Have you met Luca?

I don’t mean in the flesh; Luca has been dead and gone for a long time. But have you heard of him? An important individual was Luca. I am descended from him, and so are you. And everyone else, and everything else that is alive today. Luca is not really a him. Luca is really LUCA, which stands for Last Universal Common Ancestor. Luca lived about three and half billion years ago, and although we don’t know everything about it, we do know a lot. By definition, Luca was the organism from which all current living organisms are descended. There would have been other kinds of life around, but they didn’t last. Only the descendants of LUCA are on earth today.

We know a lot about LUCA because there are many characteristics that all current life forms share, and these are therefore characteristics that LUCA must have had.

LUCA was a small single-celled organism, with a plasma membrane. It had a cytoplasm with many proteins, each composed of either 16 or 20 amino acids arranged in a specific order as a linear polymer. The proteins made up all the structures of the cell, and, as enzymes, catalyzed all the required chemical reactions that allow life to exist. All of these proteins were produced within LUCA by a complex process that all cells today still share. The process starts with a double strand of DNA, which contains a sequence of bases arranged in a manner that codes for each of the proteins. Every group of three bases (a codon) stands for a particular amino acid. As is still true today, there were four kinds of bases, and so there were (and are) 64 possible codons, which means that some amino acids can be coded for by two, three, four or even six different codons. The specific genetic code, which is the identification of which codons code for which amino acids, is the same for you and me, oak trees, elephants, most bacteria, and LUCA[i]. (But we are all different because our DNA sequences are different, much as this blog post is different from the last one because of the sequence of the specific words, even though it’s written in the same language.

In order for this sequence to be translated into the correct proteins, LUCA used an incredibly complex molecular process that (with the rare exceptions mentioned) has not changed in any form of life for three and a half billion years.

The coded sequence is copied from one part of the DNA (called a gene) into a long stretch of RNA (the messenger RNA, or mRNA), which then interacts with another form of RNA called a ribosome. In the ribosome each codon of the RNA (which is the same as the codon on the DNA) is “read” one at a time. The reading process is both chemical and mechanical, and quite fascinating.

Since amino acids and nucleotide bases do not interact chemically, two different adapter molecules are required. One of these is a form of RNA called transfer RNA (tRNA), and there are different specific molecules of this kind of RNA for each amino acid.

There is also a group of enzymes called amino acyl tRNA synthetase (aaRS); again, different ones for each amino acid. The aaRS enzymes have binding sites for one and only one amino acid, and the same enzyme molecule has another binding site specific for the unique shape of the tRNA that has the anticodon for that amino acid. The enzyme then does the actual translation of the nucleotide-based code into the correct protein structure by joining the amino acid to the proper tRNA. The entire process has the technical name translation. Once bound together, the happy couple of tRNA and amino acid goes off to the ribosome, where the tRNA binds to the mRNA, and its amino acid is added to a growing chain making a new protein. This extremely ingenious and complex machinery operates in all living cells, and was present in LUCA as well.

We don’t know how LUCA got to be able to do this, or what happened before LUCA. In this sense, LUCA is like the big bang is for physics. Of course, we know that time existed before LUCA, and probably life did also, but what kind of life was it? And we have no idea how that life was able to produce a genetic code, and the mechanism for protein production that uses the code.

In fact, the same kind of mystery applies to all of the biochemical machinery found in all living cells. These include the mechanical wheels that produce the energy molecule ATP from sunlight or food, the membrane machines that selectively move molecules in and out of cells, the error correction systems, and a host of metabolic pathways by which all cells make the material they need.

Will we discover the answers to these mysterious origins some day? I believe we will, but not until we begin to explore new ways of thinking about biology, and the still unknown laws that control the truly miraculous processes of life.

[i] The rare, slightly different variant code that occurs in a few species of bacteria and protozoa evolved from the original LUCA code as well.)  

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8 Responses to Have you met Luca?

  1. Arnold says:

    ‘And God said, Let there be light’ is enough light for me- I think that’s coded into us too (Romans 1). I think we choose to either receive him, or analyze him into oblivion. For me, Jesus Christ is the only surefire known- everything else is optional.

  2. dgilmanjm says:

    I no longer believe in LUCA. Woese has convinced me that that hypothesis should be rejected (not that it was his intention)

  3. Maybe a naive question… but is it possible that there were some horizontal transfers at different times that might ultimately have included characteristics from more than one source of “life”?

  4. Answering both Dennis and Kumi. Yes, Woese’s work and the recognition of the kingdom of the archea has changed the way we look at the development of early life, and the reality of horizontal gene transfer had made linear trees of descendents more complicated. It is certainly possible that that there were more than one original life form, but the fact that all modern life has the same genetic code suggests that all modern life descended from one branch, and the others died out. Clearly we can only speculate as to what actually happened, and the timing and precise nature of LUCA will never be completely known. But at some point there had to be a common ancestor, if special creation is ruled out.

    • Thank you, Sy. I get what you’re saying. Regardless, this started me down another fascinating rabbit hole.
      I’ve mentioned to you before that I’m of the broad opinion that the translation is more important than the media; it matters less the specific symbols than that they’re translated into a meaningful story. In this regard, I was unaware that even the human mitochondrial code has some variations in interpretation. Interesting.

    • dgilmanjm says:

      1. Woese has convinced me that there were definitely more than one original life form.
      2. The fact that all modern life has the same genetic code also indicates that the same person wrote all the codes. To me therefore, it does not prove common descent. I started out as an agnostic, so I never excluded the possibility of special creation.

      • I don’t exclude the possibilities Dennis mentions. But mathematically, most efficient replication could also satisfy the requirements for of a preponderance of one particular code dominating the use of a resource. Given enough time in a suitable environment, forms of complexity will inevitably emerge. But a self-replicating form will quickly overwhelm mere probability. The formation of an enzyme that codes for itself, whether in RNA or simply some pattern of amino acids, would quickly proliferate. What’s important is that a proper enzyme (a “story” that works) emerges. From that point on, it “writes” for itself, and the particular media will proliferate. That there are five bases and 22 amino acids used in the genetic code suggest to me that this may initially have happened more than once.

        Question for Sy… Are there any organisms that use codons of different lengths – not three bases? Things like CC_ and GG_ have me wondering about the significance of proline and glycine. And then there’s the relative ubiquity of leucine. Just intuitively, it seems most likely that an enzyme starting point might be to utilize one or two bases, or perhaps some common amino acid in its initial self-coding. And my apologies in advance. I’m sure none of this is an original idea… just seeing what sticks.

  5. dgilmanjm says:

    Another thing: After reading everything I found on the matter, I am now convinced that no multicellular life form descended from a singular cell life form.

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