From the beginning.
Article Type: Column
Subject: Earth (Natural history)
Earth (Environmental aspects)
Author: Flannery, Maura C.
Pub Date: 02/01/2010
Publication: Name: The American Biology Teacher Publisher: National Association of Biology Teachers Audience: Academic; Professional Format: Magazine/Journal Subject: Biological sciences; Education Copyright: COPYRIGHT 2010 National Association of Biology Teachers ISSN: 0002-7685
Issue: Date: Feb, 2010 Source Volume: 72 Source Issue: 2
Geographic: Geographic Scope: United States Geographic Code: 1USA United States
Accession Number: 245037736
Full Text: There's a tremendous amount of evidence for evolution, but biologists are always looking for more. As with any delving into the past, this isn't easy to do. Time erases evidence. A number of wonderful sites of prehistoric cave art have been found over the years, from Altamira in the 19th century to Chauvet in the 1990s. But the experts still haven't come up with a plausible explanation for why this art was created (Curtis, 2006). Questions still remain: were these images meant to celebrate the diversity of life or to bring blessing upon a future hunt? Such questions are what make history both a frustrating and a fascinating endeavor, and no part of history is more frustrating or fascinating than investigating early life on earth. If it's hard to piece together what was going on in caves 20 or 30 thousand years ago, it's not surprising that figuring out what occurred 3 or 4 billion years ago would be much more difficult. The amazing thing is that it isn't totally impossible. Biologists, chemists, physicists, and geologists have worked together to come up with some plausible scenarios for the early years of life on earth. Sure, there's still much controversy about some of their explanations, but there has also been a lot of progress since the experiments by Stanley Miller and Harold Urey in the 1950s in which they attempted to recreate the chemical environment of the early earth. In this column, I want to explore several lines of evidence that together give us at least a sketchy view of what early life was like. That's not bad, considering that many of us can't trace our ancestors back more than two or three generations.

* Early Earth

Physicists and geologists agree that the earth is about 4.5-4.6 billion years old. There is also good evidence that in its early years, the earth was a hot and turbulent place. When it was only about 100 million years old, it suffered what Lynn Rothschild (2009: p. 335) calls its "worst day ever" when it was hit by a "rogue" planet. This impact resulted in the formation of the moon and also melted the earth's surface. After that, there were repeated impacts, especially during the late heavy-bombardment era, from 4.1 to 3.9 billion years ago, which left the earth hot and the oceans steamy. It also left little time for the evolution of early life, if, as some argue, that life was significant enough to leave evidence in rocks that are 3.8 billion years old. A hundred million years may seem a long time to evanescent creatures like ourselves, but Darwin was upset when the physicist Lord Kelvin calculated that the earth was only about a hundred million years old. Few, if any, rocks remain from the bombardment period, yet there are a few about 3.8 billion years old that some geologists think contain the remnants of early life. So two questions arise: how solid is this evidence, and how could life arise so rapidly when our experiments to replicate the conditions of the early earth suggest that synthesis of macromolecules would not be an easy or swift process?

Welcome to the world of early evolution! It definitely seems long on questions and short on answers, but things are hardly hopeless, and new evidence keeps being unearthed. Geologists have identified rocks in the Hudson Bay area of Canada that they date to 4.3 billion years ago. This estimate is on the basis of a new dating method using the radioactive decay of samarium-146 (Kerr, 2008). If the calculation is verified, this would make the rock part of the earth's protocrust, which formed from the earliest mantle rock. This is a first, and it's too early to tell if these results will hold up, but there are very old zircon inclusions in "younger" rocks, those dating from about 3 billion years ago (Chang, 2008). Some of these zircons may have formed almost 4.4 billion years ago. The oxygen isotopes in the zircons suggest that water was present as they formed, which indicates that the earth may not have been as hot, at least in some areas, as earlier thought. This would mean that not all the macromolecules formed early in the earth's history would have been destroyed during the late bombardment, so a date of 3.8 billion years ago for life on earth may not imply that life had to evolve from inorganic molecules within a mere 100 million years.

* How Old Is Life on Earth?

But this brings up another question: just how firm is that date of 3.8 billion years? The answer is "not very," at least if you ask some geologists. This date is again based on isotopic evidence. Metabolism favors carbon-12 over carbon-13, so chemical remains of living things have about 3% less carbon-13. Geologists have found that there are several areas where rocks about 3.8 billion years old have depleted levels of carbon-13, which suggests that these specimens contain the chemical remains of life. These are metamorphic rocks, which means they have been transformed by heat and pressure that destroyed any microfossils or biomolecules (Eiler, 2007). So, if there is no biological evidence, is the isotopic evidence strong enough to be convincing? Well, it depends on whom you ask.

The geochemists who generated these data consider them valid, especially because they come from rocks in more than one locale and differ from the ratios in older rocks. Other researchers, however, can come up with nonbiological explanations for the skewed carbon-isotope ratios, including subsequent chemical changes long after the rocks first formed. Those in this camp place the evidence for the first life on earth several hundred million years later, at about 3.5 billion years. They cite rock formations that have not only the skewed carbon ratios but also inclusions that look like bacterial cells and rock formations similar to present-day stromatolites formed by huge, long-lived colonies of cyanobacteria.

It is because of the disagreement over which type of evidence is most valid that some Web sites date the origin of life to 3.8 billion years ago and others to 3.5 billion. I think this is great for students to see: Web sites that are considered legitimate and scientific by the criteria we give students to evaluate sites (".edu" sites; web pages that provide citations for their claims; clear and detailed presentation of the supporting evidence for their claims) and yet come up with different conclusions--different by 300 million years, which is nothing to sneeze at. This particular controversy turns on the kind of evidence one considers valid. Some see so many problems with the isotope ratio data that they discount it; the approach is too indirect - it is based on chemical rather than structural evidence for life. Those in this camp consider chemical evidence too susceptible to other chemical influences in the rock to be reliable.

This is a great example both of how controversies can arise when different scientists use different criteria to evaluate evidence and of how the differences in criteria are often related to differences in scientists' training and areas of expertise. Those familiar with isotopic measurement put more stock in this technique than those who don't use it. But what is someone who has expertise in neither area to do? Well, common sense is always helpful, because it leads to asking such questions as, How much evidence is there for a particular viewpoint, and is it based on only one or a few small studies or on results from a number of locations? As more evidence accumulates, viewpoints can become much more convincing. That's why evolutionists anxiously await more geological research, and why studies on ancient stromatolite-like formations keep getting attention in the science news (Vasconcelos & McKenzie, 2009).

* How Did Life Evolve?

All this argument over when life arose on earth doesn't really get to the issue of how it arose: what chemical processes were involved? This is the question that Stanley Miller and Harold Urey began to explore in the 1950s and that Alexander Oparin had speculated about even earlier when he postulated that life arose in an atmosphere almost free of gaseous oxygen, which would have destroyed the small building blocks of macromolecules like nucleic acids and proteins. Miller and Urey demonstrated that sending a spark through a mixture of ammonia and carbon dioxide could yield amino acids as a first step in the chemistry of life. Though researchers have greatly altered views on the early atmosphere and "primordial soup" in which life arose since the original Miller-Urey experiment, they've gathered a great deal of evidence that generation of organic molecules by reactions is possible, but there is still debate about what reactions, and under what conditions. Astronomers have also identified amino acids and other organic molecules in the interstellar atmosphere, another possible source of molecules for the beginnings of life.

The "RNA world" hypothesis for the origin of life gained ground for a number of years. It's based on RNA ability both to code for information and, as ribozymes, to catalyze specific chemical reactions. The reasoning is that instead of needing separate information (DNA) and catalytic (protein) molecules and their building blocks, early life involved dual-purpose RNA, with these more specialized molecules coming later. One problem with the hypothesis, however, is that it's been difficult to create RNA nucleotides synthetically, in order to mimic what may have happened on the prebiotic earth. New work, however, takes another tack: putting the nucleotide together without first assembling the individual components. This different methodology seems to do the trick. There is also new research showing how RNA nucleotides can bond to each other in an abiotic environment (Zimmer, 2009c).

In looking at still another possible scenario for early life, researchers at Rockefeller University have discovered how RNA could serve as a template for primitive tRNAs that bond amino acids with limited selectivity. They argue that even with such a fuzzy system, the beginnings of selective coding are possible (Lehmann et al., 2009). Here is another wonderful thing about investigating the origin of life with students: I can almost bet that there will be some new, tantalizing piece of information to come out almost every week. One of my favorite examples of this is an article about the work of Mike Russell, who argues for the "metabolism first" rather than "replicator first" view of the origin of life (Whitfield, 2009). He focuses not on information molecules like RNA, but rather on how a set of metabolic reactions could have developed as an underpinning for biochemistry. His hypothesis is based on tiny chimney-like structures discovered in ancient rocks. They resemble the chimneys found near ocean hot springs but are much smaller. Russell reasons that the temperatures in such an environment wouldn't go much above 100[degrees]C, and that the environment would have been alkaline and would have allowed for the concentration of reactants. As these smokers formed, they would have been gel-like, with minerals that could catalyze organic reactions. Where this work fits in with the "information first" research has yet to be determined, but all these studies present a wonderful picture of how science often progresses: people with various viewpoints pursue very different lines of research, and at some point the pieces either begin to fit together or perhaps veer off in a totally different direction. What fun!

* Yet Other Problems

As with so many other topics in biology, genetic sequence analysis has shed much light on early life, and - as usually happens with more knowledge--the questions just proliferate. There's now a great amount of evidence for three major domains: archaea, eubacteria, and eukaryotes. But there's much less consensus on what the earliest form of life looked like genetically. Norman Pace (2006) contends that research has rendered the term "prokaryote" useless because archaea and eukaryotes are more closely related to each other than either of them are to eubacteria. The tree he presents branches in two right at its origin, thus begging the question of the characteristics of the first form of life, or of what has come to be called LUCA, the "last universal common ancestor" (Boussau et al., 2008). One reason that it's very difficult (and perhaps impossible) to identify LUCA is that there is more and more evidence for lateral transmission of genes. This means that genes have been passed not only from one generation to the next - that is, vertically,--but also across species, and even across domains. This makes for a tree of life that looks less like a tree and more like a plate of spaghetti. W. Ford Doolittle (2000), an early supporter of this idea, argues that the three domains probably arose from a number of primitive cells that differed in their genes. In other words, there is no single root to the tree of life.

I must say that as I sit here writing this, I realize that I rarely write an article that's so fuzzy, that has two sides, at least, to every point I raise. I am beginning to question why I picked this topic. Why didn't I do something "easy" like the evolution of the eye (Zimmer, 2009a) or what Darwin calls an "abominable mystery," the origin of flowering plants (Friedman, 2009). In both these cases, some real progress has been made. But with the next big problem on my list, things seem to be moving in the opposite direction, toward less rather than more clarity. The question is, how did eukaryotes arise? Biologists of the present generation were brought up on Lynn Margulis's "endosymbiont" hypothesis: that mitochondria and chloroplasts were originally free-living bacteria that became engulfed by cells and eventually developed such close symbiotic relationships with their hosts that they became part of the cellular furniture. The discovery of profuse lateral gene transfer is one thing that has clouded this picture in recent years, making it less clear that genes moved from mitochondria to the nucleus as Margulis theorized. Another new idea is the hypothesis that mitochondria originated as predators rather than prey, that they took over other cells and, in some cases, used the cells' resources instead of destroying them (Zimmer, 2009b).

Then there is the issue of when did eukaryotes arise. Many estimates go back as far as 2 billion years. These are based on geochemical evidence --eukaryotes leave different chemical remains than prokaryotes--and also on microscopic fossils that are much larger than bacteria. Some are willing to push the date back still further, to 2.8 billion years, reasoning that archaea and eukaryotes arose from a common ancestor, so that eukaryotes must be quite ancient. Here is another example of different estimates based on different kinds of evidence, with the more conservative one based on the more direct support.

* An Aside

As an aside, before I go on to tackle the multicellularity issue, I want to mention an article I found on the evolution of viruses, a group that doesn't seem to get much attention in terms of its evolutionary origins, though present-day viral evolution is a major public-health issue (Balter, 2000). This time it's not genetic sequencing but structural biology bringing about a change in perspective. Comparison of viral genetic sequences indicates broad variations, but structurally there are some seemingly odd resemblances. For example, the herpes virus HSV-1 and the bacteriophage T4 have coats that are very alike in form; they also assemble their genetic material and outer coat proteins in similar fashion even though these viruses are very different genetically. The same is true of another odd couple: human adenovirus and the bacteriophage PRD1. They each have coat proteins that, despite radically different amino acid sequences, have very similar 3-D structures and assemble in the same way in the viral coat.

I like this discovery because it's so surprising. Who would have guessed it? Now the problem is to figure out what it means. Virologists are speculating that viruses are very ancient entities that evolved even before the three domains separated from each other; if so, they are truly roots of the tree of life. Roger Hendrix of the University of Pittsburgh argues that the similarities I've described are so great that it's very unlikely they arose independently, but the great genetic differences imply they arose a very long time ago. Viruses may have existed as packages of genetic material wrapped in protein even before there were cells. This differs from the most common explanation for the origin of viruses, as rogue particles that separated themselves from chromosomes and therefore are akin to transposable elements that move about within the nucleus. I'm hardly the person to settle this question, but I love considering it because it adds still another element to the mix: now we have to try to sort out the origin not only of prokaryotes and eukaryotes, but also of viruses. What fun!

* Oxygen

One issue related to the evolution of eukaryotes is why it took them so long to get together as multicellular organisms. If they indeed arose around 2 billion or even close to 3 billion years ago, why did the Cambrian "explosion," when multicellular creatures seem to suddenly become rife, occur a mere 545 million years ago? If you are expecting me to provide the answer to this question, you really are a trusting soul. I haven't been able to find an answer for any of the other questions about early evolution that I've brought up, so why should this one be any different? However, here as elsewhere, new information is making the picture a little clearer, and, of course, more complex. Given that changes in the environment drive evolution and that oxygen is pivotal to so much of life as we know it, it's not surprising that oxygen may very well be the key here.

The simple view is that molecular oxygen may finally have become plentiful enough around this time that there was sufficient energy available to organisms to fuel more complex structures. But even if this were the case, this wasn't the first rise in oxygen levels in earth's history. The rise occurred in spurts over almost 3 billion years (Kerr, 2005). By 2.7 billion years ago, the cyanobacteria's photosynthetic processes had contributed significant amounts of oxygen, and about 2.4 billion years ago there was what had been termed the Great Oxidation Event that many now consider not that great. Studies of rocks representing ocean-floor deposits from this time and a billion years later indicate that although there was oxygen in the atmosphere and in surfaces waters, the rest of the ocean remained anoxic. This may explain the long wait for multicellularity. What is still difficult to figure out is why the oxygen levels rose when they did. Like everything else I've discussed here, the evidence is so old, so scattered, and so partial that any hypothesis remains fragile.

Another reason why the simple view of oxygen as the driver of the Cambrian explosion is questioned is that this explanation has holes in it. The first is simply that some paleontologists don't see this explosion as all that spectacular. To them it's more that multicellular organisms become more obvious in the fossil record than that they suddenly made an entrance. There are Edicaran organisms that date to at least 700 million years ago. Other paleontologists point to the importance of an extinction event about 542 million years ago, perhaps triggered by noxious waters welling up from the deep sea. This clearing of niches, tied to increased oxygen, may have led to a flurry of radiation events (Kerr, 2002). According to Helen Pilcher (2005), singled-celled organisms seem to have been poised on the threshold of multicellularity for some time. Genetic analysis indicates that all metazoans have similar "toolboxes" of genes responsible for organizing cell aggregates.

Some researchers look to sponges for clues to how multicellular animals arose, because they are considered simple. Yet they are really rather complex, having a number of cell types and a rather complex level of organization. However, examining sponges does give some sense of what the bottom line for multicellularity may have been like. They have genes for a body plan, for organizing cells structurally. They also have a differentiation process that leads to the formation of several different kinds of cell types that also occur in other animals. In addition, sponge cells exude a glue that holds them together, and the different cell types communicate with each other.

A study of choanoflagellates, which are unicellular protists that resemble the collar cells of sponges, suggests that they also have both these important tools. They express genes for cell adhesion proteins and for communication molecules as well. This indicates that the genetic toolbox may have been ready for service well before environmental conditions drove the push to multicellularity. Also, this is a good example of how important the study of what might be considered "odd" protists is to evolutionary biology. Some of them, like the choanoflagellates, seem to foreshadow evolutionary leaps, while others seem to be "fossils," retaining characteristics that have been lost by most other eukaryotes.

* No Conclusion

For the few of you who have stuck with me and read to this point, I wish I could give you some grand answer and tie all these different pieces of evidence, hypotheses, and scenarios together. But this is definitely science in the middle of being done, and I wouldn't be surprised if it remains in an unfinished state for a long time. When students ask when life began and I tell them maybe 3.5 billion years ago, maybe 3.8; or when they want to know when the first eukaryotes arose and I say, maybe 2 billion years ago, give or take a few hundred million either way, they sometimes get annoyed at me. Why can't I give them a straight answer? Isn't that what science is about? No, I'm afraid not. Science is about slogging through data and trying to come up with the best explanation possible, and sometimes that means admitting that no available explanation is that great. What fun! After all, certainty is so dull.

DOI: 10.1525/abt.2010.72.2.13

References

Balter, M. (2000). Evolution on life's fringes. Science, 289, 1866-1867. Boussau, B., Blanquart, S., Necsulea, A., Lartillot, N. & Manolo, G. (2008). Parallel adaptations to high temperatures in the Archaean eon. Nature, 456, 942-945.

Chang, K. (2008). When hell cooled down. New York Times, 2 December, pp. D1, D4.

Curtis, G. (2006). The Cave Painters: Probing the Mysteries of the World's First Artists. NY: Knopf.

Doolittle, W.F. (2000). Uprooting the tree of life. Scientific American, 282(2), 90-95.

Eiler, J.M. (2007). The oldest fossil or just another rock? Science, 317, 1046-1047.

Friedman, W.E. (2009). The meaning of Darwin's 'abominable mystery.' American Journal of Botany, 96, 5-21.

Kerr, R.A. (2002). A trigger for the Cambrian explosion? Science, 298, 1547.

Kerr, R.A. (2005). The story of [O.sub.2]. Science, 308, 1730-1732.

Kerr, R.A. (2008). Geologists find vestige of early earth-maybe world's oldest rock. Science, 321, 1755.

Lehmann, J., Cibils, M. & Libchaber, A. (2009). Emergence of a code in the polymerization of amino acids along RNA templates. PLoS One, 4(6), e5773.

Pace, N.R. (2006). Time for a change. Nature, 441, 289.

Pilcher, H. (2005). Back to our roots. Nature, 435, 1022-1023.

Rothschild, L.J. (2009). Life battered but unbowed. Nature, 459, 335-336.

Vasconcelos, C. & McKenzie, J. (2009). The descent of minerals. Science, 323, 218-219.

Whitfield, J. (2009). Nascence man. Nature, 459, 316-319.

Zimmer, C. (2009a). How the eye evolved. New York Academy of Sciences Magazine (Autumn), 23-25.

Zimmer, C. (2009b). On the origin of eukaryotes. Science, 325, 666-668.

Zimmer, C. (2009c). On the origin of life on earth. Science, 323, 198-199.

MAURA C. FLANNERY, DEPARTMENT EDITOR

MAURA C. FLANNERY is Professor of Biology and Director of the Center for Teaching and Learning at St. John's University, Jamaica, NY 11439; e-mail: flannerm@ stjohns.edu. She earned a B.S. in biology from Marymount Manhattan College; an M.S., also in biology, from Boston College; and a Ph.D. in science education from New York University. Her major interests are in communicating science to the nonscientist and in the relationship between biology and art.
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