functional proteins require a highly specific sequence of the different types of amino acids. Even minute changes in the sequence could make the protein useless.

13 Honestly, it is nearly impossible to randomly form a specific protein. Almost every single amino acid would have to be perfectly located in the sequence. For a chaperone protein, which consists of 600 amino acids, the probability of getting the correct amino acid at each of the 600 positions if we just plucked amino acids from a pool of proteinaceous amino acids at random is around (1/20)600. Further, a protein needs several chaperone proteins to fold up properly; one chaperone wouldn’t have done much.

14 Orgel has recently discovered a possible predecessor to RNA, called PNA. PNA can both self-replicate and serve as a template to form RNA. While there is no evidence that PNA could have arisen on the early Earth, Orgel’s discovery at least demonstrates to some the possibility that simple, self-replicating molecules could have formed. Remember that formaldehyde would have ruined its replicative properties, however.

15 While this might be a step in the right direction, it is very far from anything representing a cell. There is no indication of how proteins could have arisen from this process. RNA is like a blueprint: it tells the cell machinery (which consists of proteins) which amino acids it needs for making proteins. But what good is a blueprint if there is no cell machinery to use it? (Remember how difficult it would have been to form specific proteins.)

16 We have already seen how difficult it would have been to combine nucleotides. Once again, we see that scientists fail to address the problem of concentrating necessary building blocks. With nucleotides, there is also the possibility that DNA nucleotides could combine with an RNA polynucleotide. This would be like D-amino acids combining with an L-amino acid polypeptide. We have never seen that genetic material composed of mixed types of nucleotides could be functional.

17 I do not know enough about Deamer’s work to criticize it too much. I do want to mention that the formation of RNA polymerase would have been next to impossible. The simplest RNA polymerase is composed of four protein subunits—two alphas, a beta, and a beta’. (It also needs a subunit called the sigma factor, but I’m not even going to get into that.) We have already discussed how difficult it would have been to form one protein. Imagine forming two identical proteins and two others perfectly, all in the same location. The odds against this are astronomical, especially considering that each subunit is made up of about 1,000 amino acids. And, of course, even if this miracle did occur, we still would need functioning chaperone proteins to give the subunits their proper shapes and combine them.


Works Cited

Alberts, Bruce, et al. Molecular Biology of the Cell. New York: Garland, 1994.

Brock, Thomas D., et al. Biology of Microorganisms. Englewood Cliffs, NJ: Prentice Hall, 1994.

Cairns-Smith, A. G. Seven Clues to the Origin of Life. Cambridge: Cambridge UP, 1985.

Crowe, John. Personal Communication. March, 1996.

De Duve, Christian. “The Constraints of Chance.” Scientific American January 1996: 112.

Denton, Michael. Evolution: A Theory in Crisis. London: Burnett, 1985.

Futuyuma, D. J. Science on Trial. New York: Pantheon, 1983.

Hickman, Cleveland P., Jr. Integrated Principles of Zoology. Wm. C. Brown Communications, 1995.

Horgan, John. “The World According to RNA.” Scientific American January 1996: 27-30.

Johnson, Philip. Darwin On Trial. Illinois: Intervarsity Press, 1993.

Lehninger, Albert L., et al. Principles of Biochemistry. New York: Worth, 1993.

Morris, Henry, and Gary Parker. What Is Creation Science? San Diego: Creation- Life Publ., 1987.

Orgel, Leslie E. “The Origin of Life on Earth.” Scientific American, October 1994: 77-83.

— , et al. “Template Switching Between PNA and RNA Oligonucleotides.” Nature, August 1995: 578-81.

Sagan, Carl. “Ultraviolet Selection Pressure on the Earliest Organisms.” Journal of Theoretical Biology (1973), 195-200.

Thaxton, Charles, et al. The Mystery of Life’s Origin: Reassessing Current Theories. New York: Philosophical Library, 1984.

Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry. New York: W. H. Freeman, 1994.

Zimmer, Carl. “First Cell.” Discover, November 1995: 69-79.