segunda-feira, 30 de maio de 2011

From soup to cells — the origin of life

A microbe-like cellular filament found in 3.465 billion year old rock
A microbe-like cellular filament found in 3.465 billion year old rock
Evolution encompasses a wide range of phenomena: from the emergence of major lineages, to mass extinctions, to the evolution of antibiotic resistant bacteria in hospitals today. However, within the field of evolutionary biology, the origin of life is of special interest because it addresses the fundamental question of where we (and all living things) came from.
Many lines of evidence help illuminate the origin of life: ancient fossils, radiometric dating, the phylogenetics and chemistry of modern organisms, and even experiments. However, since new evidence is constantly being discovered, hypotheses about how life originated may change or be modified. It's important to keep in mind that changes to these hypotheses are a normal part of the process of science and that they do not represent a change in the basis of evolutionary theory.
Here, you can learn about important hypotheses regarding when, where and how life originated and find out how scientists study an event that occurred so long ago.

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When did life originate?
Evidence suggests that life first evolved around 3.5 billion years ago. This evidence takes the form of microfossils (fossils too small to be seen without the aid of a microscope) and ancient rock structures in South Africa and Australia called stromatolites. Stromatolites are produced by microbes (mainly photosynthesizing cyanobacteria) that form thin microbial films which trap mud; over time, layers of these mud/microbe mats can build up into a layered rock structure — the stromatolite.
Stromatolites are still produced by microbes today. These modern stromatolites are remarkably similar to the ancient stromatolites which provide evidence of some of the earliest life on Earth. Modern and ancient stromatolites have similar shapes and, when seen in cross section, both show the same fine layering produced by thin bacterial sheets. Microfossils of ancient cyanobacteria can sometimes be identified within these layers.
stromatolites at Shark Bay close up of a stromatolite at Shark Bay
Modern stromatolites in Shark Bay, Australia

cross section of fossil stromatolites cross section of fossil stromatolites
Cross sections of 1.8 billion year old fossil stromatolites at Great Slave Lake, Canada

Where did life originate?

Hydrothermal vent photo
A hydrothermal vent at the bottom of the ocean
Scientists are exploring several possible locations for the origin of life, including tide pools and hot springs. However, recently some scientists have narrowed in on the hypothesis that life originated near a deep sea hydrothermal vent. The chemicals found in these vents and the energy they provide could have fueled many of the chemical reactions necessary for the evolution of life. Furthermore, using the DNA sequences of modern organisms, biologists have tentatively traced the most recent common ancestor of all life to an aquatic microorganism that lived in extremely high temperatures — a likely candidate for a hydrothermal vent inhabitant! Although several lines of evidence are consistent with the hypothesis that life began near deep sea vents, it is far from certain: the investigation continues and may eventually point towards a different site for the origin of life.

How did life originate?
Living things (even ancient organisms like bacteria) are enormously complex. However, all this complexity did not leap fully-formed from the primordial soup. Instead life almost certainly originated in a series of small steps, each building upon the complexity that evolved previously:

  1. Simple organic molecules were formed.
    Simple organic molecules, similar to the nucleotide shown below, are the building blocks of life and must have been involved in its origin. Experiments suggest that organic molecules could have been synthesized in the atmosphere of early Earth and rained down into the oceans. RNA and DNA molecules — the genetic material for all life — are just long chains of simple nucleotides.
    a nucleotide, composed of carbon, hydrogen, nitrogen, oxygen and phosphorus atoms
  2. Replicating molecules evolved and began to undergo natural selection.
    All living things reproduce, copying their genetic material and passing it on to their offspring. Thus, the ability to copy the molecules that encode genetic information is a key step in the origin of life — without it, life could not exist. This ability probably first evolved in the form of an RNA self-replicator — an RNA molecule that could copy itself.
    a chain of nucleotides forms an RNA molecule
    Many biologists hypothesize that this step led to an "RNA world" in which RNA did many jobs, storing genetic information, copying itself, and performing basic metabolic functions. Today, these jobs are performed by many different sorts of molecules (DNA, RNA, and proteins, mostly), but in the RNA world, RNA did it all. Self-replication opened the door for natural selection. Once a self-replicating molecule formed, some variants of these early replicators would have done a better job of copying themselves than others, producing more "offspring." These super-replicators would have become more common — that is, until one of them was accidentally built in a way that allowed it to be a super-super-replicator — and then, that variant would take over. Through this process of continuous natural selection, small changes in replicating molecules eventually accumulated until a stable, efficient replicating system evolved.
  3. Replicating molecules became enclosed within a cell membrane.
    The evolution of a membrane surrounding the genetic material provided two huge advantages: the products of the genetic material could be kept close by and the internal environment of this proto-cell could be different than the external environment. Cell membranes must have been so advantageous that these encased replicators quickly out-competed "naked" replicators. This breakthrough would have given rise to an organism much like a modern bacterium.
    genetic material enclosed in membranes
    Cell membranes enclose the genetic material.

  4. Some cells began to evolve modern metabolic processes and out-competed those with older forms of metabolism.
    Up until this point, life had probably relied on RNA for most jobs (as described in Step 2 above). But everything changed when some cell or group of cells evolved to use different types of molecules for different functions: DNA (which is more stable than RNA) became the genetic material, proteins (which are often more efficient promoters of chemical reactions than RNA) became responsible for basic metabolic reactions in the cell, and RNA was demoted to the role of messenger, carrying information from the DNA to protein-building centers in the cell. Cells incorporating these innovations would have easily out-competed "old-fashioned" cells with RNA-based metabolisms, hailing the end of the RNA world.
    DNA contains instructions.  RNA copies DNA.  Proteins are made from copies instructions.
  5. Multicellularity evolved.
    As early as two billion years ago, some cells stopped going their separate ways after replicating and evolved specialized functions. They gave rise to Earth's first lineage of multicellular organisms, such as the 1.2 billion year old fossilized red algae in the photo below.
    Bangiomorpha pubescens Bangiomorpha pubescens These fossils of Bangiomorpha pubescens are 1.2 billion years old. Toward the lower end of the fossil on the left there are cells differentiated for attaching to a substrate. If you look closely at the upper part of the fossil on the right, you can see longitudinal division that has divided disc-shaped cells into a number of radially arranged wedge-shaped cells, as we would see in a modern bangiophyte red alga.

Studying the origin of life
The origin of life might seem like the ultimate cold case: no one was there to observe it and much of the relevant evidence has been lost in the intervening 3.5 billion years or so. Nonetheless, many separate lines of evidence do shed light on this event, and as biologists continue to investigate these data, they are slowly piecing together a picture of how life originated. Major lines of evidence include DNA, biochemistry, and experiments.
Origins and DNA evidence
Biologists use the DNA sequences of modern organisms to reconstruct the tree of life and to figure out the likely characteristics of the most recent common ancestor of all living things — the "trunk" of the tree of life. In fact, according to some hypotheses, this "most recent common ancestor" may actually be a set of organisms that lived at the same time and were able to swap genes easily. In either case, reconstructing the early branches on the tree of life tells us that this ancestor (or set of ancestors) probably used DNA as its genetic material and performed complex chemical reactions. But what came before it? We know that this last common ancestor must have had ancestors of its own - a long line of forebears forming the root of the tree of life - but to learn about them, we must turn to other lines of evidence.
The 3 domains that include all living things, the most recent common ancestor of all living things, and forebear lineages from before that most recent common ancestor 

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Origins and biochemical evidence
By studying the basic biochemistry shared by many organisms, we can begin to piece together how biochemical systems evolved near the root of the tree of life. However, up until the early 1980s, biologists were stumped by a "chicken and egg" problem: in all modern organisms, nucleic acids (DNA and RNA) are necessary to build proteins, and proteins are necessary to build nucleic acids - so which came first, the nucleic acid or the protein? This problem was solved when a new property of RNA was discovered: some kinds of RNA can catalyze chemical reactions — and that means that RNA can both store genetic information and cause the chemical reactions necessary to copy itself. This breakthrough tentatively solved the chicken and egg problem: nucleic acids (and specifically, RNA) came first — and later on, life switched to DNA-based inheritance.
Another important line of biochemical evidence comes in the form of surprisingly common molecules. As you might expect, many of the chemical reactions occurring in your own cells, in the cells of a fungus, and in a bacterial cell are quite different from one another; however, many of them (such as those that release energy to power cellular work) are exactly the same and rely on the exact same molecules. Because these molecules are widespread and are critically important to all life, they are thought to have arisen very early in the history of life and have been nicknamed "molecular fossils." ATP, adenosine triphosphate (shown below), is one such molecule; it is essential for powering cellular processes and is used by all modern life. Studying ATP and other molecular fossils, has revealed a surprising commonality: many molecular fossils are closely related to nucleic acids, as shown below.
adenine nucleotide and ATP
The discoveries of catalytic RNA and of molecular fossils closely related to nucleic acids suggest that nucleic acids (and specifically, RNA) were crucial to Earth's first life. These observations support the RNA world hypothesis, that early life used RNA for basic cellular processes (instead of the mix of proteins, RNA, and DNA used by modern

Origins and experimental evidence
Experiments can help scientists figure out how the molecules involved in the RNA world arose. These experiments serve as "proofs of concept" for hypotheses about steps in the origin of life — in other words, if a particular chemical reaction happens in a modern lab under conditions similar to those on early Earth, the same reaction could have happened on early Earth and could have played a role in the origin of life. The 1953 Miller-Urey experiment, for example, simulated early Earth's atmosphere with nothing more than water, hydrogen, ammonia, and methane and an electrical charge standing in for lightning, and produced complex organic compounds like amino acids. Now, scientists have learned more about the environmental and atmospheric conditions on early Earth and no longer think that the conditions used by Miller and Urey were quite right. However, since Miller and Urey, many scientists have performed experiments using more accurate environmental conditions and exploring alternate scenarios for these reactions. These experiments yielded similar results - complex molecules could have formed in the conditions on early Earth.
This experimental approach can also help scientists study the functioning of the RNA world itself. For example, origins biochemist, Andy Ellington, hypothesizes that in the early RNA world, RNA copied itself, not by matching individual units of the molecules (as in modern DNA), but by matching short strings of units — it's a bit like assembling a house from prefabricated walls instead of brick by brick. He is studying this hypothesis by performing experiments to search for molecules that copy themselves like this and to study how they evolve.
Two views of RNA replication in the early RNA world 

A knotty problem...
All the evidence gathered thus far has revealed a great deal about the origin of life, but there is still much to learn. Because of the enormous length of time and the tremendous change that has occurred since then, much of the evidence relevant to origins has been lost and we may never know certain details. Nevertheless, many of the gaps in our knowledge (gaps that seemed unbridgeable just 20 years ago) have been filled in recent years, and continuing research and new technologies hold the promise of more insights. As Ellington puts it, "Origins is a huge knotty problem — but that doesn't mean it's an insoluble one."
The Origins Problem: knotty, but not insoluble.

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