The Origins of Life

(This post was originally posted at Disjointed Thinking.)

When someone states that they do not believe in God, often one of the first questions in response is, “Then how did life get here?” Of course, “God did it” is not a good explanation for, well, much of anything, because it does not actually provide any details about the process it claims to explain.¹ Regardless of this, however, it is still a valid question to ask: Without invoking a God, is there a reasonable explanation for how life arose from non-life? This is where the field of abiogenesis comes in.

My goal with this article is to provide a general overview, in simple terms, of the theories and models that scientists have created to explain the development of life from non-life.² I will try to use a minimum of jargon and technical terminology, although some, of course, cannot be avoided. First, the current  biological system will be briefly described, and then two major competing models in the field will be presented.

The Current Creature

DNA Transcription and Translation

As you are no doubt aware, all present-day life on earth is comprised of cells, which store information in DNA (deoxyribonucleic acid). But this is far from the whole picture. DNA is made up of long strands of nucleotides known as “base pairs”, which could be compared to letters in an alphabet. In order to use this information in the DNA molecule, it must betranscribed and translated. This is done with the help of enzymes (proteins that help to facilitate chemical reactions). These enzymes break apart the double helix of the DNA, and then go through each base pair, matching it up to a corresponding base pair which is attached to an RNA (ribonucleic acid) molecule. The major difference between DNA and RNA is that DNA is double-stranded (like a ladder), while RNA is single-stranded (like a broken ladder, with one of the vertical supports missing). After the base pairs are copied to RNA, this RNA then moves to another area of the cell, where more enzymes “read” the different base pairs and translate them into amino acids.³ Certain sets of base pairs correspond to certain amino acids, so the enzymes assemble these amino acids into a long chain. These chains (if formed correctly) are known as proteins. And proteins are the compounds that actually do the work within the cell. Some of them are even responsible for transcribing and translating the DNA in the process that I just described!

The Dividing Line

This outlines the major question to be resolved. DNA/RNA molecules contain the information needed to assemble proteins, but proteins are needed to read that information. Like the chicken or the egg, it becomes a question of which came first: DNA/RNA or proteins? And that is essentially where researchers are divided. Some believe that RNA came first (the RNA world hypothesis), whereas others believe that proteins arrived first (the metabolism first model). But with either model, it is important to note that both RNA and proteins are still present and play vital roles in today’s more complex systems. Evolution has had about four billion years to improve on the systems with which early life started off.

Because of these two major models, there is no consensus in the field as of yet. Abiogenesis is a fairly young field of study, which started around the time of the Miller–Urey experiments in 1952. In comparison to, say, physics, which had its origins in Aristotle (300s BCE) and was developed by others such as Galileo (early 1600s) and Newton (late 1600s), abiogenesis is virtually in its infancy. So it is not unexpected that biologists have yet to come to a firm conclusion on the processes that drove the beginning of life. It is also common for relatively new fields of study to “cast the nets wide” and explore many possibilities. In other words, a lack of consensus is not detrimental to the field. On the contrary, it means the field is healthy and active.

Much Ado about Metabolism

Reverse Krebs Cycle

The first model that will be discussed is the model which posits that proteins and metabolic processes came first. Metabolism deals with the usage of energy, and so researchers who advocate the “metabolism first” model argue that metabolic processes must have been present in order to produce organic molecules such as RNA. Central to this model is the reverse Krebs cycle, a set of chemical reactions which are used by some bacteria today to produce organic molecules from carbon dioxide and water. These chemicals were present on the early earth, and primarily near deep-sea hydrothermal vents. However, the biggest obstacle for this model is that the Krebs cycle has 10 steps to it, and it is difficult to see how such a process could come about without some sort of genetic system to store information and provide the enzymes necessary to keep the cycle going. Zhang and Martin (2006) have found that three of these steps can be driven by zinc sulfide particles, which were present in early Earth waters.⁴ They suggest the possibility that a more complex mineral compound could drive the remainder of the reactions. If this is the case, given an environment where these minerals are plentiful, this could drive the production of complex carbon molecules such as amino acids and nucleotides, which could then be used to create proteins and RNA as the processes became more organized. Some research has demonstrated the ability of some single amino acids to catalyze reactions, which opens the possibility that the reverse Krebs cycle could have been driven to create amino acids for the purposes of facilitating better efficiencies in metabolic processes. In this case, the development of RNA might have been a beneficial by-product of the process.

Despite the work of many researchers on this model, from what I gather (and I am, admittedly, not an expert), it seems that this model is less widely accepted as the next one, which I am about to share with you. There is some evidence that metabolic processes could have arisen without any genetic input, but it seems more likely to be the case that small chains of reactions were eventually connected into larger cycles with the help of genetic information.

The Run-Down on RNA

Miller-Urey Experimental Setup

This brings us to the second major model of abiogenesis: The RNA world model. This suggests that RNA was the first to form, and only later did metabolic cycles, proteins, and enzymes appear. The evidence for this is, in my view, more substantial. To begin with, the work of Miller and Urey demonstrated that, given conditions believed to be present on the early earth (methane, hydrogen, ammonia, and water), many amino acids could form spontaneously. They were able to produce 13 of the 22 amino acids that are used to make proteins in living cells, although a more recent analysis of the sealed vials from the original experiments has found that well over 20 were actually produced. Although this is an impressive result, there is some debate over whether the early atmosphere on Earth differed somewhat from how Miller and Urey believed it to be. Some scientists argue that there would have been large amounts of oxygen (which essentially prevents the creation of amino acids), while others argue that the atmosphere had large quantities of hydrogen (which would facilitate the reactions). However, these are highly technical discussions that are beyond the scope of this article. Either way, Miller and Urey demonstrated that there are conditions under which virtually all the amino acids necessary for life can arise.

In addition to this evidence, the unique properties of RNA make it an excellent candidate for the precursor to life. Although its primary function today is to carry genetic information, much like DNA does, it can also operate as a catalyst for reactions, much like protein enzymes do. Indeed, even in modern cells, ribozymes (catalytic strands of RNA) play a role in synthesizing proteins. Because of this dual property, it is at least possible that RNA could be self-replicating, i.e. catalyze its own replication. And indeed, RNA polymerase is an example of a modern ribozyme that is capable of replicating parts of its own strand.

Of course, the big question is how such an RNA molecule could form in the first place. For many years, scientists could not figure out a chemical reaction that would fuse the nucleobases (the “rungs” of the ladder) to the chain of sugars that make up the base. However, Powner, Gerland, and Sutherland (2009) recently discovered a set of reactions that would allow these components to fuse, which works for two of the four nucleobases used in RNA.⁵ It is possible that in the next few years, similar methods will uncover a way that works for the other two.

Synthesis of Pyrimidine Nucleotides. The previously assumed reactions follow the blue arrows, but they fail to fuse together where the red X indicates. The new successful synthesis follows the green arrows.

Cultivating Complexity

Let’s presume for the moment that a self-replicating RNA strand was at one point able to be produced. If this was the case, the build-up of complexity from that point forward is simple in comparison. Due to their properties, fatty acids (the main component of the modern cell membrane) can form “bubbles” spontaneously. Thus, it is plausible that a primitive fatty acid membrane could have surrounded the first self-replicating RNA strands. This would protect them somewhat from destruction, and also keep them in close proximity to each other to continue replication. These conditions would allow natural selection to occur.

Natural Selection

In order to function, natural selection needs at least four conditions to be met: a (1) population of organisms capable of (2) self-replication, and (3) variation in that population that leads to (4) differential survival. If these conditions are met, natural selection can and will occur. Although it is a stretch to call RNA molecules “organisms”, they do fulfill the conditions. This group of early, self-replicating RNA strands would fulfill the first two conditions to start off. In addition, with no checks or balances to the replication process such as are found in the modern cell, mutations were bound to occur with relative frequency, which would lead to variation in the population. And inevitably, these mutations would lead to differential survival, in the sense that some mutations would lead to an inability to continue self-replication. Thus, natural selection would kick in and begin to select for RNA strands that could replicate with high fidelity, quickly, and more efficiently. Mistakes in the replicating process might often be “fatal”, but many mutations might simply be neutral, or even add extra benefit. And from there, complexity could develop. Protein synthesis may have developed over time, as it would lead to increased efficiencies in further replication. (Proteins are much better catalysts than RNA.) Wolf and Koonin (2007) have outlined a stepwise model for the origin of the protein translation system (which reads RNA and assembles proteins), each step of which would create a distinct advantage for that organism.⁶ And eventually, down the road, when enough complexity had been achieved, similar benefits would lead to the usage of DNA instead of RNA, since the double-stranded structure of DNA is stronger than the single strand of RNA.

Conclusion

What I have written above is just the briefest of summaries regarding the major theories that scientists have developed to describe abiogenesis. These theories rely on much more detailed explanations than I could possibly convey in this article. But the message to take away is that, although there is still certainly much left to discover about the nature and development of early life on Earth, the explanations provided are plausible. Like a detective solving a murder mystery, these scientists are trying to piece together, bit by bit, a coherent narrative based on the clues. We see the yet-unfinished product of four billion years of evolutionary pressures, but the challenge is to reduce life to its most basic elements. And from what scientists have discovered so far, it seems that RNA has the characteristics necessary to be the most fundamental unit of life. Hopefully further research will uncover the details about how it was first formed and the way in which the complexity developed into the beautiful engine that drives us all today.

Notes:

1. See ‘God Did It’ is a Terrible Explanation for more details.
2. As a non-expert in the field myself, I have drawn much of this information from summaries of the research, such as here and here. Readers who would like more information are highly encouraged to visit these well-referenced articles and comb through their source material.
3. I use quotation marks around “read” because these enzymes are anything but literate. They are not reading information like you are reading this article. They simply have certain chemical properties which react to certain sets of base pairs. It is all very much dependent on the physical and chemical properties of the RNA strand and the enzyme.
4. Zhang, X.V., Martin, S.T. (2006). Driving parts of Krebs cycle in reverse through mineral photochemistry. Journal of the American Chemical Society, 128(5), 16032-16033. The article can be found here.
5. Powner, M.W., Gerland, B., Sutherland, J.D. (2009). Synthesis of activated pyrimidine ribonucleotides in prebiotically plausible conditions. Nature, 459(7244), 239-242. The article can be found here.
6. Wolf, Y.I., Koonin, E.V. (2007). On the origin of the translation system and the genetic code in the RNA world by means of natural selection, exaptation, and subfunctionalization. Biology Direct, 2(14). The free full text is available here.