Darwin and LUCA are sitting in a tree…

Deep sea volcano.
LUCA was forged in this hell.
Ancestor to all.

Charles Darwin’s most spectacularly prescient hypotheses was not about evolution. It was about the origin of life on Earth. In his most famous work about natural selection, On the Origin of Species, published in 1859, Darwin stated:

“…probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed…”

Darwin proposed that simple cells somehow arose on the infant Earth, and gave rise to all other organisms that have ever lived. Darwin thought this idea was so important that he linked it to evolution in the beautiful final lines of his masterpiece:

“…whilst this planet has gone circling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being evolved.”

There are two main paths scientists struggle along to test Darwin’s ideas on the origin of life.

One of the main routes is to follow the arrow of time forward, using physics and chemistry to recreate how the solar system and early earth stepped like clockwork from simple chemicals towards the complex majesty of life.

The other way is to work backwards, using our intimate knowledge of organisms today to re-trace their evolutionary path and snatch a glimpse of the original primordial form, the precursor of all life today. What we call the last universal common ancestor, or LUCA.

Building a tree to find LUCA…

Bacterial genes
and proteins trace back in time.
The trunk of our tree.

Biologists want to build family trees of all living things the way we try to build trees of our own ancestors, as far back as we can go. Where we search through databases of things like birth certificates, burial records, and high school yearbooks, biologists use databases of genes and proteins. A phylogenetic tree is a biologist’s fancy term for a family tree.

Today, biologists have access to immense databases and powerful computers to build their phylogenetic trees. Their computers crunch the information encoded in all the genes and proteins in thousands of organisms. Such massive amounts of data and canny coding draw even more accurate trees, sketching many more of the twigs and leaves, but more importantly, drawing the main branches and trunk of the tree.

This is exactly what William F. Martin, Ph.D. does. This former Dallas, Texas carpenter now runs a lab at the Heinrich Heine University in Dusseldorf, Germany, where they crunch massive amounts of data in their search for LUCA.

Martin’s data revealed that the organism which is the great-great-great… grand organism of us all, LUCA, is something that looked superficially like the bacteria which occupy our guts or soils or ponds. But, under the hood, LUCA looked more like the bacteria that thrive near volcanic vents that spew boiling poisonous metals and gases into the dark cold abyss of the sea.

Martin’s team believes that LUCA was anerobic (did not use oxygen), obtained energy from hydrogen, converted carbon dioxide and nitrogen into essential organic compounds, and was heat loving. Extreme heat loving.

Some biologists and oceanographers studying hydrothermal vents believe the energy released by these ocean-floor wounds in the earth’s crust power chemical reactions. Today, we know that the ocean-floor vents produce many organic compounds and the raw materials for life to thrive. These vents support an immensely rich diversity of life. But, did they originate life? Based on his analysis, Martin thinks so.

One of the enzymes Martin found at the base of the tree, within LUCA, is called reverse gyrase. Reverse gyrase protects DNA at high temperatures. Other enzymes in LUCA are consistent with organisms that thrive in hydrothermal vents.

Martin also found that LUCA obtained energy from inorganic compounds and lived without oxygen. The gases hydrogen, carbon dioxide and nitrogen were all LUCA needed to survive (unlike us who need organic compounds we call food and oxygen to survive).

Finally, LUCA contained a number of ancient enzymes. Biologists have long considered modern proteins that require iron-sulfur (FS) clusters to be relics of ancient enzymes, based on tracing amino acids through a variety of bacteria to eukaryotes. FS clusters are among the most common cofactor (something required for an enzyme’s activity) in LUCA’s proteins.

Trouble in paradise…

Scientific wars
Over data and methods.
Truth remains aloof.

Science is a full-contact sport, with hair-pulling and shin-kicking amongst researchers seemingly the normal course of scientific dialog.

A hypothesis like Martin’s does not occur in a vacuum. There are many competing hypotheses and researchers all vying for research grants, publications, and bragging rights.

Claiming that deep-sea vents are where life began on earth is bound to attract critics in a crowded field of science.

One of many other competing hypotheses, for example, suggests life began in a warm, shallow pond on the surface of a volcanic island, exposed to the atmosphere. This hypothesis is actually a direct descendant of Darwin’s thoughts, expressed in a letter to his good friend J.D. Hooker:

“…But if (& oh what a big if) we could conceive in some warm little pond with all sorts of ammonia & phosphoric salts, — light, heat, electricity &c present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter wd be instantly devoured, or absorbed, which would not have been the case before living creatures were formed…”

The modern version of the warm little pond hypothesis provides several critical conditions for the creation of life, according to its supporters. One of the most important is a repeated wet-dry cycle, which helps to concentrate chemical precursors, and drive their reaction to form complex polymers like DNA or proteins.

We can imagine that those objecting to the Weiss paper would have strong opinions, expressed bluntly:

“To the Editor — We wish to comment on several claims made in the paper by Weiss et al., which describes a genomic analysis that they believe is consistent with the origin of life and emergence of a progenote-like last universal common ancestor (LUCA) in hydrothermal vent conditions….”

That is the academic equivalent of a two-by-four applied with vigor and thoroughness to the opponent’s heads.

And we have the Martin Lab’s feisty response.

“Weiss et al. reply — In response to our recent paper, Gogarten and Deamer write in with five paragraphs. They focus on traditional views concerning the nature of the last universal common ancestor (LUCA). We find the current exchange worthwhile in that it highlights several important differences in older and newer concepts concerning both LUCA and approaches to inference of its properties…”

The lead author of the Martin Lab’s paper, Madeline Weiss, beautifully pointed out that Gogarten and Deamer’s hypothesis was outdated, “traditional”, old. That new data and methods have come to light.

Science constantly evolves, and old hypotheses must either adjust or retire.

Despite the complaints of the old, white, male scientists, Gogarten and Deamer, one comment they made was absolutely spot on:

“…We hope that in the future, the authors will propose feasible experiments that will either support or falsify their conjecture about the origin of life in hydrothermal vents…”

That of course is just how science works. Weiss et al. close their paper with the following comment, that their data favors:

“…theories that posit a single hydrothermal environment rich in H2 and transition metals for LUCA’s origin over theories that entail many different kinds of chemical environments catalysing one reaction each.”

The obvious experiment suggested by that comment is also a very hard one, and that is to replicate a hydrothermal environment and demonstrate that a single set of conditions can give rise to a minimal set of complex biochemicals necessary for the origin of life, and that is also consistent with LUCA’s genome.

References…

The physiology and habitat of the last universal common ancestor, Madeline C. Weiss, et al.

Thank you for reading!

If you find this interesting and want a deeper dive, please check out my first and more detailed article on LUCA, here: