Anaerobic carbon fixation in ancient prokaryotes

Most of us were taught that plants are the main source of fixing carbon from carbon dioxide. Some of us even had to memorize the enzymes and reactions of the Calvin Cycle including the complicated reaction catalyzed by rubisco, the main CO₂ fixing enzyme. [Fixing Carbon: the Rubisco Reaction].

We were led to believe that plants were the main source of sugars and other organic molecules but that's because undergraduate biochemistry education emphasizes human biochemistry. Photosynthesis and plants are only important because they are food. We were also taught, incorrectly, that photosynthesis is defined as a carbon-fixation process. [What is photosynthesis?]

It turns out that the Calvin Cycle isn't restricted to plants and it doesn't even require oxygen. Anaerobic bacteria also have a version of the Calvin Cycle and they are perfectly capable of fixing carbon without a major energy source like photosynthesis. [Carbon Dioxide Fixation in the Dark Ocean]

This makes sense since the earliest forms of life had to be able to turn inorganic molecules (e.g. CO₂) into organic molecules so they had to be able to fix carbon. Current models of the origin of life are referred to as Metabolism First models because they postulate that life began with simple metabolic reactions that made organic molecules from inorganic molecules. One of the most important of these early reactions is the fixation of two molecules of CO₂ into a two carbon compound (acetate).

Paralogs and LUCA

We're interested in the last universal common ancestor of all life (LUCA). In theory, this is a species that gave rise to both Bacteria and Archaea. The general assumption is that this is a single species with a well-defined set of genes that can now be found in all, or almost all, living species.

There are some scientists who question that assumption because they see massive transfers of genes between "species" during the early history of life. This gives rise to a web of life and not a well-defined tree. [The Three Domain Hypothesis: RIP] [The Web of Life] If that model is correct, then the ancestor of all living species could be a group of species that contributed different genes to a pool of organisms that lived billions of years ago. Early Bacterial and Archaeal ancestors could have independently acquired some genes by horizontal gene transfer.

On the evolution of the glycolytic pathway (glycolysis)

Jonathan McLatchie has a PhD in Evolutionary Biology from Newcastle University (UK) and he is currently "resident biologist" and a fellow at the Center for Science and Culture at the Discovery Institute. He is an intelligent design creationist who attacks evolution by questioning standard explanations in the fields of biochemistry and molecular biology.

I've debated him frequently over the years since those are my areas of interest as well. The last time we met was at an evolution conference in London (UK) in 2016 (see photo).

I've always found Jonathan to be more honest and more willing to learn than most of his creationist colleagues so that's why I'm addressing his latest post on Evolution News (sic) where he challenges the evolutionary origins of the glycolytic pathway. As you might expect, his argument is largely based on the idea that since the glycolytic pathway is very complicated, there's no way it could have arisen all at once. He then goes on to reject the idea that the pathway could have evolved incrementally, one step at a time.

The Fermi Paradox: Are we alone in the universe?

All available evidence suggests that we are quite likely the only advanced life form in the Milky Way galaxy. Maybe our planet harbors the only life in the entire universe.

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Where did the glucose come from?

Currently there are two distinct views on the origin of life. The majority of scientists think that life arose in a prebiotic soup of complex organic molecules. Most of them think this "warm little pond" was the ocean (!) and most of them have bought into the stories about asteroids and comets delivering complex organic molecules to create a soup of amino acids and sugars. Presumably, all the earliest forms of life had to do was to join together the amino acids to make proteins and hook up the nucleotides to make RNA. The energy for these reactions was derived from breaking down all the glucose in the sweet ocean.

The origin of eukaryotes and the ring of life

The latest issue of Philosophical Transactions of the Royal Society B (Sept. 26, 2015) is devoted to Eukaryotic origins: progress and challenges. There are 16 articles and anyone interested in this subject has to read all of them.

Many (most) of you aren't going to do that so let me try and summarize the problem and the best current ideas on how to solve it. We begin with the introduction to the issue by the editors, Tom Williams, Martin Embley (Williams and Embly, 2015). Here's the abstract ...

Comets and meteorites CAN NOT create a primordial soup in the ocean

I want to talk about two recent press releases on the origin of life.

The first one is from the BBC and it talks about the work of Haruna Sugahara and Koicha Mimura who presented their results at a recent conference [Comet impacts cook up 'soup of life']. They noted that the impact of a comet carrying organic molecules can produce more complex organic molecules.

The second report is from ScienceDaily. It reports a similar study by Furukawa et al. (2015) who examined the idea that the impact of meteorites in the primitive ocean could create more complex organic molecules than those already found in meteors [Meteorite impacts can create DNA building blocks].

The problem of the origin of life has been solved and creationists are terrified

You learn something new every day. Today I learned that a young physics professor at MIT has figured out how life originated without god(s). Salon let's us know about this amazing discovery: God is on the ropes: The brilliant new science that has creationists and the Christian right terrified.

The Christian right’s obsessive hatred of Darwin is a wonder to behold, but it could someday be rivaled by the hatred of someone you’ve probably never even heard of. Darwin earned their hatred because he explained the evolution of life in a way that doesn’t require the hand of God. Darwin didn’t exclude God, of course, though many creationists seem incapable of grasping this point. But he didn’t require God, either, and that was enough to drive some people mad.

Darwin also didn’t have anything to say about how life got started in the first place — which still leaves a mighty big role for God to play, for those who are so inclined. But that could be about to change, and things could get a whole lot worse for creationists because of Jeremy England, a young MIT professor who’s proposed a theory, based in thermodynamics, showing that the emergence of life was not accidental, but necessary. “[U]nder certain conditions, matter inexorably acquires the key physical attribute associated with life,” he was quoted as saying in an article in Quanta magazine early in 2014, that’s since been republished by Scientific American and, more recently, by Business Insider. In essence, he’s saying, life itself evolved out of simpler non-living systems.

Jerremy England's ideas are too complex for me. Watch this video to see for yourself.

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More primordial soup nonsense

I just discovered a new paper on the origin of life (Keller et al. 2014). The authors think they are looking at the first primitive biochemical pathways, which they identify as glycolysis and the pentose phosphate pathways.

Here's what they did. They took a bunch of pure sugar phosphates¹ and dissolved them in water containing salts and metal ions that were likely present in the primordial oceans. They heated the solution up to 70° C and looked at the degradation products. Low and behold, the sugar phosphates degraded and sometime the products were other intermediates in the glycolytic and pentose phosphate pathway, including pyruvate and glucose.

They conclude that ...

Origin Stories

Here's a podcast on the origin of life. Check out the website to see who's talking [Origin Stories].

For some strange reason the show begins with Greek mythology. Then it moves on to real science. There are three origin of life scenarios ...

1. Darwin's warm little pond ... equivalent to primordial soup.
2. Panspermia ... which doesn't solve anything.
3. Hydrothermal vents ... which aren't explained

The moderator seems to think that primordial soup has problems and panspermia is a nonstarter but he doesn't explain the hydrothermal vent story and doesn't even mention Metabolism First.

The second half of the show features soundbites suggesting that the origin of complex organic molecules on Earth is a problem but they could form in interstellar space. But this is exactly the "problem" that Metabolism First tries to explain so it's puzzling that there was no advocate of this view on the show.

This is a complicated topic that is not compatible with the format of this show. How do you, dear readers, think it rates as science journalism? Is this a good way to get the general public interested in science?

The blurb on the website suggests that the series is highly rated by fellow journalists.

A show that explores the bigger questions. Winner of "Top New Artists" and "Most Licensed by Public Radio Remix" awards at PRX's 2011 Zeitfunk Awards.

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Metabolism First and the Origin of Life

There are several competing hypotheses about the origin of life. Most people know about the Primordial Soup scenario; that's the one where complex organic molecules are created by spontaneous chemical reactions. Over time these complex molecules, such as amino acids and nucleotides, accumulate in a warm little pond and eventually they come together to form proteins and nucleic acids.

The RNA World scenario is similar except that nucleic acids (RNA) are thought to form before proteins. For a while, RNA molecules are the main catalysts in the primordial soup. Later on, proteins take over some of the catalytic roles. One of the problems with the RNA world hypothesis is that you have to have a reasonable concentration of nucleotides before the process can begin.

The third hypothesis is called Metabolism First. In this scheme, the first reactions involve spontaneous formation of simple molecules such as acetate, a two-carbon compound formed from carbon dioxide and water. Pathways leading to the synthesis of simple organic molecules might be promoted by natural catalysts such as minerals and porous surfaces in rocks. The point is that the origin of life is triggered by the accumulation of very simple organic molecules in thermodynamically favorable circumstances.

Simple organic molecules can then be combined in various ways that result in simple amino acids, lipids, etc. These, in turn, could act as catalysts for the formation of more organic molecules. This is the beginning of metabolism.

Eventually simple peptides will be formed and this could lead to better catalysts. Nucleic acids and complex amino acids will only form near the end of this process.

One of the advantages of the metabolism first scenario is that it offers a simple "solution" to the chirality/racemization problem by explaining why all naturally occurring amino acids are left-handed [see Can watery asteroids explain why life is 'left-handed'?]. Another advantage is that it doesn't require spontaneous formation of nucleotides—a major limitation of the RNA world scenario since spontaneous formation of such molecules is very improbable.¹

James Trefil, Harold Morowitz, and Eric Smith have written up a very nice summary of the Metabolism First hypothesis for American Scientist: The Origin of Life. The subtitle, "A case is made for the descent of electrons," is a clever play on words. It illustrates the point that synthesis of simple organic molecules such as acetate are thermodynamically favorable. This is science writing at its best.²

The authors have reconstructed the simplest, most fundamental, biochemical pathways concluding that a reductive citric acid cycle is probably the best example of the first metabolic pathway. In this pathway, the two-carbon acetate molecule is made from carbon dioxide and water in the reverse of the common citric acid pathway found in eukaryotes.

In fact, the reductive pathway occurs in many bacteria. They can still use it to fix carbon. The authors use the figure on the left to illustrate the basic pathway.

Almost all of the common molecules of life are synthesized from acetate or the molecules of the citric acid cycle. The simple amino acids, for example, are formed in one step. More complex amino acids are derived from the simple amino acids, etc. Similarly, simple fatty acids can be formed from acetate and more complex ones come later; once the simple ones accumulate.

The central role of citric acid cycle metabolism in biochemistry has been known for decades. It's involvement in biosynthesis pathways is often ignored in introductory biochemistry courses because they are heavily focused on fuel metabolism in mammals and biosynthetic pathways get short shrift in such courses.



The essence of Metabolism First is that the various complex molecules of life came after the spontaneous formation of very simple molecules. Pathways leading to the complex molecules evolved and their evolution was assisted by the evolution of various catalysts, some of which were biological in nature.

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1. In spite of the claims surrounding a recent paper in Nature: RNA world easier to make.

2. Probably good science editing as well. My friend Morgan Ryan is managing editor and he is very good.

[Photo Credit: American Scientist, courtesy of Scripps Institution of Oceanography, University of California, San Diego.]