{"id":300041,"date":"2020-11-04T11:00:00","date_gmt":"2020-11-04T19:00:00","guid":{"rendered":""},"modified":"2020-11-04T11:00:00","modified_gmt":"2020-11-04T19:00:00","slug":"have-researchers-developed-a-computer-algorithm-that-explains-the-origin-of-life","status":"publish","type":"post","link":"https:\/\/reasons.org\/creation\/evolution\/have-researchers-developed-a-computer-algorithm-that-explains-the-origin-of-life","title":{"rendered":"Have Researchers Developed a Computer Algorithm that Explains the Origin of Life?"},"content":{"rendered":"
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As a chemistry major at West Virginia State College during the early 1980s, I was required to take a library course on the chemical literature before I could graduate. During the class, we learned how to use the many library reference materials devoted to cataloging and retrieving the vast amount of chemistry research published in the scientific literature. Included in this list was the multivolume Beilstein\u2019s Handbook of Organic Chemistry<\/em>.<\/p>\n

Beilstein\u2019s Handbook of Organic Chemistry<\/em><\/strong><\/p>\n

Beilstein\u2019s Handbook<\/em> consists of hundreds of volumes with entries for well over 10 million compounds. The books that originally made up Beilstein\u2019s Handbook<\/em> took up rows of shelves in the library with new volumes ad<\/span>ded to the collection every few years. Today, the Beilstein\u2019s<\/em> volumes are no longer published as printed editions. Instead the entries are now housed online in the Beilstein\u2019s Handbook <\/em><\/a>database, with the old print volumes serving as little more than artifacts of a bygone era in the annals of chemistry.<\/span><\/p>\n

Learning to master Beilstein\u2019s Handbook <\/em>is<\/span> no easy task. In fact, there are textbooks devoted to teaching chemists how to use this massive database effectively. It is well worth the effort. If you know what you are doing, Beilstein\u2019s Handbook<\/em> holds the key to finding quickly anything you need to know about any organic compound, provided it has been published somewhere.<\/p>\n

Beilstein Synthesis and the Origin-of-Life Problem<\/strong><\/p>\n

The utility of Beilstein\u2019s Handbook<\/em> is endless and its applications far-reaching. In fact, Beilstein\u2019s<\/em> has even served as the inspiration for origin-of-life chemists seeking to make sense of prebiotic chemistry and chemical evolution. These investigators think that if they can master an approach to prebiotic chemistry called a Beilstein synthesis, then they may well gain key insight into how chemical evolution generated the first life on Earth. In short, a Beilstein synthesis involves a chemical reaction taking place in a single flask with a large number of chemical compounds serving as the reactants. This process is so named as a nod to the 10 million entries in the Beilstein\u2019s database.<\/span><\/p>\n

Origin-of-life scientists are interested in Beilstein synthesis because they think that these types of reactions more closely reflect the chemical and physical complexity of early Earth\u2019s environment. Yet, very few origin-of-life researchers have even attempted this type of reaction. Understanding what transpired during a Beilstein synthesis has long been an intractable problem. Until very recently, the analytical capabilities didn\u2019t exist to efficiently and effectively characterize the myriad products that would form during a Beilstein reaction, let alone identify and characterize the different chemical routes in play. For this reason, origin-of-life researchers have focused on singular prebiotic processes involving a limited number of compounds, reacting under highly controlled laboratory conditions. In these types of reactions, it is far easier to make sense of experimental outcomes\u2014but the ease of interpretation comes with a cost.<\/p>\n

Over the last 70 years, the focus on singular sets of reactions and highly controlled conditions has produced some successes for origin-of-life researchers\u2014albeit qualified ones. Focusing on isolated reactions and specific sets of conditions has made it possible for researchers to identify a number of physicochemical processes that could have contributed to the early stages of chemical evolution\u2014at least, in principle<\/em>. Unfortunately, serious concerns remain about the geochemical relevance of these types of experiments. These reactions perform well in the laboratory, under the auspices of chemists, but significant questions abound about the productivity of the same laboratory processes in the milieu of early Earth. (For a detailed discussion of this problem, I recommend my blog article \u201cPrebiotic Chemistry and the Hand of God<\/a>.\u201d)<\/p>\n

Additionally, these highly controlled reactions\u2014carried out under pristine conditions\u2014fail to take into account the chemical and physical complexity of early Earth. Undoubtedly, this complexity will impact the physicochemical processes on early Earth, shaping the outcome of plausible prebiotic reaction routes. No one really knows if this complexity will facilitate chemical evolution or frustrate it, but now we have some idea, thanks to the work of a research team from the Polish Academy of Sciences. These investigators moved the origin-of-life research community closer to achieving a prebiotic Beilstein synthesis by developing and deploying a computer algorithm (called Allchemy) to perform computer-assisted organic chemistry designed to mimic the earliest stages of chemical evolution. In effect, they performed an in silico Beilstein reaction with some rather intriguing results.1<\/sup><\/p>\n

Allchemy and the Prebiotic Chemistry<\/strong><\/p>\n

The researchers used Allchemy to identify the reaction pathways and products that could have formed under plausible early Earth conditions. They initiated the computer-assisted reactions by starting with hydrogen sulfide, water, ammonia, nitrogen, methane, and hydrogen cyanide as the original set of reactants, under the assumption that these small molecules would have been present on early Earth. After the reactions reached completion, the researchers removed any products that possessed an \u201cinvalid\u201d chemical structure, then incorporated the remaining reaction products into the original set of starting compounds, and ran the computer-assisted reactions again. They repeated this process 7 times.<\/p>\n

For each generation of reactions, they \u201ccomputed\u201d reaction pathways and products using a set of 614 rules. These rules were developed by encoding into the algorithm all of the known prebiotic reactions published in the scientific literature. They also encoded plausible conditions of early Earth. As they developed the list of rules, the researchers also paid close attention to chemical functional groups that would be incompatible with one another. As it turns out, it was possible to group these 614 rules into 72 chemical reaction classes. The algorithm began each generation of reactions by identifying suitable reactants for each class of reactions and then \u201creacting\u201d them to discover the types of products that would form.<\/p>\n

Allchemy Results<\/strong><\/p>\n

Through the course of 7 generations of reactions, Allchemy produced almost 37,000 chemical compounds from the initial set of 6 gaseous molecules. Of these compounds, only 82 were biotic. And, of this collection, 41 were peptides (formed when amino acids react together to form an adduct).<\/p>\n

As it turns out the biotic compounds had some unusual properties that distinguished them from the vast collection of abiotic molecules. These compounds:<\/p>\n