When did life first appear?

The Earth’s rock record begins around 3.8 billion years ago with a period that is known as the Archaean.  The Archean can be split into different eras, where the early Archaean extends from 3.8 to 3.6 billion years ago, the Paleoarchaean extends from 3.6 to 3.2 billion years ago, the Mesoarchaean extends from 3.2 to 2.8 billion years ago, and the Neoarchaean extends from 2.8 to 2.5 billion years ago.  At this point, a new period known as the Proterzoic begins and it will extend all the way until about 550 million years ago, the time of the Precambrian.

I have long assumed that life appeared on this planet approximately 3.5 billion years ago.  But lately, the evidence for such ancient life seems to be evaporating.  The crown jewel among the ancient microbial fossils has been the filamentous cyanobacteria from 3.5-billion-old Australian chert that were first described by William Schopf from UCLA.  Yet in 2002, Martin Brasier and colleagues made a strong case that those fossils are not remnants of living things, but represent the activity of ancient and exotic geochemical processes [1].  And a recent study has just confirmed these are not fossils (HT to Joe):

Introns and Metazoans again

Recall that I hypothesized that introns have played a key role in facilitating metaozoan evolution.  Here’s some more support support for that hypothesis:

Darwin’s warm pond idea fails test

Life on Earth was unlikely to have emerged from volcanic springs or hydrothermal vents, according to a leading US researcher.

Experiments carried out in volcanic pools suggest they do not provide the right conditions to spawn life.

MORE

Metazoan transcription factors predate metazoans

I run across many papers that support the hypothesis of front-loading, but never seem to find the time these days to write up blog entries that explain the findings and how they relate to FLE.  So instead of just sitting on them, I thought I would share them by posting the abstracts.  In the future, I hope to comment on them.  If you have read the book or follow this blog, you should be able to pick out the relevance of the findings.  So here’s the first one about transcription factors, which are proteins that regulate the expression of genes:

The Archaean Expansion

[Edit added 4/27/11.

PZ Myers, the atheist activist who recently helped organize a smear campaign against Nick Matzke, has offered some opinions about this blog entry. He writes:

One of the creationist summaries is by an intelligent design creationist. He looks at the paper and claims it supports this silly idea called front-loading: the Designer seeded the Earth with creatures that carried a teleological evolutionary program, loading them up with genes at the beginning that would only find utility later. The unsurprising fact that many gene families are of ancient origin seems to him to confirm his weird idea of a designed source, when of course it does nothing of the kind, and fits quite well in an evolutionary history with no supernatural interventions at all.

I’ll ignore the use of stereotype in calling me a “creationist,” as Myers also calls Ken Miller a creationist. That should clue you in to the level of intellectual rigor that is involved in his labeling. The main problem is that his description is a total misrepresentation of my position.

First, front-loading has nothing to do with “loading them up with genes at the beginning that would only find utility later.” I explained the error of this interpretation two years ago. Secondly, no where do I argue for a supernatural intervention in evolutionary history. I agree there is no evidence of supernatural intervention in evolutionary history.

Myers characterization of my views are rooted in a form of ignorance that is sustained by stereotype. In fact, what is ironic is that the conclusions from the summary figure he cites are the very ones I picked out before he got around to the paper.

Myers: If you draw any conclusions from the graph, it's that life on earth was essentially done generating new genes about one billion years ago…but we know that all the multicellular diversity visible to our eyes arose after that period. What gives?

Me (from below): Note that gene births, shown in red, explode on to the scene and then become insignificant about a billion years ago, long before the Cambrian explosion.

Myers: That's what the blue and green areas tell us. We live in a world now rich in genetic diversity, most of it in the bacterial genomes, and our morphological diversity isn't a product so much of creating completely new genes, but of taking existing, well-tested and functional genes and duplicating them (blue) or shuffling them around to new lineages via horizontal gene transfer (green). This makes evolutionary sense. What will produce a quicker response to changing conditions, taking an existing circuit module off the shelf and repurposing it, or shaping a whole new module from scratch through random change and selection?

Me (from below): This is a visual pattern that maps nicely to the dynamics of front-loading that I have been discussing for years, as gene duplication is an excellent strategy of forwarding designs into the future and allowing them to function as feelers.

And from the linked essay:

So while most are content to view gene duplication and pseudogenes merely as a sign of common descent, there is a deeper perspective available that will help you to begin to appreciate the logic of evolution.

You don't refute the hypothesis of front-loaded evolution by agreeing with me. So, as it stands, nothing Myers offers leads me to think there is anything wrong in thinking this new research strengthens the case for the design of evolution.]

Check this out:

MIT scientists have created a sort of genomic fossil that shows that the collective genome of all life underwent an enormous expansion about 3 billion years ago, which they’re calling the Archean Expansion.

[…]

The scientists traced thousands of genes from 100 modern genomes back to those genes’ first appearance on Earth to create a genomic fossil telling not only when genes came into being but also which ancient microbes possessed those genes. The work suggests that the collective genome of all life underwent an expansion between 3.3 and 2.8 billion years ago, during which time 27 percent of all presently existing gene families came into being.

So one out of four gene families that are known to exist came into existence about 3 billion years ago.Actually, it would be higher than this, as the researcher’s excluded genes that we already present at the Last Universal Common Ancestor.  So if we are to add in the universal genes, it’s probably closer to one out of three or two gene families originating near the origin of life.  Thus, it is important to remember that all subsequent evolution took place in the context of this ancient genetic information.

This new research strengthens the case for the design of evolution:

So if we posit that the original life forms were designed, instead of viewing the composition and architecture of life as something that natural forces cannot possibly account for, consider the more tantalizing possibility that the composition and architecture of the first cells as representing a choice architecture designed to influence/nudge the “choices” made during subsequent evolution. The manner in which the various pieces and parts of life were hooked up would represent the architecture of life and this, in turn, would amount to a logic that would help guide and facilitate subsequent evolution. The actual pieces and parts of life would represent the composition of life and this, in turn, would amount to various preadaptations that would favor certain evolutionary trajectories over others.

This recent research has helped to show more clearly that a huge chunk of the composition and architecture of life is very ancient and could thus serve the objective of nudging subsequent evolution.  In fact, consider one figure from the study:

Lateral transfer climbs up the tree

Though researchers now generally agree that horizontal gene transfer is relatively common among simple organisms like bacteria, they have continued to assume that it remained relatively rare among complex organisms like plants and animals.

“The thinking has been that there is very little horizontal gene transfer among plants and animals except for a few big, ancient events and maybe the occasional transfer of a single gene here or there,” Slot said. “Our discovery suggests that the horizontal transfer of gene clusters may have been a big player not only in the evolution of bacteria but also in more complex organisms.”

Discovery of Jumping Gene Cluster Tangles Tree of Life

Eukaryotes and Prokaryotes

I’ve long found it fascinating that every living thing on this planet can be cleanly split into two categories – prokaryotes and eukaryotes.  The prokaryotes consist of all the bacteria while the eukaryotes include animals, plants, fungi, and various protozoa.  The core life processes of the two cells are much the same, being built around the triad of proteins, RNA, and DNA, relying on the ribosome to build the proteins that synthesize everything else, including RNA and DNA, using ATP as the primary energy currency, and using lipid bilayer membranes to compartmentalize.  So what makes the two cell plans so different?

Below is a nice figure that helps you answer this question.

 

As you can see, there are two primary differences: size and level of compartmentalization.  Typical eukaryotic cells are much larger than bacteria and show a much more extensive level of compartmentalization given the numerous membrane-bound organelles and membranous folds.

Yet a question to ponder is why there are two cell types and only two cell types?  The non-telic perspective would explain this (away?) as simply an artifact of a contingent past.  There is no reason to ponder the question “why?”  It just happened that way.  But the telic perspective allows us to think of these two cell plans at a level that runs deeper.

Moonlight Sonata