Tag Archives: evolution

The end of the evolutionary road on a far future earth

The question of how life first came to be on early earth  has been of fascination to scientists for decades. By stark contrast, the question of how life may end on Earth in the distant future has received little attention, probably because the question itself forces us to face the rather depressing reality that one day, our star will die, our planet’s center will cool, and Earth will no longer be capable of supporting life. But the end of the road for life on Earth will not dawn on us overnight. Just as it took billions of years for our earliest prokaryotic ancestors to evolve into complex, multicellular life (these early microbial communities, spread far and wide across the earth, had the big responsibility of oxidizing the atmosphere so that multicellular organisms could have something to breathe) it will likely take millions if not billions of years for life on Earth to devolve as the planetary systems that allow complex ecosystems to exist slowly shut down.

How will the end of life happen?  On present day Earth, the weathering of silicate rocks draws carbon dioxide out of the atmosphere and returns it to the continental and oceanic crusts. This process occurs quite slowly (millions – billions of year timescales), but ultimately if there were no source of carbon to replenish the CO2 drawn out of the atmosphere by weathering, it would eventually be depleted. This would make our planet inhospitable to plant life, which requires CO2 to do photosynthesis. Unfortunately this is exactly what will happen when our star begins to die. As the Sun ages, its luminosity will increase, meaning Earth’s surface is going to get hotter. This will speed up silicate weathering and the speed with which CO2 leaves our atmosphere. Normally, this CO2 would be replenished with carbon recycled through the crust and mantle due to tectonic activity. However, the heating up of the planet’s surface will also increase surface water loss due to evaporation, which will increase the friction between the plates until eventually plate tectonics shuts down entirely.

When atmospheric CO2 concentrations drop below a critical threshold (< 10 ppm), plants will begin to die off. With the plants will go both the food and oxygen source for animals. Large ectotherms (large mammals and birds) will likely go first, due to their high oxygen requirements, followed by smaller ectotherms (i.e., small birds, rodents). Reptiles, amphibians and fish will likely outlast the rest of us due to their lower oxygen requirements, with marine species lasting longer in general because the oceans will likely heat up less rapidly than the land. Eventually, within perhaps 100 million years of the end of plant life, the world will be returned to the microbes.

And what might the final microbes on Earth be? In all likelihood, they will be extremophiles capable of tolerating multiple environmental stressors (polyextremophiles)- low oxygen concentrations and high temperatures, for example. They will recede from the planet’s surface where high heat and rapid evaporation will be too stressful. In all likelihood, they will return to deep ocean vents and similar subsurface environments that are both buffered from surface temperatures and capable of supplying their own source of energy.

I’ve just described the devolving (or perhaps mass extinction occurring on along a trajectory of evolutionary complexity over geologic timescales) of life of Earth in broad brushstrokes. As with most scientific theories, there are details, nuances, unanswered questions and questionable assumptions. Of course, this is also assuming that some anthropogenic force doesn’t end life on Earth far sooner (nuclear war, chemical warfare, climate change, GMOs, encountering an unfriendly and technologically superior alien race, creation and subsequent uprising of AI, zombie apocalypse). And it’s also possible that I’m being far too pessimistic, and some future technological or geoengineering solution will be able to keep our planet liveable far beyond its natural lifetime.

I’ll leave you with a plug for SpaceRip, a really awesome astronomy youtube show that has several episodes focused on questions of planetary habitability. These guys know way more than I do.

The Search for Earth-Like Planets

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The tree of life becomes clearer with Next-Generation sequencing

Since the dawn of molecular genetics, scientists have been developing new ways to reconstruct evolutionary relationships among organisms. While historically, taxonomy was a field that relied on comparative anatomy of living organisms, or even more challenging, comparative anatomy of fossils, the comparison of genetic code allows for precise measurements of relatedness among different species. However, sequencing an entire genome was, until quite recently, prohibitively expensive for everything except well-characterized model organisms, and therefore not a viable way to measure the evolutionary relatedness of, say, two rare species of fish.

Next-generation sequencing techniques are rapidly opening new doors in the field of genomics- making it faster, more efficient, and significantly cheaper to sequence entire genomes. Scientists are finally beginning to examine the geneti code of non-model, and even very rare organisms to determine their “evolutionary place” in the tree of life. For example, micrognathozoa is a small, wormlike invertebrate with complex jaw architecture. It was entirely unknown to science until 1994, when the first specimins were discovered on an island off the west coast of Greenland. From anatomical characteristics alone, micrognathozoa was impossible to place into any existing phylum, suggesting that it diverged from other modern relatives very deep in evolutionary history. Researchers at Brown University have recently collected samples of micronathozoa and are now sequencing its bulk DNA. They are hoping to identify specific genes that will allow them to properly place the bug in a phylogenetic tree.

In addition to simply classifying organisms based on relatedness, Next-Generation sequencing is allowing scientists to study evolutionary dynamics and discern how changes in gene expression patterns lead to the divergence of species. A particularly exciting new technique, known as RNA-seq, can be used to gauge genetic activity by measuring cDNA copy number. cDNA, or complementary DNA, is produced when genes are activated. The amount of cDNA in a sample therefore reflects the relative “usage” of that gene. This technology could provide answers to questions as fundamental as how flight or swimming evolved ona  genetic level- was the activity of certain genes upregulated or downregulated?

 

 

Reference: Elizabeth Pennisi, “Tracing the Tree of Life”. Science 331: 1005-1006.

Crystal structure of 40S ribosomal subunit determined

The structure fo the 40S ribosomal subunit of eukaryotic ribosomes has recently been determined through x-ray crystallography, a method that allows scientists to reconstruct a 3-dimensional model of a protein in its native conformation. This discovery represents a significant breakthrough that scientists are hopeful will lead to an understanding of the evolution of ribosomes and eukaryote-specific mechanisms of protein synthesis.

Ribosomes, the small organelles that exist in millions of copies in all living cells, are responsible for one of life’s most essential processes- the creation of specific proteins with millions of different functions. Composed of a small and a large “subunit”, ribosomes are essentially tiny factories that process RNA and match specific RNA sequences with the amino acids necessary for building a particular protein. Because of this vital role, they have remained relatively highly conserved over evolutionary time. However, enough changes have accrued in ribosomes that, over time, they have become important biomarkers for distinguishing species. This technique has proved incredibly useful in describing the diversity of microbial communities. In particular, when  scientists want to get a sense of the ” species diversity” in a particular environmental sample, extraction and genetic sequencing of the small ribosomal subunit has become the gold standard.

Compared to prokaryotes, less is known about the structure and function of the eukaryotic ribosome. Not only are eukaryotic ribsomes larger and somewhat more complex, eukaryotic protein synthesis involves complex regulation and feedback pathways that are not present in prokaryotes. For example, the new crystal structure of the 40S subunit, or small eukaryotic ribosome subunit, reveals an interaction with a small protein known as an “initiation factor” that helps signal the ribsome to begin produciton of a new protein. The small subunit is responsible for binding numerous such initiation factors, and the new 3D structure promises to provide insight into eukaryotic-specific aspects of proteins synthesis, as well insight into the evolution of ribsomes by comparison of structures across a diverse range of species.

Evolution in Action!

A really great interactive phylogenetic tree showing all major extant taxa on Earth today and their evolutionary relationships.

Tree of Life

Simulation of plant evolution

This video shows results from a research project involving simulated Darwinian evolutions of virtual block creatures

microbiologists watch evolution in action

rapid advances in molecular genetics are now allowing scientists to watch, and even manipulate, evolution. this may seem hard to reconcile with the idea that evolution is a very gradual, long-term process, whose effects are seen only on timescales of thousands or millions of years. the misconception here is that time governs the rate of evolution. time in the abstract is relentless and constant, moving forward endlessly. this conception of time does not take the broad range of life strategies that evolution has produced into account.

in fact it is generation time that governs rates of evolution. human beings, who tend to have several children over the course of a multi-decadal life, have relatively slow generation times. it can take millions of years for noticeable evolutionary shifts to occur in a population that grows and reproduces slowly, simply because the genetic mutations that lead to evolution are very rare, and advantageous mutations take a long time to become established in a population.

it has long been known that microbial evolution occurs rapidly- noticeable genetic shifts can be observed in a manner of days or weeks. the evolution of pathogen resistance to pesticides or medicine occurs through natural selection for a rare genetic mutation that allows survival. because microbial populations often grow exponentially and generation time can be as short as twenty minutes, rare genetic mutations can sweep through a population and become ubiquitous rapidly. this is evolution in action!

historically, experiments in microbial genetics have focused on determining the function of an existing gene. this is generally accomplished by creating a strain with a defective, mutant version of the gene of interest, and observing how its function differs from the normal gene. studying defective mutants, however, does not provide insight into how gene pools can be improved.

now scientists are growing microbial cultures whose entire genetic makeup is known, and performing experiments that test evolutionary theory. any number of questions are being asked- how do the bugs evolve in response to an environmental change? a new food source? the introduction of a genetically different strain? for example, if a microbial population that requires oxygen to breathe is suddenly placed in a low oxygen environment, will genetic shifts occur that allow the microbes to use oxygen more efficiently? this certainly seems to be the case with humans- human populations that have existed for centuries at high altitudes, where oxygen is scarce, exhibit slight alterations in genes that encode hemoglobin, the protein that binds oxygen and transports it throughout the body. controlled evolution experiments allow replication, which means that scientists can now ask how frequently a positive evolutionary outcome, such as increased oxygen efficiency, occurs.

though such experiments may only provide a simplistic illustration of evolution, the mechanisms leading to genetic changes in microbial populations are remarkably similar to the basic mechanisms governing genetic change in higher organisms, including humans. insights developed from these experiments may be a first step towards unraveling the complex chain of events that has created the extraordinary diversity of adaptive traits across all types of life.

the meaning of life

when most people hear the word “virus”, the first image that comes to mind is generally something along the lines of a sick person, an epidemic, trips to the doctors office, vaccinations, or, for those with some biology background, a crystalline, nightmarish spider-alien injecting DNA into a defenseless cell. viruses are generally perceived as perpetrators of malaise, a scourge to society that modern science can and will eventually eradicate. only in the past decade, since the advent of fast and relatively cheap genetic sequencing technology, have scientists begun to recognize the staggering diversity of viruses in the world, many of which are entirely benign and have no known ecological function. the dawning realization that really are just about everywhere- they are ten times more abundant than bacteria in the ocean- indicates an incredibly effective strategy for self-propagation. this strategy in turn represents  a form of existence so simple that scientists have been debating for decades whether or not viruses can be classified as life.

despite their apparent simplicity, understanding viruses has been one of biology’s greatest challenges since the beginnings of the molecular revolution. the traits that we have discovered to be ubiquitous among viruses are relatively straightforward. generally, a virus consists of a single piece of naked DNA, encapsulated in some sort of protein-based coat. viruses cannot be considered cells because they contain none of the internal machinery necessary for growth or self-replication. instead, many viruses replicate by inserting their DNA into the cells of a host. this invading DNA is able to co-opt the host cell’s own replication proteins, and turn the host into a small factory for new viruses.

many but not all of the viruses that cause human disease use this strategy, and they often do so with alarming efficiency. another common viral replication strategy is to insert DNA into a host, and integrate that DNA into the hosts own DNA. viruses that employ this strategy are effectively choosing symbiosis inside a host, and replicate themselves in step with the host cell’s own cycle.

it may seem strange that some viruses act aggressively- invading, replicating and moving on once they have plundered all the resources available, while others choose a life of harmless symbiosis within their host. how can we come up with a general definition for all viruses if this is the case? shouldn’t we classify these critters as two unique types – neither truly alive perhaps, but fundamentally different in their non-living existence?

to answer this question, one must think carefully not about what viruses are doing but why. in both cases, a fragment of DNA is simply trying to replicate itself in the most effective way possible. for some, this means integrating itself into an organism, and reproducing in concert with the organisms own generations. for others, it means rape, kill, pillage and burn. viruses  are the ultimate narcissists- no ambitions for complex structure or function,, simply a raw, unabashed need for self-propagation.

if existence driven entirely by the need to replicate and produce more of oneself what it means to be a virus, i don’t think it’s a far stretch of the imagination to draw parallels with organisms that we officially classify as “alive”. with simple single-celled life, the similarity is easy to see. unicellular bacteria are essentially DNA vessels, but with extra compartments for the tools and machinery required to replicate. some single-celled bacteria do reproduce sexually and, in exchanging DNA, produce offspring that are not genetic clones. nevertheless, the idea is essentially still simple propagation of genes, but given one more level of complexity in that the replication process is self-sufficient.

but how much similarity can there possibly be between a complex, multi-cellular organism, and a single replicating strand of DNA? try thinking of a complex organism, like a cat, horse, or even human, as a nation of cells. each cell is an individual citizen, and each citizen has a specialized job that he must perform as an effective member of the community. if too many citizens dissent, or get lazy, and choose not to perform their allocated jobs, the community falls apart. and what do these citizens, many of whom look and act very different, and would certainly never be caught getting coffee or drinks together, all have in common? dependency on each other for replication.

a human being is orders of magnitude more complex than a virus, and I am not trying to diminish that complexity, or even to claim that it can be reduced to aggregate of cells driven by a simple process. but the common purpose of genes, in everything from their rawest form that do not even consider living, to the most complex organism evolution has produced, speaks to the ancestry we all share.

wyrd evolution

A population essentially evolves through the accumulation of random changes in its genetic makeup over time. These genetic changes modify organisms’ phenotypes, and over time change the distribution of traits in a population. Many traits which become prevalent in a population do so because they make the population more “evolutionarily fit”- better able survive and reproduce in its environment. Darwin coined the famous term “natural selection”to describe this phenomenon, though he wasn’t aware of the complex genetic mechanisms underlying it.

Evolutionary theory is anchored on the principle that the biology of the past has shaped the diversity we see today. Though countless examples in nature substantiate the important role of natural selection in evolution, it is important to understand that natural selection itself is not a conscious force. Rather, it is it is a pattern that produces predictable outcomes. Stochastic probability tells us that, over a long enough time and with large enough populations, traits that allow organisms to produce more offspring will come to dominate a population, simply because the individuals possessing these traits will pass along more of their genes into the next generation.

Because evolution by natural selection is not a conscious force, and because it must work to improve upon what already exists in nature, evolution cannot rapidly produce superanimals that are perfectly adapted to their environments. As the French biochemist Francois Jacob once eloquently described it, evolution is a tinkerer that works to improve upon what is already there, but its creative freedom is heavily constrained by existing body plans and biochemical pathways. Moreover, natural selection works to optimize organisms, not isolated systems. A trait that may seem advantageous, such as a genetic mutation producing enhanced night vision, may be helpful for a large predator on the Savannah, but useless for a cave fish that is rarely exposed to any sunlight and must use other sensory systems to perceive its environment. The cave fish would not develop improved eyesight because the selective advantage conferred by this ability would not outweigh its energetic costs.

As this last example begins to illustrate, natural selection is often working in concert with another force known as selective constraint. When a gene, biochemical pathway, or phenotypic trait is under selective constraint, it is maintained over evolutionary time. There are many reasons that selective constraint could operate. A biochemical pathway could be so fundamental to an organisms ability to survive that any small alterations to that pathway would be lethal. A limb or sensory organ could already be well suited for its environment, or the benefits of  making any changes to it may not outweigh the costs. A single mutation event in a gene encoding an essential protein could alter the protein’s structure and make it useless.

Natural selection and selective constraint are two important paradigms for understanding evolution. They are not the entire story, but they do help us to understand how evolution produces produces change but also propagates sameness. An alien visiting earth 3 billion years ago could not have imagined that the simple life he discovered would lead to the overwhelming diversity we see today. And yet in spite of all the novelty and innovation that has appeared over evolutionary time, this diversity has drawn upon itself, reaching outwards without  breaking its ties to the past.