Abiogenesis

Abiogenesis is the process by which life arises naturally from non-living matter. Scientists speculate that life may have arisen as a result of random chemical processes happening to produce self-replicating molecules. One of the popular current hypotheses involves chemical reactivity around hydrothermal vents. This hypothesis has yet to be empirically proven, although the current evidence is generally supportive of it.

History: spontaneous generation
Before recent centuries, it was widely believed that abiogenesis happens all around us — in other words, that many individual present-day organisms had originated from nonliving matter. Frogs and mice seem to come from mud, and maggots from rotting meat. In this form, abiogenesis is more usually called "spontaneous generation".

In the ancient Greco-Roman world, it was advocated by some notable philosophers, such as Anaximander or Aristotle (History of Animals, Generation of Animals). Their medieval successors also advocated it, pointing to parts of the Bible that seem to support it, like Genesis 1:20. In 1648, Jan Baptista van Helmont proposed this recipe for mice :

But in 1646, Sir Thomas Browne published a book Pseudodoxia Epidemica ("Vulgar Errors" or "Popular False Beliefs"), in which he expressed skepticism about a variety of common beliefs, including spontaneous generation. Alexander Ross wrote a response to him, which included: He doubts whether mice can be procreated of putrifaction. So he may doubt whether in cheese and timber worms are generated; Or if Betels and wasps in cowes dung; Or if butterflies, locusts, grashoppers, shel-fish, snails, eeles, and such like, be procreated of putrified matter, which is apt to receive the form of that creature to which it is by the formative power disposed. To question this, is to question Reason, Sense, and Experience: If he doubts of this, let him go to Ægypt, and there he will finde the fields swarming with mice begot of the mud of Nylus, to the great calamity of the Inhabitants. Some years later, Francesco Redi became doubtful of the spontaneous generation of flies, so around 1668, he did some classic experiments in which he showed that keeping flies away from rotting meat keeps maggots and flies from appearing in it. However, he still thought that spontaneous generation happens in some other circumstances. Though spontaneous generation was soon discredited for macroscopic organisms, it still seemed true of microscopic "animalcules". But even there, spontaneous generation was gradually discredited by Redi-like experiments, with Louis Pasteur delivering the final blow in 1861.

Still to this day, however, there are cranks who insist that spontaneous generation happens. Wilhelm Reich, for example, saw microscopic vesicles he called "bions" which he claimed could organize themselves into full-blown amoebas. (He rejected the notion that he was merely reconstituting amoebic cysts, because he didn't believe in the "air infection" hypothesis.)

Evolution and abiogenesis
Often brought up in the origins debate is how evolution does not explain the origin of life. Let's get something abundantly clear: abiogenesis and evolution are two completely different things. The theory of evolution says absolutely nothing about the origin of life. It merely describes the processes that take place once life has started. There may also be multiple pathways to producing naturally occurring "life", depending, of course, on the definition of life. This is something that Ben Stein is apparently willfully ignorant of.

An objection to the distinction is that it is goalpost moving, but this would only be true if evolution at some point did try to explain the origin of life and then people moved away from it. This is not the case at all. Evolutionary theory started with the observation of the mutability of species — a property that only exists post-abiogenesis; indeed, later definitions of "life" have often used the ability to evolve as a key component. This, of course, has been known for some time, as animals and crops have been selectively bred for thousands of years. Later, the idea was refined by Charles Darwin in the form of natural selection, where nature provides the selection criteria to drive evolution. At no point was evolution, nor natural selection, about explaining the origin of life — just as we don't fault chemistry for not explaining where atoms come from: it explains how substances behave once they exist, not how they came about.

One objection is that explaining the origin of life is a natural extension to what evolution has to explain. In fairness this is true, and theories surrounding abiogenesis often use natural selection as a jumping point for how organised molecules could themselves develop further (thus making such molecule groups "alive" by the definition discussed above). But whether evolution and natural selection can explain this stage in the development of life is irrelevant to living creatures post-abiogenesis. A common analogy to the fallacy of rejecting evolution due to it not explaining the origin of life is that gravity doesn't explain the origin of life. The analogies are heavily challenged because it leaves people assuming life always existing when it's known otherwise. (Also, gravity and the origin of life have virtually nothing to do with one another, outside of gravity being one of the core forces that defines physics as we know it.)

Aspects
Abiogenesis is not a single step event, but a process. Biological life has the properties or capabilities of organization, metabolism, homeostasis, growth, reproduction, response, and evolution. All cellular life that has those capabilities is alive. Whether viruses are alive or not is more controversial. At least, viruses do reproduce and evolve, but are unable to do so independently from the host cells they invade.

Conversely, first "life" very possibly lacked many important properties, such as homeostasis and response, as in viruses. However, unlike viruses, first life very possibly had (partially or wholly independent) reproduction and metabolism, but which came first is unclear.

DNA or proteins first?
Proteins came before DNA. Reductases convert ribonucleotides into deoxyribonucleotides, a chemically-demanding task which is unlikely to have ever been carried out by ribozymes. No prebiotic pathways for deoxyribonucleotides have been proposed.

Some claim that DNA and proteins must have appeared simultaneously, rising a “chicken or egg” problem: DNA is needed to code proteins for its own replication, so which came first? This question dismisses that RNA is also needed for the existence of both, and that it can and does serve both functions. DNA can be thought of as RNA specialized for genetic storage. Enzymatic properties are of no use for this and the 2-OH' group that allows them makes RNA one hundred times more unstable than DNA.

Artificial abiogenesis
In the 1950s, several experiments by Stanley Miller and Harold Urey verified that the natural formation of amino acids, components of proteins, and other organic compounds out of inorganic materials was possible under the atmospheric conditions of Primordial Earth. The UV radiations from the Sun would've made it impossible on land. Today, it is generally accepted that abiogenesis happened not solely on land or in oceans, but a combination of both.

Lipid Magic
In 1965, Alec Bangham was the first to discover the autocatalytic properties of phospholipids. How you can prove this aspect of nature and disprove the creationist version of the second law:
 * 1) Get a glass of water.
 * 2) Get a yolk of an egg.
 * 3) Put the egg yolk in the water.
 * 4) Profit!!!!
 * 1) Profit!!!!

What actually is happening: the amphipathic lipids arrange themselves based on their interaction with water molecules. It may not be the most extravagant example, but it does show spontaneous order.

Pier Luigi Luisi has shown that vesicles made of these lipids can grow by incorporating new lipids, and can make new vesicles leading to a primitive replication.

Abiogenesis experiments
In 2001, Louis Allamandola demonstrated that organic material can be synthesized in deep space using a "Chill vacuum chamber" — a lot of biomolecules: nitriles, ethers, alcohols, ring-like hydrocarbons, and others.

In a complementary experiment, Jennifer Blank at Lawrence Berkeley National Laboratory reported: "Through subsequent chemical analysis, the team discovered that the initial amino acids in the mixture had linked together to form peptides, from which proteins can be formed."

In 2010, and his colleagues inserted a wholly artificial chromosome into a bacterial cell and produced the first artificial life form (a.k.a. "dial-a-genome"). While it may seem like artificial abiogenesis, it nevertheless involved some major cheating: the artificial chromosome was constructed using gene sequences of an existing organism.

As of 2011, Lee Cronin at the University of Glasgow is trying to start an evolutionary process in polyoxometalate-based "cells".

In 2014, a group of researchers managed to produce all four components of RNA by simulating an asteroid impact in primordial conditions.

A 2015 paper showed that the chemical precursors for the synthesis of amino acids, lipids, and nucleotides, which would be required in a primitive cell, could have all arisen simultaneously through reactions driven by ultraviolet light.

In 2015, the lander discovered 16 organic compounds, four of which had never been detected on a comet before, on the comet 67P/Churyumov–Gerasimenko. Many of the organic compounds are important building-blocks of life.

In 2015, NASA scientists studying the origin of life managed to reproduce uracil, cytosine, and thymine from an ice sample containing pyrimidine under conditions found in space.

A 2016 study showed that the building blocks of life can be replicated in deep-sea vents. These experiments have for the first time demonstrated that RNA molecules can form in alkaline hydrothermal chimneys.

A 2022 study found all four DNA/RNA bases in each of three meteorites from Australia, Canada, and the United States.

Creationists and abiogenesis
Certain creationists correctly point out that abiogenesis must have taken place at some point to begin the process of evolution. They then attempt to use this premise to "disprove" evolution, claiming that Louis Pasteur had conclusively refuted it. However, he only showed that it is not a typical present-day occurrence even for the simplest of free-living organisms — and that complex life forms such as mice don't spring forth fully formed from things like cloth and grain.

Creationists also like to rebut abiogenesis by pointing out seeming prebiotic environments where it does not happen, like in their Peanut Butter Argument, thus highlighting their confusion of abiogenesis with spontaneous generation. However, the most suitable environment has been the subject of active research, like that of Günter Wächtershäuser with his hypothesis of an iron-sulfur world of hydrothermal vents.

Another creationist statement often made is that evolution is abiogenesis; this is simply ignorance of scientific terminology. Evolution is the gradual change of organisms over time, whereas abiogenesis is the start of life itself. The creationists may also be projecting their belief in separate creations onto mainstream biologists.

Yet more creationist illogic is, "Scientists can't explain the origin of life yet, therefore it must have been God, and specifically, the version of God I believe in" (Protestant, Roman Catholic, Islamic version, etc., according to choice).

Probability of abiogenesis
The probability of abiogenesis occurring in a given situation appears important, both for assessing whether abiogenesis was likely to be the origin of life, but also for assessing the likelihood of extraterrestrial life. Naive estimates of probability focusing on the probability of individual chemicals or organisms suggest that abiogenesis is vanishingly improbable: the chance of a specific 300 amino acid protein being created from a set of atoms may be 2.04 x 10390 to 1 against, but this ignores the fact that the process was almost certainly more incremental than that, and that you're not looking for the probability of a specific protein but that of any protein that can be called alive. The same problem arises with creationists' use of Hoyle and Wickramasinghe's argument that the probability of all the chemicals in a bacterium arose by chance is around 1040,000; nobody suggests that bacteria appeared by chance with no simpler precursor. Estimating the actual probablity of life requires a knowledge of not merely the precise conditions of the world at the time of life's origin, and the precise chemical path followed, but the sum total of the probabilities of all possible paths that could produce life. Any estimate must also consider the number of life-supporting planets in the universe, as we are here because abiogenesis occurred on one world, possibly one of billions of candidates. Hence it is incredibly difficult, perhaps impossible, to accurately calculate the probability of life.

Creationists commonly use the improbability of abiogenesis as a disproof of abiogenesis relying on a misapplication of Borel's Law. Intuitions about improbability ignore the difficulty of estimating the probabilities and the failure of our intuitions to handle the vast numbers of molecules and vast time frames available. The number of atoms in the earth has been estimated at around 1051, while there may be around 1047 in the world's oceans (mostly small hydrogen atoms), although neither figure represents the amount of atoms available for abiogenesis. Similarly, while it's not clear exactly what parts of the Earth's history were most conducive, life had hundreds of millions, if not billions of years, to come about, and for much of that time conditions were very different from today. This explains why nobody has seen abiogenesis in a lab or peanut butter jar.

Oil
Oil is now understood to be biogenic in origin, not abiogenic. A hypothesis that oil was abiogenic in origin was popular in the Soviet Union until the 1980s. The abiogenic origin hypothesis proposed that oil formation results from chemical reactions taking place within the earth, and that oil is thus continually replenished and not a fossil fuel. A few (notably astronomer Thomas Gold until his 2004 death, and Jack Kenney) have continued to promote the abiogenic origin hypothesis.

Understanding of origin sciences by the wider community
Many people don’t understand origin sciences. This is caused by a couple of factors.
 * 1) Religious views can get in the way of wanting to understand abiogenesis, preferring explanations involving a miraculous event.
 * 2) Comprehending that unlikely does not equal impossible and, furthermore, that, given sufficient time and opportunity the unlikely becomes likely, is difficult for many non-specialists to understand, and harder yet for the wilfully ignorant and the scientifically illiterate. Furthermore, there is but a small field of scientists who are sufficiently trained in chemistry and geology to be able to properly review abiogenesis. There is, however, a dedicated society to studying the origin of life.

Specifically for origins of life research

 * Origins of life and evolution of the biosphere

Other journals

 * The journal of molecular evolution
 * The journal of molecular biology

Some papers
https://onlinelibrary.wiley.com/doi/abs/10.1002/ijch.201400180
 * Origin of the RNA world: The fate of nucleobases in warm little ponds.
 * Extreme accumulation of nucleotides in simulated hydrothermal pore systems
 * On the Origin of Life
 * Isolation of New Ribozymes from a Large Pool of Random Sequences
 * Nebula-Relay theory: primitive life in nebula and the origin of life on the earth
 * THE LIPID-RNA WORLD
 * Emergence of life in an inflationary universe
 * Possible origin of life between mica sheets: does life imitate mica?
 * The Landscape of the Emergence of Life
 * The Narrow Road to the Deep Past: In Search of the Chemistry of the Origin of Life