Evolution Gets More Predictable

According to a recent study, it has become clear that the genetic circuit for segmentation “was inherited from a common segmented ancestor thought to have lived 600 million years ago and whose presence “changed the face of the world.””  According to the abstract of the study itself:

Annelids and arthropods share a similar segmented organization of the body whose evolutionary origin remains unclear. The Hedgehog signaling pathway, prominent in arthropod embryonic segment patterning, has not been shown to have a similar function outside arthropods. We show that the ligand Hedgehog, the receptor Patched, and the transcription factor Gli are all expressed in striped patterns before the morphological appearance of segments in the annelid Platynereis dumerilii. Treatments with small molecules antagonistic to Hedgehog signaling disrupt segment formation. Platynereis Hedgehog is not necessary to establish early segment patterns but is required to maintain them. The molecular similarity of segment patterning functions of the Hedgehog pathway in an annelid and in arthropods supports a common origin of segmentation in protostomes.

The researchers are now working on confirming the same circuit is behind vertebrate segmentation.  Apart from this being another example of deep homology, where architecture and components shape and channel subsequent evolution for hundreds of millions of years, there is another feature to this story with telic echoes.

Mainstreamin’ the Matrix

Previously, I wrote,

There is no reason to think something as complex as the eukaryotic cell, or the metazoan body plan, would have emerged without oxygen.

and

In other words, the blind watchmaker was not able to cobble some metazoan-like life forms without sufficient oxygen, even though there was almost a billion years of trial and error. Apparently, there are not lots of ways to string together something like a metazoan. As it stands, it is quite reasonable to propose that the blind watchmaker had needs – it needed a eukaryotic cell plan and it needed oxygen (a biological output) to generate metazoa.

Today we read:

Another strategy that physicist Werner von Bloh at the Potsdam Institute for Climate Impact Research in Germany and his colleagues suggest is to focus on the zones around stars where photosynthesis might be possible, since nearly all life on Earth depends on it one way or another for energy.

Although primitive life can exist without photosynthesis, the researchers argue it would be necessary for more complex multi-cellular organisms to emerge. This is because the main source for oxygen on Earth comes from photosynthetic life, and oxygen is thought to be necessary for multi-cellular life to arise.

There ya go.  There are two lessons we can draw from this.

Connections

No, not chemical connections.Not genetic connections.  Not conceptual connections.   How about electrical connections?

Deep on the ocean floor, colonies of bacteria appear to have connected themselves via microscopic power grids that would be the envy of any small town. Much remains unknown about the process, but if confirmed the findings could revolutionize scientists’ understanding of how the world’s smallest ecosystems operate.

Oxygen-breathing bacteria that live on the ocean bottom have a problem. Those sitting atop the sediment have ready access to oxygen in the water but not to the precious mineral nutrients that lie out of reach a centimeter or so below the ground. Meanwhile, those microbes that live in the sediment can access the nutrients, but they lack oxygen. How do both groups survive?

Shaping the Environment

Before looking at a more radical example whereby symbiogenesis with bacteria played a key role in the evolution of a certain metazoan lineage, I thought it a good idea to stress the significance of the terraformers.

The common perception of bacteria is that they are primitive, single-celled organisms. Yet they are not primitive; they are extremely sophisticated in many ways. That’s something most readers of this blog can probably agree with. But I would also argue that, on balance, it is also misleading to think of bacteria as single-celled organisms when, in reality, they are more like cells that are part of superorganism. They form a web of connections. We’ll explore that in future blog entries.

But for now, consider another common perception of bacteria – they are minor players and easy to ignore except when they cause disease. Wrong. Our existence is built on the back of bacteria. Consider a recent survey of the ocean’s biotic diversity:

marine microbes account for up to 90% of all ocean biomass and collectively weigh the equivalent of 240 billion African elephants.

240 billion African elephants. And it’s safe to say that the majority of this microbial biomass is bacterial. Consider this from “Prokaryotes: The unseen majority” by William B. Whitman, David C. Coleman, and William J. Wiebe:

Thus, the total amount of prokaryotic carbon is 60–100% of the estimated total carbon in plants, and inclusion of prokaryotic carbon in global models will almost double estimates of the amount of carbon stored in living organisms. In addition, the earth’s prokaryotes contain 85–130 Pg of N and 9–14 Pg of P, or about 10-fold more of these nutrients than do plants, and represent the largest pool of these nutrients in living organisms.

In fact, how many bacterial cells exist on the planet? Answer – 5 x 10^30

And as any microbiologist will tell you, these cells are found everywhere we find life, including places where bacteria are the only life forms.

So why is all this significant?

Hard Workers of Evolution

Over a year and half ago, I laid out the four general expectations that arise from the hypothesis of front-loading evolution.  One such expectation was that “front-loading would be linked to terraforming.”  As I explained,

So if we are to front-load the existence of mice-like creatures into the genomes of single-celled organisms, we also need to ensure the Earth will be prepared, at some point, to receive the mice. And it is the preparation of a receptive Earth that we can call terraforming

Bacteria are easily viewed as the terraformers, where one of their most glorious successes was to draw from the ancient Earth’s abundant supplies of water and use this to oxygenate the atmosphere which in turn would facilitate the evolutionary emergence of eukaryotes, then metazoan.  Yet there is much more to bacteria.

When it became clear that the genome of a single-celled eukaryotic organism did not need to be radically retooled to transition to the multicellular state of an organism like Volvox, one of Jerry Coyne’s colleagues commented, “Maybe all the hard work was done by bacteria.”

Indeed.  Not only have bacteria terraformed our planet, but they probably facilitated metazoan evolution itself.  In fact, they may have assisted metazoan evolution such that nothing like a metazoan would have emerged had bacteria not existed.

As a tease for this shift in thinking, consider some recent research:

Adaptation

Conventional thinking would have us believe that evolution is all about organisms adapting to the environments over time.  Sure, but it probably goes deeper than this. There is no good reason to think that such adaptation is a purely a passive process, as if the environment itself molds organisms like an artist might shape clay.  On the contrary, there is good reason to think organisms play an active role in this process, as if the clay was participating its own shape changes.

Tiny Marine Microbes Exert Influence on Global Climate

New research indicates that the interactions of microscopic organisms around a particular organic material may alter the chemical properties of the ocean and ultimately influence global climate by affecting cloud formation in the atmosphere.

[…]

The fact that the microbes actively moved toward the DMSP indicates that the tiny organisms play a role in ocean sulphur and carbon cycles, which exert a powerful influence on Earth’s climate. How fast the microorganisms consume DMSP — rather than converting it into DMS — is important because DMS is involved in the formation of clouds in the atmosphere. This in turn affects the heat balance of the atmosphere.

Here

Expectations vs. No Expectations

From here:

The genes that make a fruit fly’s eyes red also produce red wing patterns in the Heliconius butterfly found in South and Central America, finds a new study by a UC Irvine entomologist….”We found that evolution is achieved primarily through recycling old genes into new functions, as opposed to evolving entirely new genes from scratch,” Reed said.

Yes indeed, evolution is achieved primarily through recycling old genes into new functions, as opposed to evolving entirely new genes from scratch. That’s one reason front-loading is plausible. How so?

Duck Absorbs More Data

We’ve just seen another study that echoes front-loading.  Let’s now consider how a hardcore non-teleological viewpoint would  assimilate these findings.  Evolutionary biologist Jerry Coyne – who once wrote, “any injection of teleology into evolutionary biology violates precisely the great advance of Darwin’s theory: to explain the appearance of design by a purely materialistic process” – set things up as follows:

One of the key innovations in the history of life—at least, looking back at it from the viewpoint of a complex species—was the origin of multicellularity.  Having many cells that are differentiated, so that different cells can do different things, allows the specialization of tissues and organs that opens up many new ways of life…. In their important book The Major Transitions in Evolution, John Maynard Smith and Eörs Szathmáry considered multicellularity one of the nine most critical evolutionary innovations.

So how did multicellularity come about? How much genetic change was needed to get those single cells on their own to form colonies, with some of them specializing in reproduction and the others in locomotion, nutrition, and the like?  Did it take a wholesale restructuring of the genome?

[….]

In their new paper Prochnik et al. asked a simple question: if we sequence the whole genome of Volvox carteri, how much difference does it show from its fairly close unicellular relative C. reinhardtii?  Does the initial evolution of multicellularity require many new types of genes, or will a few simple changes suffice?

The first thing to notice from this introduction is the Missing Duck.  That is, where is the guidance from the Duck?  Doesn’t it have a preference, expectation, or prediction?  Isn’t it willing to place a bet?  It would seem not.

In striking contrast, the Rabbit is quite eager to wager.

Unicellular to Multicellular Transition Doesn’t Require Much Retooling

Yet more reason to think the hypothesis of front-loading is both reasonable and plausible:

One of the most pivotal steps in evolution-the transition from unicellular to multicellular organisms-may not have required as much retooling as commonly believed, found a globe-spanning collaboration of scientists led by researchers at the Salk Institute for Biological Studies and the US Department of Energy’s Joint Genome Institute.

A comparison of the genomes of the multicellular algae Volvox carteri and its closest unicellular relative Chlamydomonas reinhardtii revealed that multicellular organisms may have been able to build their more complex molecular machinery largely from the same list of parts that was already available to their unicellular ancestors.

“If you think of proteins in terms of lego bricks Chlamydomonas already had a great lego set,” says James Umen, Ph.D., assistant professor in the Plant Molecular and Cellular Biology Laboratory at the Salk Institute. “Volvox didn’t have to buy a new one, and instead could experiment with what it had inherited from its ancestor.”

Altogether the findings, published in the journal Science, suggest that very limited protein-coding innovation occurred in the Volvox lineage. “We expected that there would be some major differences in genome size, number of genes, or gene families sizes between Volvox and Chlamydomonas,” says Umen. “Mostly that turned out not to be the case.”