First Life (Inevitable Life?)

Update #5 to Human Origins: How diet, climate and landscape shaped us

John S. Compton (www.johnscompton.com)

Several recent papers present evidence that life was established early on, soon after Earth’s fiery and cataclysmic assembly had ended and its surface had cooled down into a watery world capable of sustaining life. Such an early start implies that life, rather than being unique to Earth may be, if not inevitable, then at least a highly likely outcome here as well as on other Earth-like planets. Give life half a chance and it will rise up and thrive. A result which perhaps shouldn’t come as too big a surprise considering the tenacity with which life has persisted and diversified over the many billions of years since it first emerged. One way to ascertain if life on Earth was a highly likely or inevitable outcome is to find it elsewhere. The recent discovery of thousands of distant planets (exoplanets) orbiting within the watery, and hence potentially habitable zone of their stars is a promising sign that we may be closing in on evidence that life does exists out there in the great beyond. Confirming life on just one exoplanet would imply that our universe is home to a multitude of living worlds peppered across its enormous expanse. This is a mind-boggling concept even if our chances of ever directly interfacing with life elsewhere is remote given the distances involved. As our search for life on distant planets continues, we can also look long and hard for evidence of the earliest life here on Earth. Establishing when life first appeared on Earth can provide us with valuable insights into how life might have come about, but finding convincing evidence of life in the ancient rock record is a difficult task.

The first problem is that most life never leaves even a hint of its existence in the rock record. Life is fragile and readily decomposes such that most living things upon death rapidly vanish, recycled back into the world of non-living elements. Hence, fossil remains of life are rarely preserved in rocks of any age, never mind long ago when the abundance and types of life forms were far more limited than today. The other problem is that older rocks become increasingly difficult to find the further back in time you go. This is because Earth is dynamic, with the movement of its crustal plates (plate tectonics) constantly recycling older rocks into younger rocks. The evidence of life can only be found in the rock record and, therefore, the oldest rocks define the limit of how far back we can potentially detect life. And even for those oldest rocks that we are lucky enough to find and that once harboured fossils, most have since been subjected to intense pressures and temperatures over the dynamic history of their long existence. Such abuse is likely to obscure, if not destroy, whatever original fossil evidence the now transformed rocks may have once contained. Despite these problems, what does the rock record reveal about the earliest life on Earth?

The oldest rocks yet found are around 4 billion years old and occur in Canada and Greenland. We know from the age and composition of meteorites that our solar system formed initially 4.56 billion years ago. It was at this time that Earth’s assembly began by the collision of the many small rocky and metallic bits circling the Sun in our planet’s orbit. Initially gravity pulled in surrounding dust and rock to form small planets (planetissmals) and then these collided gradually to form larger planets. The final, major planetissmal collision that went into the making of Earth occurred 4.44 billion years ago. Our Moon formed from the debris of this collision and the force of the collision transformed Earth into a magma ball, too hot to sustain life. Life could have conceivably been established once the magma ball had cooled and crusted over, and the water vapour had condensed to form the oceans. Conditions on Earth however remained challenging to life as it had to contend with periods of intense bombardment by the sweeping up of the remaining rocky bits. This time of heavy meteorite bombardment is known as the Hadean, named after Hades, god of the underworld. The intense bombardment and the Hadean ended 4 billion years ago to give way to the Archean. To whatever extent life may have started during the Hadean, it was only by the start of the Archean that Earth presented a relatively stable setting for life to persist.

hellish hadean

Archean Earth
The Hadean (top) was a hellish period of intense meteorite bombardment and vaporised oceans, conditions that were generally not favourable to life, while the Archean world (bottom) included oceans of water and conditions suitable for the earliest microbial life forms.

 

The oldest, direct fossil evidence of life is in the form of stromatolites. Stromatolites are mound-shaped structures that form from the activities of microbial mat communities. Stromatolites are common throughout much of the early rock record and some still form today in places like Shark Bay, Western Australia. The minute microorganisms themselves are rarely preserved, but the layered stromatolite structures they build as a result of their activities often are preserved. The distinctive features of stromatolites rule out alternative, non-biological origins for the layered structures, such as the deposition of mineral crusts. The oldest stromatolites were recently discovered in rocks from Greenland 3.7 billion years old (Nutman and others, 2016), significantly older than the previously oldest stromatolites known from Australia dated to 3.48 billion years.

1-Nutman stromatolites
Small conical-shaped mounds (dashed lines) in rocks from Greenland 3.7 billion years old are interpreted to be stromatolites formed by microbial communities (photo by Allen Nutman adapted from Allwood, 2017).

Going back beyond 3.7 billion years, the evidence of life relies on the chemical signature of what is interpreted to be the remains of once living organisms as well as possible fossils. Life on Earth is carbon based and hence most organisms are made up of a significant amount of carbon. For life that grows by taking up carbon directly as CO2, the lighter carbon isotope (carbon 12) is taken up preferentially to the heavier isotope (carbon 13) (the heaviest isotope (carbon 14) is radioactive and has a short life span). The preferential uptake of the light isotope gives life a distinct, negative carbon isotopic composition. When organisms die and their organic matter decomposes, most of the other elements besides carbon, such as nitrogen, phosphorus, oxygen and hydrogen are lost and eventually all that remains is carbon. When heated up under pressure the remaining organic carbon can form the mineral graphite (a soft, grey mineral that is familiar to us as pencil lead). At extreme pressures graphite can transform to diamond. Some have found organic matter in rocks from Greenland greater than 3.7 billion years old that still contains some oxygen, hydrogen, nitrogen and phosphorus because it was preserved as inclusions within the metamorphic mineral garnet (Hassenkam and others, 2017). But in most cases all that remains is pure carbon in the form of graphite. Graphite from rocks in Labrador Canada greater than 3.95 billion years old have carbon isotope values that suggest the carbon was originally part of living organisms. Some of the graphite takes on globular shapes common to some microorganisms (Tashiro and others, 2017). Structures in rocks at least 3.77 billion year old from Quebec Canada interpreted to represent fossil microorganisms suggest that mid-ocean ridge submarine hydrothermal vents or ‘black smokers’ are a potential setting in which early life evolved on Earth (Dodd and others, 2017). Unfortunately, the structures interpreted to be fossil bacteria and the carbon isotope values of graphite interpreted to indicate life processes can both be produced by reactions that do not involve living organisms. Therefore, the indications of life earlier than the 3.7-billion-year-old stromatolites are compelling, but remain ambiguous.

3.95 Ga graphite spheres

black smoker
Cluster of globular graphite in quartz chert from Canada is suggestive of fossilised microbial organisms (top, from Tashiro and others, 2017). A modern submarine volcanic vent or ‘black smoker’ is a possible setting where life first emerged on Earth (image from NOAA).

 

The oldest known rocks are around 4 billion years old, so how can we say anything about earlier periods of Earth history? Some younger rocks contain mineral grains derived from the erosion of older rocks. Zircon is a highly durable mineral that often ends up being eroded out of older rocks but is not destroyed by weathering and ends up being recycled into younger rocks. In fact, the oldest known mineral is zircon dated to as old as 4.38 billion years in rocks from Jack Hills, Western Australia. A small number of these zircon grains have minute inclusions of graphite. The graphite in a zircon grain dated to 4.1 billion years has a carbon isotope signature consistent with a biological origin, but again not unambiguously (Bell and others, 2015). Therefore, the recent evidence pushes back the earliest life on Earth from around 1000 million years to at least 700 million and possibly 300 million years following the final major collisional event 4.44 billion years ago. Assuming it took on the order of 100 million years for Earth to become habitable after the final major collisional event, reduces the time span of life’s emergence to between 600 and 200 million years.

timeline early Earth
Timeline of early Earth history from its formation as a molten, magma ball, through the hellish Hadean and into the Archean. Oldest direct fossil evidence of life is from stromatolites in rocks 3.7 billion year old and indirect chemical evidence of life comes from rocks around 4 billion year old and from graphite inclusions in zircon minerals 4.1 billion years old.

What is the significance of the suggested narrowing of the time it took life to emerge on Earth? The more rapidly life was established, the less difficult or improbable it would appear to be. The origin of life remains a major unknown. We know that early Earth likely had an enormous diversity of chemical compounds to work with including amino acids, which are the building blocks of all life today. But whether life was inevitable or even highly likely to come about is open to debate, because it remains unclear how these compounds became organised into self-replicating, evolving organisms. It could be that the emergence of life is simply too slow a process for us to replicate in the lab. Even the simplest of life forms, bacteria, involve an incredibly complex array of biochemical reactions and processes that would have taken time to evolve from the diverse pool of chemical compounds available. Although less than previously thought, several hundred million years is still a long span of time over which life could have gradually emerged.

It seems unlikely that the rock record will allow us to refine the timing much more or to push it back much further. Thus, the implied ease at which life can emerge on a place like Earth will perhaps have to wait for the discovery of life on another planet. Just what form life will take on other planets is unknown, but if at all like Earth, life is most likely to be dominated by diverse yet small, simple microbial organisms. Perhaps quick to get started, life on Earth appears to have remained fairly simple for a long period of time. It took around a billion years before the more complex eukaryotic cells evolved and another two billion years or so after that before animals evolved. The delay in the evolution of animals has been attributed to the need of an oxygen-rich atmosphere.  For the latest ideas on what may have controlled oxygen levels in the atmosphere and how the level became high enough for animals, check out my next blog update #6: First Animals.

Further reading

Allwood, A.C., 2016. Evidence of life in Earth’s oldest rocks. Nature 537, 500-501 (doi:10.1038/nature19429).

Bell, E.A., and others, 2015. Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon. PNAS 112, 14518–14521 (www.pnas.org/cgi/doi/10.1073/pnas.1517557112).

Dodd, M.S., and others 2017. Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature 543, 60-64 (doi:10.1038/nature21377).

Hassenkam, T., and others, 2017. Elements of Eoarchean life trapped in mineral inclusions. Nature 548, 78-81 (doi:10.1038/nature23261).

Nutman, A.P., and others, 2016. Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures. Nature 537, 535-538 (doi:10.1038/nature19355).

Tashiro, T., and others, 2017. Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada. Nature 549, 516-518 (doi:10.1038/nature24019).

© John S. Compton (www.johnscompton.com)

 

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The first Australians

Update #4 to Human Origins: How diet, climate and landscape shaped us

John S. Compton (www.johnscompton.com)

Australia is home to some of our species’ most ancient roots outside of Africa. When the first of our human (Homo) lineage arrived in Australia has long been debated. Although early members of our lineage (Homo erectus, for example) were living nearby on the island of Java as early as 1.7 million years ago, it was only much later that humans entered Australia. Dated archaeological sites suggest that our species, Homo sapiens was the first to arrive by around 50 thousand years ago (50 ka) and that we had become widespread throughout the continent by 45 ka (Hamm and others, 2016). This chronology generally fits with the proposed timing of the ‘Great Expansion,’ when our species rapidly spread out of Africa around 60 to 50 ka and effectively conquered the world. Our species had earlier forays out of Africa prior to the Great Expansion, but these never appear to have amounted to much. In my book Human Origins I refer to those who left Africa prior to the Great Expansion as anatomically modern humans (AMHs) and those that left as part of the Great Expansion as people having cultures on a par with modern hunter-gatherers. Our species evolved in Africa 200 to 160 ka, but appears to have only slowly acquired cultures equivalent to modern hunter-gatherers between 100 and 70 ka while in Africa. This may explain, in part, why earlier exits were relatively unsuccessful: the Great Expansion had to wait until modern hunter-gatherers had emerged in Africa and their movement beyond Africa, in turn, had to wait until the Sahara-Arabian Desert became sufficiently green to let them out 60 to 50 ka. However, a recent study by Clarkson and others (2017) proposes that modern people had arrived in Australia by at least 59.3 ka and possibly as early as 70 ka. Such an early arrival of people in Australia would be at odds with the Great Expansion scenario.

Great expansion

Going global: possible pathways and timing of the Great Expansion, when modern people conquered the world.

The study by Clarkson and others revisited and expanded upon earlier work carried out at the Madjedbebe rock shelter located in northern Australia. From the lowest and oldest layers of human occupation they recovered over 10,000 artefacts that, in addition to an in place hearth, included many stone flakes, ground ochre (associated with mica), edge-ground hatchets and a grinding stone. The age of the deposit was determined by optically stimulated luminescence (OSL), a method by which the measured luminescence of many individual sand grains is related to the time it took for them to accumulate their luminescence from exposure to radioactivity in the surrounding sediment. The artefacts and their associated OSL ages establish that the sequence of layers at the site has not been significantly disturbed or mixed and indicate, quite convincingly, that our species was in Australia as early as 65±5 ka. Such an early arrival of modern hunter-gatherers is inconsistent with all other archaeological evidence indicating that the peopling of the Eurasian continent occurred between 55 and 45 ka.

A critical question is who were these first Australians? If they were part of one of the earlier waves of our species (AMHs) that expanded out of Africa between 130 and 80 ka, then there is no problem with the timing of their arrival. Instead, the potential problem is with their cultural artefacts, which appear to be inconsistent with those associated with earlier waves of our species out of Africa. On the other hand, if they were part of the exodus from Africa of modern hunter-gatherers that successfully filled the world, then the problem lies not with their artefacts but with the time of their arrival, which would appear too early relative to other sites. At this stage, the best explanation appears to be that the first to arrive were AMHs from an earlier exodus out of Africa that had developed some cultural artefacts similar to modern hunter-gatherers. Despite their cultural artefacts, these early arrivals in Australia, as elsewhere, appear to have had a limited presence in the archaeological record and were largely replaced by the later arrival of modern hunter-gatherers by around 50 ka as part of the Great Expansion.

The authors of the paper argue that those living at the Madjedbebe rock shelter were behaviourally modern people based on the presence of an edge-ground hatchet, a grinding stone and ochre (a red coloured pigment) mixed with highly reflective mica flakes. The use of ochre dates back to our predecessor species, already widespread in Africa by 230 ka. However, these earlier ochre occurrences are not associated with highly reflective mica flakes, for which the Madjedbebe site is the earliest known example. Ground hatchets and a grinding stone at the site may also be the earliest occurrences known, but the lack of fine stone tools (such as backed microlithic stone tools for spear or bow and arrow), along with art or jewellery (micaceous ochre aside) suggest that these earliest arrivals were perhaps not yet in possession of a complete modern hunter-gatherer culture.

Interpreting the significance of these artefacts is difficult because cultures evolve over time and can be lost. Loss of cultures may result if specific cultural items are no longer needed or if groups are too small to sustain them. There is evidence that humans living in Southeast Asia developed different cultures to those elsewhere in Eurasia, with a lack of stone tools in particular. The lack of stone tools may reflect their use of wood (bamboo), which is much less likely to be preserved than stone tools. There is evidence that those associated with the Great Expansion were innovative, using fire ash to detoxify yams and tree nuts by 46 ka in Borneo, as well as artistic, making some of the earliest cave paintings 40 ka on Sulawesi (Aubert and others, 2014). What the archaeological record suggests in Australia is that the first to cross over did not arrive with the typical modern hunter-gatherer toolkit but managed to reinvent it over time, with bone points appearing by 40 ka and backed microliths by 30 to 20 ka (Hamm and others, 2016).

If Homo erectus was already in Java by 1.7 Ma, why did it take so long for humans to cross over to Australia? The difficulty in reaching Australia is that it requires crossing over water to get there. This is true today as well as in the past when many of the islands were joined into one large landmass during periods of lowered sea level when ice sheets built up in the Northern Hemisphere. Homo erectus survived in Southeast Asia until around 300 ka. Some among them managed to cross narrow, calm seaways to reach the island of Flores, where they underwent island dwarfism to become the one-metre tall ‘hobbit’ (Homo floresiensis) who lived there until around 50 ka. But crossing the larger seaways required to reach New Guinea – Australia (collectively called Sahul) was apparently too great for earlier members of our lineage to manage. There is evidence that our species was living in Sumatra sometime between 78 and 58 ka, but unfortunately no cultural items were found associated with the fossil evidence (Westaway and others, 2017). Perhaps these were AMHs for an earlier exit and among those who the first to successfully navigate their way as far as Australia.

SahulWallacea

Humans could expand into Southeast Asia when sea level was lower (pale blue areas of Sunda) but had to island-hop their way through Wallacea to reach the connected landmasses of New Guinea and Australia (Sahul).

Therefore, it would appear that the first arrivals in Australia were AMHs from an earlier exit out of Africa. As elsewhere in Eurasia, the AMHs who arrived in Australia had a relatively subdued impact and were largely displaced by the later arrival of modern hunter-gatherers as part of the Great Expansion who reached Australia by around 50 ka. This Great Expansion scenario is supported by genetic studies which indicate that all people today outside of Africa descend from a single population that exited out of Africa and that they acquired DNA from intermingling with Denisovans and Neanderthals along the way between 53 to 45 ka. DNA studies of indigenous Australians (aborigines) indicate that those who arrived with the Great Expansion rapidly colonized the continent by 45 ka (Tobler and others, 2017). To whatever extent earlier expansions of our species may have taken place prior to the Great Expansion, none feature strongly in either the archaeological or genetic evidence, their existence appears to have been swamped out by the rapid peopling of the world during the Great Expansion. However, the earlier forays of our species out of Africa were perhaps not completely erased, with some genetic studies suggesting that a few percent of the DNA from these earlier expansions survives in modern populations (Pagani and others, 2016).

 

Further reading

Aubert, M., and others, 2014. Pleistocene cave art from Sulawesi, Indonesia. Nature 514, 223-227. doi:10.1038/nature13422

Clarkson, C., and others, 2017. Human occupation of northern Australia by 65,000 years ago. Nature 547, 306-310. doi:10.1038/nature22968

Gibbon, A., 2017. The first Australians arrived early. Science 357, 238-239. doi: 10.1126/science.357.6348.238

Hamm, G., and others, 2016. Cultural innovation and megafauna interaction in the early settlement of arid Australia. Nature 539, 280-283. doi:10.1038/nature20125

Marean, C.W., 2017. Early signs of human presence in Australia. Nature 547, 285-287.

Pagani, L., and others, 2016. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538, 238-241. doi:10.1038/nature19792

Tobler, R., and others, 2017. Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. Nature 544, 180-184. doi:10.1038/nature21416

Westaway, K.E., and others, 2017. An early modern human presence in Sumatra 73,000–63,000 years ago. Nature 548, 322-325. doi:10.1038/nature23452

 

© John S. Compton (www.johnscompton.com)

The first humans in America

Update #3 to Human Origins: How diet, climate and landscape shaped us
John S. Compton (www.johnscompton.com)

 

A recent study presents evidence that members of our human (Homo) lineage were in North America around 130 thousand years ago (Holen and others, 2017; Wade, 2017a). This is a shocking claim because it is more than 100 thousand years before the previously established timing of 14 thousand years ago for when humans first entered the Americas. This latest report is not the first to argue for a much earlier presence of humans in the Americas, but it provides by far the most compelling and best dated evidence yet.

The evidence consists of scattered mastodon bones lying immediately adjacent to several large stones. The bed in which the bones and stones occur were recovered from a 12-m-thick succession of river deposits discovered at a construction site near San Diego, California. The mastodon is a distant relative of elephants and was common in North America (along with the woolly mammoth and other large animals) up until people hunted them to extinction by around 12 thousand years ago. The authors of the study argue that the physical damage of some mastodon bones and associated stones indicate that the stones were used as hammerstones and anvils to break open the large mastodon bones. Breaking of the bones was done most likely to access the oozing, nutrient-rich marrow inside. The large stones were locally sourced but, oddly, none was modified or shaped in any way by removal of smaller stone flakes. Although no human bones were found at the site, it is assumed that humans were responsible because no other animal capable of smashing large mastodon bones with large stones is known to have lived at this time in the Americas.

mastodon

Many of the large animals shown here (including the mastodon, upper right) became extinct soon after people arrived in North America 14 thousand years ago (human with spear for scale).

The site was determined to be 130.7 ± 9.4 thousand years old based on the decay of the radioactive element uranium contained within the bones. There was no organic carbon left in the bones to date using radiocarbon methods and the application of optically stimulated luminescence (OSL) indicated that the sediment at the site was deposited at least 60 thousand years ago. The age uncertainty of plus/minus nearly ten thousand years reflects, in part, the model assumptions made in using the uranium-series disequilibrium method. However, the uranium-derived ages appear to be robust and indicate that the deposit most likely formed sometime between 140 and 120 thousand years ago.

The lack of human bones, as well as any other stone tools or cultural artefacts besides the hammerstones and anvils, make it difficult to say which member of our human lineage was active at the site. It is certainly conceivable that members of our lineage living in Eurasia may have crossed over to North America when the Beringia land bridge was exposed. The Beringia land bridge today is flooded by the Bering Sea, but the lowering of sea level at times in the past was sufficient to expose the Bering Sea as a land bridge connecting Eurasia and North America. For example, the Beringia land bridge could have been crossed roughly 134 to 131 thousand years ago, within the age window of the mastodon site. Any humans living in eastern Siberia at that time may have made the journey across on foot without necessarily making use of boats.

Beringia

Siberia was connected to North America periodically when sea level was lowered by major ice build up. Humans living in Siberia could have crossed over to North America either by boat along a coastal route or on foot overland through ice-free corridors.

The highly successful crossing 14 thousand years ago was part of the Great Expansion of behaviourally modern people who left Africa around 60 to 50 thousand years ago. There are numerous archaeological sites that show modern people had entered and become widespread throughout the Americas, reaching the southern coast of Chile by around 14 thousand years ago. The timing of initial entry into the Americas is thought to be mostly determined by when people living in the Far East and eastern Siberia could cross over the Beringia land bridge connecting Eurasia and North America during the Last Glacial Maximum when sea level was lowered in response to the build-up of major ice sheets. Passage into North America from Beringia was delayed until the large ice sheet blocking the way had started to melt back with the onset of warmer climates 18 to 14 thousand years ago. There was a relatively brief window to pass over the land bridge before it was flooded by the rising sea as the ice sheets quickly melted. Most are sceptical that humans had crossed over before 14 thousand years ago, with the current debate centred on when people crossed over, where they came from and whether they travelled by canoe along a coastal route or overland on foot through ice-free corridors that opened as the large Laurentide ice sheet melted back (Wade, 2017b).

It is not too far-fetched that some of our ancestors living in Eurasia might have crossed over to the Americas much earlier than the well-documented crossing of people by 14 thousand years ago. This is because the Beringia land bridge was repeatedly exposed as Earth cycled through glacial and interglacial periods over the last million years. Any of our ancestors adapted to living at relatively high latitudes may have inadvertently crossed over Beringia in pursuit of game and, once across, they could expand and fill the virgin American landscapes.

SL and Beringia

Sea-level cycles over the last million years and the periodic exposure of the Beringia land bridge in the transition from glacial to interglacial periods when animals (including humans) may have crossed over to North America (brown columns). The mastodon archaeological site reported from southern California implies humans crossed over sometime prior to 134 to 131 thousand years ago during the MIS 6 glacial to MIS 5 interglacial transition (third brown column on the right) when Neanderthals and Denisovans, but probably not our species (Homo sapiens) or the ‘hobbit’ (H. floresiensis), were living at high latitudes in Eurasia.

Could it have been our species, Homo sapiens, who crossed over? This seems unlikely because, although our species had appeared in Africa by around 200 to 160 thousand years ago, the earliest evidence of when we left Africa is 131 to 113 thousand years ago (MIS 5). After crossing over, our species appears to have largely been confined to the Middle East region. There is, as yet, no evidence that they had expanded into Siberia as early as when the Beringia land bridge to the Americas was exposed 134 to 131 thousand years ago. So, if not our species, then what other member of our lineage may have crossed over prior to 140 to 120 thousand years ago?

We know that Neanderthals, Denisovans and the ‘hobbit’ (Homo floresiensis) were all living in Eurasia at this time. Homo erectus were widespread throughout Eurasia even earlier, but do not appear to have lived at high enough latitudes, above 40°N, to have crossed over the Beringia land bridge located at latitudes above 55°N. The ‘hobbit’ is only known from the Indonesian island of Flores where it lived from 700 up until 50 thousand years ago, whereas Neanderthals and Denisovans are known to have lived at high latitudes, including Siberia. However, it is unclear which of the two crossed over the Beringia land bridge because the only stone tools (hammerstones and anvils) yet to be recovered from the site are not shaped in any way. Almost all contemporaneous stone tools documented in Eurasia (and Africa) were intentionally shaped by the removal of stone flakes. The lack of shaped stone tools is an unusual, and difficult to comprehend, aspect of the mastodon site.

Another surprising aspect about the mastodon site besides its lack of shaped stone tools, is that there has been so little convincing evidence of an earlier human presence in the Americas before now. If humans did managed to cross over, then it is predicted that they would have rapidly spread into the virgin landscapes, landscapes never before occupied by humans and full of large animals relatively easy to hunt. The Americas are two enormous continents no more difficult for humans to thrive in than Eurasia. So why are traces of humans living there so difficult to see in comparison to the record in Eurasia? Has the abundance of archaeological sites younger than 14 thousand years old obscured older, less abundant evidence? Perhaps if people dig a bit deeper and consciously look for it, an older record of humans in the Americas will be revealed. Now that the first compelling site has been discovered, perhaps more will follow.

Further reading

Holen, S. R., and others, 2017. A 130,000-year-old archaeological site in southern California, USA. Nature 544, 479–483. doi:10.1038/nature22065

Wade, L., 2017a. Claim of very early humans in Americas shocks researchers. Science 356, 361. doi: 10.1126/science.356.6336.361

Wade, L., 2017b. On the trail of ancient mariners. Science 357, 542-545. doi: 10.1126/science.357.6351.542

© John S. Compton (www.johnscompton.com)

 

 

Surprisingly young age of the Homo naledi fossil site

 

Update #2 to Human Origins: How diet, climate and landscape shaped us

The age of the fossil-rich Homo naledi fossil site within the Rising Star cave system in the Cradle of Humankind World Heritage Site near Johannesburg, South Africa was frustratingly unknown until recently. The exceptionally large number of fossil bones scattered on the cave floor proved difficult to date, but an international team of scientists has applied several dating techniques (optically stimulated luminescence, uranium/thorium and palaeomagnetism) to constrain the age of the deposit to between 414 and 236 thousand years old (Dirks and others, 2017). This age is supported by the estimated age of several fossil teeth from the deposit, independently dated to between 335 and 183 thousand years old using a combination of uranium series and electron spin resonance (US-ESR) methods. The US-ESR methods directly date the fossils, but rely on a number of complex model assumptions that result in a large amount of uncertainty. Although not terribly precise, these ages are considered fairly robust and are surprisingly young for fossils whose features (or traits) suggest that they are much older. Prior to the age determinations, many estimated that the fossils, given their mix of australopith and early Homo features, would date to around when our genus Homo first appeared in the fossil record between 3 and 2 million years ago (Ma). How, then, is such a young age explained for fossils that retain so many old features?

A mosaic of features

One of the striking aspects of the Homo naledi fossils is the odd mix or mosaic of features they display. The amazingly rich fossil find from the Rising Star cave system includes a total of over 1500 bones from the Dinaledi Chamber alone (Berger and others, 2015), with more bones recently discovered in the separate Lesedi Chamber (Hawks and others, 2017). All of the bones recovered from both caves are considered to belong to Homo naledi and comprise a minimum of 15 individuals. Such a large number of bones provides a fairly complete skeleton of Homo naledi who stood 1.4-1.6 m high and weighed 40-55 kg. One of the most notable features is the small size of the skull, having an interior volume (endocranial capacity) of between 460 and 610 cc. This range in volume is based on three skulls and is intermediate between the mean skull size of the australopiths and the earliest Homo species for which skulls are available that date to around 2 Ma. Such a small skull suggested that Homo naledi represented one of the earliest members of our genus Homo, which branched from the australopiths around 2.8 to 2.3 Ma, based on fossil teeth and jaws from East Africa (Villmoare and others, 2015). In contrast, its foot shares many features similar to ours. Comparing Homo naledi to other species is difficult to do because for most other species there are simply not enough fossil bones to compare. However, overall, Homo naledi much more closely resembles early Homo (H. habilis and H. erectus) than it does us (H. sapiens) or our predecessor species (‘archaic’ H. sapiens). The close resemblance to early Homo suggested to many that the age of the deposit would be similar in age to when early Homo appeared circa 2.5 Ma and not the reported age of less than 0.5 Ma.

Hawks et al 2017 H naledi skull   Hawks et al 2017 H naledi endocranial LES1

Skull of Homo naledi (LES1) from the Lesedi Chamber (scale bar 5 cm) and the digital reconstruction of the endocranial volume of 610 cc, scale sphere is 10 mm (Hawks and others, 2017).

The most likely explanation is that Homo naledi represents one of the earliest members of our Homo lineage and that it managed to retain many features of early Homo up until at least 414 to 236 thousand years ago. While retaining many of its early features, it also appears to have acquired features that closely resemble later features, which either evolved independently (convergent evolution) or were acquired through interbreeding (hybridization) with other, later-evolved Homo species (but probably not our species, which only appeared by around 200 to 150 thousand years ago).

What is remarkable is that Homo naledi persisted for so long in a region occupied by other, later-evolved Homo species. For example, the skull from the Florisbad fossil site is thought to represent our predecessor species and was likely contemporary with Homo naledi, the two living within several hundred kilometres of one another. One possible explanation of their co-existence is that they occupied distinctly different habitats. Although their feet and aspects of their hands are similar to ours, Homo naledi’s fingers are curved. Curved fingers suggest that they were adapted for living in and moving about in trees. Therefore, they may have resided within heavily treed habitats, such as forest canopies, whereas our predecessor species was living primarily in more open grassland and savannah habitats. Although such niche partitioning may explain the co-existence of different species of Homo, it is remarkable that a species with so many early features, including such a small brain, managed to survive until just prior to when our species Homo sapiens evolved onto the scene.

Hangers on

Homo naledi is not the only member of our Homo lineage who managed to persist over such a long period of time. Homo erectus, for example, managed to survive in Asia long after they had become locally extinct in Africa, surviving up until around 300 thousand years ago in China and Java. And, in many respects, the suite of unusual features of Homo naledi reflect those of Homo floresiensis, the ‘hobbit”, which also retains features of early Homo (H. habilis and H. erectus) and lived up until just 50 thousand years ago on the island of Flores (Sutikna and others, 2016). The persistence of H. floresiensis on the somewhat remote island of Flores seems more plausible than a group within the African continent, but perhaps this reflects the fact that groups in Africa were adapted to specific habitats that effectively isolated them from other groups. Population densities were likely low and, along with the diversity of habitats, may have facilitated the survival of earlier groups for long periods of time. More recently evolved species might have been widely dispersed in part because of their big brain, sophisticated tools and control of fire, but were perhaps spread thinly enough over the landscape to have permitted pockets of earlier evolved groups to hang on. What the hobbit and Homo naledi seem to indicate is that among the more recently evolved members of our lineage, older groups managed to persist, either within distinct habitat or niche holdouts  ̶  perhaps culturally as much as physically isolated from other groups. The fossil record is so limited it may have hidden from us or we may have tended to underestimate the amount of variability in features, such as brain and body size that existed in the past.

Homo naledi culture?

Typically an archaeological site has hundreds to thousands of stone artefacts but very few if any fossil bones of those who made the artefacts. And whether or not any bones of the makers of the stone tools are found, it is common to find the bones of other animals at many archaeological sites. Hence, the Rising Star cave sites present the most unusual case: many bones of Homo naledi not in association with any stone tools or other cultural artefacts, nor any other large animal bones. Hence, although we know a lot about what Homo naledi looked like, we have very little idea of what they made or what other animals they lived among.

This lack of context makes it difficult to know much about the habitat in which they lived and how they lived. They most clearly did not live in the deep caves where they ended up as fossils. It is conceivable that they fell into or were washed down into the caves through surface openings connected to deep cave chambers. But in that case we would expect other large animals to have fallen in or been washed into the caves along with them. Some have proposed that they were intentionally disposed of into cave openings and that this disposal may indicate a type of ritual burial (Berger and others, 2017). Ritual burial is a cultural behaviour that has so far only been associated with our species, with the earliest hints (mortuary defleshing) dating to around 160 thousand years ago, and proper burials with grave goods not until around 100 thousand years ago. It is possible they disposed of their dead into the caves as a form of good housekeeping, but it is hard to imagine that small-brained Homo naledi had the mental ability to practice ritual burials, and evidence to substantiate ritual disposal into the caves remains lacking.

The complete absence of stone tools makes it difficult to know what stone tools, if any, were used by Homo naledi. They possess the wrists and hands capable of making and using stone tools, but did they? The age of the site falls within the Middle Stone Age (MSA), a time of regionally diverse stone tool industries throughout Africa. Some have suggested that Homo naledi may have been the maker of some of these stone tools (Berger and others, 2017), but so far there is no direct evidence to support this idea. The appearance of stone tool use has been dated as far back as 3.3 Ma and associated with australopiths having brains similar to or smaller sized than Homo naledi, but these early stone tools are a far cry from the diversity and sophistication of MSA stone tools that existed throughout much of Africa by 300 thousand years ago. Hopefully future finds of Homo naledi in association with cultural artefacts will shed some light on where and how they lived.

Lomekwian tool           MSA tools across Africa

A 3.3 Ma Lomekwian stone tool (left; Harmand and others, 2015) and regionally diverse MSA stone tools throughout Africa 300-100 thousand years ago (right).

Further Reading

Berger. L., and others, 2017. Homo naledi and Pleistocene hominin evolution in subequatorial Africa. eLife 2017;6:e24234. DOI: 10.7554/eLife.24234

Berger, L., and others, 2015. Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. eLife 2015;4:e09560. DOI: 10.7554/eLife.09560

Dirks, P., and others, 2017. The age of Homo naledi and associated sediments in the rising star Cave, South Africa. eLife 6:e24231. doi: 10.7554/eLife.24231

Harmand, S., and others, 2015. 3.3-million-year-old stone tools from Lomekwi 3, West Turkana, Kenya. Nature 521, 310–318.

Hawks, J., and others, 2017. New fossil remains of Homo naledi from the Lesedi Chamber, South Africa. eLife 6:e24232. DOI: 10.7554/eLife.24232

Sutikna, T., and others, 2016. Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia. Nature 532, 366–369.

Villmoare, B., and others, 2015. Early Homo at 2.8 Ma from Ledi-Geraru, Afar, Ethiopia. Science 347, 1352–1355.

New ages from Jebel Irhoud, Morocco

Update #1 to Human Origins: How diet, climate and landscape shaped us

John S. Compton

The date

New fossil finds and a better constrained age for the Jebel Irhoud fossil site in Morocco shed new light on our evolution. The new ages indicate that the site is approximately 315 thousand years old (315 ka), or nearly twice as old as the previous estimated age of 160 ka for the site. The new, older age was obtained by applying the thermoluminescence dating method, which estimates the amount of time lapsed since stone flint tools found from the same layer as the fossil bones had been heated by fires made by those living at the site. The thermoluminescence method measures the amount of light given off by the stones tools (the amount of luminescence) as they are heated to higher temperatures. The idea is that the fires at the site were hot enough to completely erase any luminescence trapped in the stones. Once cooled, and so long as they were never exposed to the heat of a fire again, the stones gradually accumulated stored luminescence through time from natural radiation received from the surrounding sediment. The present-day background radiation dose of the deposit was measured from where the stone tools were recovered and was assumed to have remained more or less constant back through time. Heating of the stone flints in the lab causes the stored luminescence to be released, and the amount released could be measured. Dividing the total released luminescence by the radiation dose rate measured at the site allows an age to be calculated.

Luminescence dating, both thermoluminescence and optically stimulated luminescence (or OSL), has revolutionized our ability to date archaeological sites beyond what was previoulsy limited to the last 50 thousand years by the radiocarbon method. The drawback to luminescence dating is that it too has limits in how far back it can reach because the amount of luminescence that can accumulate is limited. Once the stones have acquired maximum luminescence they can acquire no more, making it difficult to apply the method to samples older than 200 ka. So, the new age determined at Jebel Irhoud by thermoluminescence in excess of 300 ka is remarkable.

The other drawback with the thermoluminescence method is that the dates are not nearly as precise as those obtained by the radiocarbon dating method. The weighted average age of 14 samples from the fossil-bearing layer at Jebel Irhoud is 315 ka, but this age is associated with a fairly large uncertainty, with a 68% probability that the age of the site is between 349 ka and 281 ka, and a 95% probability that the age of the site is between 383 ka and 247 ka. The age range of 383 ka to 247 ka is consistent with both the range in age of a human tooth recovered from the site determined by a different method known as electron spin resonance (a far more complicated method than thermoluminescence that I will not try to explain here), and the known age ranges of fossil animals found at the site. Therefore, although not terribly precise, the new age is a huge improvement on previous ones for the site and, as we shall see, the new age provides valuable insights into the interpretation of the Jebel Irhoud fossils and their possible connection to other fossil sites in Africa.

The fossils

The Jebel Irhoud site has yielded a rich human fossil assemblage comprising skulls, jaws, teeth, leg and arm bones from at least five individuals, including a child and adolescent. Although the original location of all the fossils is not known, they are all assumed to have come from the same layer at the site associated with the new date of circa 315 ka. The face, jaw and teeth are considered to be similar to our own, although the jaw and teeth are unusually large, and the size of the browridge is variable. The most significant difference appears to be in the shape of the skull, being lower in height and more elongate (less bulbous) than ours (see figure below). The features of the skull resemble those of other skulls of similar age, such as the 260 ka skull from the Florisbad site in South Africa. These differences in the shape of the skull suggest that those living at Jebel Irhoud, and more broadly throughout Africa from around 330 to 230 ka, were not yet fully us (Homo sapiens).

The line of descent in our Homo lineage is thought to be from early Homo species (Homo habilis, for example) to Homo erectus to Homo heidelbergensis to our predecessor species, and finally, to us Homo sapiens. As I discuss in my book, the range of variations within a species and the complexity of speciation in a large continent such as Africa, makes it difficult from the limited number of fossils available to delineate species clearly. Some experts, the ‘lumpers’, view the changes in our lineage as gradational and refer to the Jebel Irhoud fossils as ‘archaic’ Homo sapiens. Other experts are ‘splitters’ and argue for stepwise evolution of distinct species. I believe there are enough physical differences and culture differences (see below) to support an intermediary species in the evolution of H. heidelbergensis to H. sapiens, an intermediary species that would take the place of the lumpers’ archaic Homo sapiens. However, this intermediary species lacks a generally accepted species name, and so I refer to it as our ‘predecessor’ species.

To my view, the new age indicates that the fossils at Jebel Irhoud represent some of the earliest members of our predecessor species and not, as implied by many of the news stories, that our species Homo sapiens now has an age range that extends back to around 300 thousand years. The oldest yet recovered fossils of our species Homo sapiens, ones that represent anatomically modern humans (AMHs) remain those found in East Africa that date to between 200 ka and 150 ka. The earliest members of our species most probably descended from our predecessor species, who were widespread throughout Africa by around 280 ka as represented by the fossil skulls found at Jebel Irhoud in Morocco, Florisbad in South Africa and Laetoli and Ileret in East Africa.

predecessor skulls.pngFossil skulls dated between 315 and 260 thousand years old that are possibly representative of our predecessor species intermediate between H. heidelbergensis and H. sapiens (from left to right: Florisbad, Laetoli (Smithsonian Institution) and Jebel Irhoud (Natural History Museum, London)).

Herto 1.png   Herto 2.png  modern skull 1.png  modern skull 2.png

Fossil skulls of our species Homo sapiens from 160 thousand years ago (Herto, two images on left; photos by David Brill (humanoriginsphotos.com)) and modern (two images on the right). Our species is largely defined by its bulbous shaped skull.

 

Cultural differences

The arrival of our predecessor species is associated with the major transition from the Earlier Stone Age to the Middle Stone Age (MSA), a transition marked by smaller, more regionally-diverse stone tools. Jebel Irhoud is now the oldest site known having a direct association of fossils with MSA tools. MSA tools are widespread throughout Africa from around 300 ka to 230 ka, but most often not associated with human fossil remains. Some of the MSA stone points recovered from Ethiopia have been interpreted from their edge damage to have been used as thrown spears by at least 279 ka. The stone points from Jebel Irhoud have not yet been interpreted as having been thrown as spears (javelins). Those living at Jebel Irhoud were competent hunters based on the animal bones found. It may be that they made effective use of sharpened wooden spears without stone armatures, something their predecessor Homo heidelbergensis was doing.

 

spear tips.png    San throwing.png

Obsidian projectile spear tips from Ethiopia dating to at least 279 ka (Sahle et al., 2013) and a photo of a !Kung San throwing a spear (photo courtesy of Neil Roach).

 

The presence of burnt bones and charcoal suggests they had control of fire. However, they do not appear to have used fire to intentionally heat the stones (pyrotechnology). The earliest evidence for intentional heating of stones to improve their work-ability dates from 164 ka at the Pinnacle Point site in South Africa, presumably made by H. sapiens. Heating was probably not necessary in the case of the raw stone material available at Jebel Irhoud and the heating of about a third of the stone tools there was likely because they inadvertently ended up beneath where later fires were made.

The other cultural artefact to appear for the first time in the MSA is ochre, an iron-rich rock used for, among other things, symbolic body painting based on the specific collection of the reddest coloured stones. The earliest use of ochre is in East Africa, but no ochre has been reported from the Jebel Irhoud site. The absence of thrown stone-tipped spears and ochre at Jebel Irhoud may indicate that these cultural innovations were only developed later among groups of our predecessor species. Alternatively, these cultural items may have been present among groups in sub-Saharan Africa but were lost by groups too small to sustain these cultures after they had expanded into North Africa where soon became isolated from other groups.

ochre.png  ochre powder.png

Ochre stones and grinding ochre into a red powder.

 

Speciation events

Do the fossils at Jebel Irhoud suggest that the geographical region of origin of our predecessor species was North Africa? I argue in my book that the Maghreb, located at the northernmost tip of Africa was a potential geographical region of origin for species within our human lineage. This was based primarily on the periodic isolation of the Maghreb, separated from the rest of Africa and Eurasia by the Sahara-Arabian Desert and the Mediterranean Sea. Relatively small groups living in isolation in the Maghreb over long periods of time may have evolved away from other groups. These substantial physical barriers would have made exchange highly unlikely, except during relative brief periods when the Sahara-Arabian Desert ‘greened’ by receiving enough rainfall for the transformation of the desert into grassland and lakes.

These greening events may have made it possible for the periodic mixing of previously isolated groups living in the Maghreb, sub-Saharan Africa and Eurasia. We know the Sahara-Arabian Desert greened most recently 9 to 6 ka, with large impacts on the movement and interaction of people throughout the region. There is also good evidence of widespread greening 130 to 120 ka go associated with the movement of our species out of Africa into the Levant, and possibly into North Africa as indicated by the first appearance there of distinctive Aterian stone tools. What the groups represented by Jebel Irhoud fossils had evolved into by the time of the 130 ka greening event and to what extent they may have intermingled with Homo sapiens coming from sub-Saharan Africa is unknown. There were other greening events, such as the one associated with when modern people left Africa as part of the Great Expansion 60 thousand years ago, but the timing and extent of past greening events remains poorly known.

The interglacial period that occurs within the dated range of the Jebel Irhoud fossil site of 383-247 ka that is most likely to have had a significant greening event is Marine Isotope Stage (MIS) 9  ̶̶   roughly 330 ka. The fossils at Jebel Irhoud may represent early members of our predecessor species who evolved there among small, isolated populations of H. heidelbergensis and then spread out into the African continent with the greening of the Sahara associated with the MIS 9 interglacial period. Alternatively, our predecessor species may have evolved from H. heidelbergensis somewhere in sub-Saharan Africa and moved into the Maghreb during the MIS 9 or another greening event. Unfortunately, the age resolution of archaeological sites and number of sites are not sufficient to determine at this stage where in Africa our predecessor species evolved.

MIS 9.png

Ochre, javelins and diverse Middle Stone Age regional cultures are associated with the evolution of our predecessor species from H. heidelbergensis in Africa. The age range of 383-247 ka of the Jebel Irhoud site places it around the time of the MIS 9 Interglacial period when a greening of the Sahara may have allowed movement of groups living in North Africa and sub-Saharan Africa.

 

What we know from the dated MSA stone tool assemblages in North Africa, East Africa Rift Valley and South Africa is that our predecessor species was widespread throughout Africa by around 280 ka, but from which of these areas they evolved into us Homo sapiens remains unresolved. In my book I suggest that the currently available information favors South Africa as our species’ geographical region of origin  ̶̶  check it out and see if you agree.

 

Further Reading

Richter, D. et al., 2017. The age of the Jebel Irhoud (Morocco) hominins and the origins of the Middle Stone Age. Nature http://www.nature.com/doifinder/10.1038/nature22335.

Hublin, J.-J. et al., 2017. New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens. Nature http://dx.doi.org/10.1038/nature22336.

Stringer, C. and Galway-Witham, J., 2017. On the origin of our species. Nature 456, 212-214.

Gibbons, A., 2017. Oldest members of our species discovered in Morocco. Science 356, 993-994. [doi: 10.1126/science.356.6342.993]

Compton, J.S., 2016. Human Origins, How diet, climate and landscape shaped us. Earthspun Books, www.johnscompton.com.

Sahle Y., Hutchings W.K., Braun D.R., Sealy J.C., Morgan L.E., et al., 2013. Earliest stone-tipped projectiles from the Ethiopian Rift date to >279,000 years ago. PLoS ONE 8(11): e78092. doi:10.1371/journal.pone.0078092.

 

 

First and forever a microbial world

They are so small, we rarely give them a thought and yet they are out there in numbers too enormous for us to comprehend. In fact, they are estimated to constitute no less than half of the total mass of all life on Earth. So, when you next look out over the landscape covered by plants and teeming with insects, birds and animals, think of the roughly equivalent mass of life that you don’t see. This invisible other half of life is the microbial world, made up of a great variety of microorganisms, so called because they typically measure only 0.5 to 5 micrometres across (that is about one-thousandth to one-hundredth the width of the 0.5 millimeter sized dot atop the letter i).  Although they are nearly everywhere, to see them requires a microscope (although some exceptionally large species are visible to our naked eye, such as Thiomargarita namibiensis, which lives by accumulating spheres of elemental sulphur in its elongate cells in shelf sediments offshore Namibia in southwest Africa).

For what they lack in size, microorganisms make up for by their ubiquitous multitudes: 10 to 1000 billion in every teaspoon of soil, a billion or so in every 20 drops (one millilitre) of water, and each of us hosts on the order of 40,000 billion microbes thriving inside our body and out. Microbes have evolved to eke out a living in nearly every habitat on Earth, even those we don’t normally associate with the living world: kilometres below the surface in deep rock fractures, and deep below the surface of massive ice sheets. Microbes can even survive in the vacuum of space, and include those left behind on the Moon by astronauts (most likely in a dormant, resting state). We tend to consider microbes as dangerous and something to kill off indiscriminately with antibiotics and disinfectants. Although some are pathogens, most microbes are benign and many others beneficial, if not essential to our well-being. We are only beginning to appreciate the roles played by the highly diverse microbes that thrive in our gut, our mouths and in every nook and cranny of our skin.

Staphylococcus_aureus_VISA_2

The bacteria Staphylococcus aureus (colourised from CDC/Matthew J. Arduino, DRPH/Photo Credit: Janice Haney Carr, scale bar is 1 micrometre).

e_coli

Escherichia coli (E. coli) bacteria (credit: NIAID, each around 2 micrometres long)

Microorganisms are unicellular, with each individual consisting of a single cell whose features are either relatively simple or complex. Those with generally small, simple cells are referred to as prokaryotes and include two main groups: bacteria and archaea. Their simple cells contain a single, circular loose strand of DNA along with ribosomes housed within a cell wall and membrane. Those with generally bigger and more complex cells in which the DNA occurs tightly coiled within a separate nucleus enclosed by a membrane and, along with ribosomes, contain organelle structures are referred to as eukaryotes. The eukaryotes are thought to have evolved from the merging of different prokaryotes. For example, mitochondria organelles, which act as the energy furnace within eukaryotes, were once separate bacteria that were at some stage taken in by and subsumed by archaea. Bacteria and archaea evolved by around 3.5 billion years ago, while the eukaryotes only evolved later by around 2 to 1.5 billion years ago.  The evolution of eukaryotes was critical to the eventual evolution of all the big, visible organisms like plants and animals whose many cells are eukaryotic.

Ch1_p21_iii

Even magnified under a microscope, the many different species of bacteria and archaea can be difficult to tell apart. Some species have many tiny hair-like cilia or long thread-like tails (flagella) to whip them about (see photo top from http://www.cdc.gov/ecoli/), while others can bind together to form filaments or thin-film colonies. But most individual cells are either spherical to elongate in shape and difficult to tell apart from outward appearances. And this partially explains why archaea were only recently appreciated as being different from bacteria. One way to tell them apart is by what they do chemically, for bacteria and archaea are extremely versatile in the ways in which they metabolise. Some reduce carbon dioxide to methane, others fix nitrogen into nitrate while others convert nitrate to nitrogen, some oxidize sulphur to sulphate while others reduce sulphate to sulphide, and so on…each occupying the chemical niche best suited to their way of life. In essence, bacteria and archaea run most global elemental cycles at Earth’s surface, accelerating the pace of chemical reactions so vital to all life forms big and small. Just how many species there are remains largely unknown, but the application of genetics has facilitated our ability to identify them, with thousands of species typically analysed within any given soil or water sample.

Ch1_p24_iv

No sex please, we are prokaryotes! Bacteria and archaea reproduce by binary fission, where an individual makes an identical copy of itself and splits into two – a parent and its clone. They can also take up bits of DNA of interest that happen to be floating about in their surroundings or they can transfer specific bits of DNA among themselves. Such horizontal or lateral transfer of DNA helps them adapt to changes and to survive stressful times. They can also shut down and stay holed up as microbial cysts until better conditions return, even if that means remaining dormant for centuries or perhaps millions of years. Although microbes living today are probably not terribly different from the first of their kind that appeared 3.5 billion years ago, they can evolve rapidly. For example, so-called ‘superbugs’ evolve in hospitals by surviving the continuous onslaught of antibiotics and disinfectants.

Being the first to live on Earth, bacteria and archaea form the two deepest domains of life, and they are the life forms most likely to endure. Their small size, widespread distribution, genetic diversity and ability to shutdown make them far more likely than other organisms to survive whatever future catastrophes come along. As long as Earth is capable of supporting life it will always include a microbial world. In this sense, the meek shall inherit the earth, if the meekest among us are the smallest and simplest microorganisms. And if life exists on other Earth-like rocky planets orbiting within the wet and warm habitable zone of their stars, it too will most likely be microbial. When considering the abundance and amazing chemical promiscuity demonstrated by the element carbon on Earth, it seems reasonable to conjecture that microbes on other rocky planets are likely to be similar in many respects to our own. It is partly for this reason that we must take every precaution not to contaminate other worlds if we hope to determine unambiguously if life exists elsewhere.

©John S. Compton (www.johnscompton.com)       Earthspun logotan

Origin of life

How did life first came about? Our planet started out as a molten magma ball too hot for life, but the oldest fossils indicate that life was established soon after Earth had cooled sufficiently to be covered by oceans of water suitable for life. Evolutionary theory allows us to understand how life, once arrived, diversified over deep geological time into the abundant life forms we observe today. However, how life first evolved on Earth remains largely unknown. We have only ever observed life to spring from existing life, and we have yet to find convincing evidence that life exists elsewhere beyond our planet. And although we have extensively modified the DNA of existing organisms, including the synthesis of a simple microbe ( C. A. Hutchison III et al., Science 351, aad6253 (2016). DOI: 10.1126/science.aad6253), we have yet to synthesis life from scratch, from its basic organic molecular building blocks such as amino and nucleic acids.

All the diverse life forms on Earth today, including us, appear to be ultimately related to one another and to share a common ancestor. This gives rise to the concept that ‘all life is one,’ which stems from the fact that all life is based on DNA and RNA, the double and single helical molecules that contain the code of life. Similarities in genetic DNA and RNA make-up, as well as the many shared biochemical processes across many different organisms, suggest that we and all other life forms descend from a distant common ancestor. This shared great-great-greatest of grandparents to everything that is living today is known as life’s Last Universal Common Ancestor, or ‘LUCA’ for short.

Charles Darwin commented on this profound concept that ‘all life is one’ in his book On the Origin of Species, published in 1859:

‘It is a truly wonderful fact – the wonder of which we are apt to overlook from familiarity – that all animals and all plants throughout all time and space should be related to each other…Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.’

LUCA is Darwin’s ‘primordial form into which life was first breathed’ and from which all life forms on Earth descended. Hence, the myriad species we see today are each from a long line of descent that includes many now extinct ancestors over the eons of deep geological time and which converge all the way back to LUCA.

There have been many ideas put forth on where and how did LUCA evolved, but the upshot is we do not know. What we do know is that LUCA must have evolved sometime between when Earth had first become habitable (4 to 3.8 billion years ago) and the oldest fossil life forms yet found in rocks 3.4 billion years old.

Sugitani1

The earliest fossil evidence of life on Earth comes from organic structures such as these observed in thin slices of rock 3.4 billion years old from Australia and South Africa (image 0.16 mm across, courtesy of Ken Sugitani; K. Sugitani, and others, 2015. Early evolution of large micro-organisms with cytological complexity revealed by microanalyses of 3.4 Ga organic-walled microfossils. Geobiology DOI: 10.1111/gbi.12148)

These oldest fossils reveal the overall cell morphologies, but tell us little about the biology of these early organisms. However, they are generally assumed to be representative of the simplest single-celled microorganisms living today. But even the simplest bacteria today include many complex organic structures (DNA, RNA and ribosomes) and intricate biochemical processes that occur within their cell-wall structures. Our general understanding of evolution suggests that the complex biology represented by these fossil organisms evolved gradually over the hundreds of millions of years available from the modification of existing, simpler structures. These first organic structures were not in themselves living entities, but they may have nevertheless evolved as molecules by way of random mutations and natural selection in much the same way that Darwin proposed species do today. These selective forces may have promoted the merging of different ‘molecular species’ in ways that enhanced their mutual stability and replication in what could be viewed as a continuum leading up to the first bona fide life forms, out of which LUCA would evolve to give rise to all life as we know it.

Earth’s surface had an abundance of all the elements necessary for life: carbon, nitrogen, oxygen, phosphorus, etc. It also included organic compounds, such as amino acids, sugar and sugar alcohols, either formed naturally on Earth or delivered by meteorites. Besides water, life forms are mostly made up of amino acids organized into many different proteins, which are the large, complexly folded, three-dimensional organic compounds that make up our blood, muscles, skin, hair, etc. Amino acids existed before life, but how did they become organized into complex proteins under the direction of DNA and RNA housed within cellular membranes?

One idea is that early organic compounds may have included simple, self-replicating molecules, with those that replicated the fastest or most accurately persisting instead of perishing. Gradually, compounds as complex as small RNA-type molecules may have emerged whose information-storage capabilities could code for different amino acids in the production of proteins essential for a broad spectrum of biochemical functions. For example, phospholipid protein molecules capable of forming impermeable bubbles may have been precursors to cell membranes providing barriers to the outside world. Over time, incremental Darwinian selection led to improvements in replication and the coordinated merging of different organic structures and protein enzymes into the first simple cellular ensembles capable of extracting energy to grow, replicate and evolve, which in a nutshell is what life does. Of course, much of the above generalized scenario is highly speculative and we are a long way from understanding the many intricate processes by which life arose on Earth.

Where on Earth might life have first evolved? A likely ‘primordial soup’ from which life was concocted is in the vicinity of volcanic hot springs located along the axis of the mid-ocean ridge mountain chain in the deep, dark ocean. These volcanic hot springs are called ‘black smokers’ (see image below), because they spew turbulent smoke-like billows of black sulfide particles through mounds and chimney-like columns. The mid-ocean ridge represents the most recently formed oceanic crust. The large temperature contrast between the newly emplaced, hot crustal rocks and cold, overlying seawater drives the intense circulation of seawater through the oceanic crust. Hot, altered seawater is eventually shot back out into the sea via black smoker vents. These and other ocean vents are home to thriving communities of organisms, such as tube worms, clams and shrimp. At the base of the vent food chain are chemosynthetic microbes, which derive their energy from chemical reactions associated with the vents rather than from sunlight energy as do algae and plants living today in the sunlit uppermost surface of the ocean. Support for a black smoker origin of life comes from the fact that some of the most primitive microbes (archaea) live there today in waters as hot as 113°C.

 

NOAA Ocean Explorer: Okeanos Explorer: Galapagos Rift Expedition

Is this where life began? Hydrothermal (hot water) vents, such as this one on the Galápagos Rift mid-ocean ridge, are host to a diverse community of organisms (mostly white and red tube worms in the photo above). The vibrant vent community ultimately exists from the energy available from chemical reactions. Some of these reactions are expressed in the precipitation of the dark sulfide minerals that give ‘black smokers’ their name.  (photo from NOAA PMEL Vents Program; source: http://oceanexplorer.noaa.gov/okeanos/explorations/ex1103/logs/july20/media/tubeworms_smokers.html)

2008_age_of_oceans_noplates

The mid-ocean ridge forms a long, continuous submarine mountain chain (red) along which black smokers and other vent systems occur. Early Earth is likely to have included a mid-ocean ridge with black smokers, with the continents only forming later.

We don’t know how many variations on early life there were before LUCA had evolved. In fact, we know very little about LUCA itself, except that it likely included features of the simplest microbes found today residing in the vicinity of deep, dark ocean vents. Wherever and however LUCA first appeared, its descendants soon ventured out to other parts of the ocean and along the way evolved into many different types of microorganisms. These, in turn, gradually gave rise to the rich diversity of life we are familiar with today in the sea and on the continents.

©John S. Compton (www.johnscompton.com)                                                      Earthspun logotan

 

Are we alone?

Earth could be considered rarefied if it belongs to a small, esoteric and exclusive group of planets that are rocky, orbit within the habitable zone of their stars and support life. NASA’s Kepler space observatory has now confirmed the existence of at least 2000 planets beyond our solar system (exoplanets). Considering that Kepler has searched within a very small patch of the sky, it is probable that exoplanets are out there in abundance. Some, like the exoplanets Kepler 542b and 186f, appear to be Earth-like: rocky planets up to two times bigger than Earth that orbit within the habitable zone of their star. But whether any of these Earth-like exoplanets also support life remains unknown.

The discovery of these distant rocky exoplanets, along with our Sun’s four inner rocky planets Mercury, Venus, Earth and Mars, suggests that rocky planets are not rare. However, they tend to be small and difficult to detect. Rocky planets are unusual in that they concentrate all the heavies, those elements heavier than the two lightest elements hydrogen (H) and helium (He). Most of the atoms in our solar system, as well as our universe as a whole, consist of H and He, with H making up 73% and He 25% of all atoms. All the other elements known on the periodic table make up the remaining 2%. These heavies were forged from H and He within large stars or during the explosion of large stars (supernovas) since the big bang 13.7 billion years ago. Because large stars are relatively rare, not much of the original H and He that formed at the time of the big bang have managed to be forged into the heavier elements.

H and He are great for making stars but it is difficult to imagine how they could ever form the building blocks of life. Life as we know it requires elements such as carbon, oxygen, nitrogen, phosphorus, sulfur and a whole host of trace metals and other elements. So, the key initial step in making a living planet is making one that, like the rocky planets, concentrates the heavies. But all we need to do is look at our rocky planet neighbours to realise that the other critical factor for life is that the planet orbits within the habitable zone. Venus is too hot and Mars is too cold, but Earth is ‘just right’ – neither too hot nor too cold for liquid water to exist in abundance. Earth, the ‘blue marble’ planet (see image above from NASA Goddard Space Flight Center/Reto Stöckli), is unique among our solar system’s rocky planets, with our big blue ocean and swirling white clouds indicating that we orbit within our Sun’s habitable or just right ‘Goldilocks’ zone. There have been recent discoveries of planets from other solar systems that appear to orbit within their star’s habitable zone, but whether they too are blue marble planets is more difficult to discern (see artist’s image below from NASA Ames/JPL-Caltech/T. Pyle).

The ideal rocky exoplanet, one that may support life, would be the same size or up to twice as big as Earth and orbit a star similar to our Sun as does the best candidate, Kepler 542b. Size matters because a planet needs to be big enough to retain an atmosphere of gases heavier than H and He. Like a child’s helium balloon, Earth’s initial H and He gases floated off into space, eventually joining up with their multitudinous kin residing in our Sun. However, the heavier gases, including water vapour, were retained and once conditions had cooled enough this water vapour rained out to form the oceans. And it was soon after the oceans formed that life was established on Earth. It is the presence of life that may or may not be the most rarefied aspect of our planet. Besides extraterrestrial visitors or communiqués from outer space, how might we detect life on other planets? What features could we look for uniquely associated with life?

Earth can also be thought of as rarefied in terms of its outermost layer, its atmosphere. While iron sank to the core, the lightest elements buoyantly made their way to the surface to form Earth’s atmosphere – its most elevated and lofty, least dense layer composed of a thin mix of gases. Earth’s atmosphere initially had no oxygen gas (O2), but today oxygen gas is abundant making up 21% by volume. The oxygen gas content increased as a by-product of photosynthesis, the process by which algae and plants use sunlight energy to combine carbon dioxide (CO2) and water to grow. It is thought that it was the rise in oxygen gas to threshold levels, for example, that allowed for the rapid evolution of animals during the Cambrian explosion 541 million years ago. And life as we know it, based on carbon and photosynthesis, seems the most likely for other rocky worlds given that their chemistry would be similar to ours and life arose here so soon after it was possible.

Currently we are unable to see potential Earth-like exoplanets well enough to know if they are blue marbles having oxygen-rich atmospheres. However, far more powerful space telescopes are in the works and these might be able to provide the first solid evidence for life elsewhere. If we could find evidence for life on just one other planet the implication would be that Earth is not rarefied after all. In that case, the equation: ‘chemistry (of a rocky planet) plus energy (from its star) plus time equals life’ just may apply, and we would be only one of many, many living worlds in our universe.  Given how science has humbled our rarefied views of our place in the universe in the past (for example, Earth is not the centre of the solar system; we are not separate from but are in fact related to all other organisms on Earth), it should not come as too big a surprise to learn that we are not alone. Of course, Earth is special and its particular life forms are undoubtedly unique in many respects, but it seems likely that there are many other worlds out there, equally alive and special.

kepler186f_artistconcept_2

An artist’s interpretation of a ‘blue-marble’ exoplanet (Kepler 186f) (NASA Ames/JPL-Caltech/T. Pyle).

Deep Time/Big History

Where did you come from? Like many questions, the answer depends on the timeframe. At the one, most recent extreme is the seemingly straightforward response that you came from your mother, grown in the space of nine months from one of her eggs fertilized by one of your father’s sperm. At the other, most distant extreme is the origin of the many atomic elements that went into making you. The carbon, nitrogen, oxygen, and other elements that make up your complex organic compounds were made long, long ago from the fusing of lighter elements in the interior of enormous stars and as these stars blew asunder in enormous explosions (supernovae, such as the one pictured above, the Carina Nebula from NASAESA, and M. Livio and the Hubble 20th Anniversary Team (STScI)) since the big bang 13.8 billion years ago. So, in this sense, it would be correct to say we come from ancient star dust. But what about the intervening time that separates these two extremes? How is it that the minute, elemental bits of star dust once made were able to assemble eventually into something as miraculous as you or any other living life form on Earth? This is the realm of deep time or what has become known as ‘big history,’ covering all events prior to the written word 5000 years ago.

And it turns out, it took a long time and a lot had to happen before anything even remotely resembling us lived on Earth. Hence, from the perspective of deep time we are a very late arrival. There are many ways to try and understand just how recent our arrival is – such as the arrival of our species (Homo sapiens) seven and a half minutes before midnight on the 31 December relative to a start of the big bang on January first of that same year.  Farming only arrives around 20 seconds before midnight, written history 10 seconds before and Edison’s first commercial light bulb literally in the final wink of an eye (300 milliseconds) before the end of an all-time-encapsulated-in-one-year timeframe. But whatever device is used, deep time remains a difficult concept for most of us to grasp fully.  Even in the course of our lives our perception of the passage of time changes, from the agonising wait for our birthday as children to the speed at which the years appear to fly by to an octogenarian.

The figure below provides a graphical representation of deep time from the big bang to the present day, a span of 13.8 billion years.  More recent times are expanded successively in the columns from right to left. The second column on the right represents the classic geologic timescale, with the major ancient past epochs of the last 540 million years, including, for example, the Cambrian when trilobites crawled about and the Cretaceous when dinosaurs ruled. The third and final columns to the left represent the last three and the last half million years, respectively – the time span over which our human (Homo) lineage evolved. The last three million years, and particularly the last million, are demarcated by a wiggly line that represents fluctuations in climate from cold to warm and back again. These climate wiggles are important to our evolution because they are believed to have played a decisive role in shaping who we are.

Refer to Figure of deep (geological) time from big bang to today below.

Climate change in many respects was the ‘master variable’ because climate ultimately determines the types of habitats our ancestors adapted to in order to survive – the types of food on offer, the other animals we shared our habitat with, the frequency of fire, the severity of seasonal differences, just to name a few.  All of these factors influenced how our features were selected for over time. But is deep time still relevant to us today? For some among us, curiosity and a wanting to know how it happened is ample justification for learning about our deep past.  Most of us love stories and what better story is there than our big history, writ large over millions of years? So many things could have happened differently from the way they did, and yet the unique events that did unfold are what ended up shaping us into who we are today.  If we are to understand ourselves in the deepest sense, we need to know our deep past.

We forget most of our past but embody all of it.

(Quote from John Updike in his Introduction to Rabbit Angstrom)

We do quite literally embody our past – from our cellular functions, to upright walking, to our unusually large brain – these and all of our other features have origins rooted in our deep evolutionary past, origins that link us in many respects to all other life forms on Earth. There are many events that shaped each of our individual lives that we have forgotten and there are many events in the deep past that shaped who we are today that are unknown to us. But for some of these past events we have bits of evidence preserved in the rock and archaeological records that allow us to speculate on our big history; to tell the story of how it happened that we came to be.

©John S. Compton (www.johnscompton.com)

 

deep time

Figure of deep, geological time (from www.johnscompton.com based on the big bang image from NASA/WMAP Science Team; timescale adapted from Walker, J.D., Geissman, J.W., Bowring, S.A., and Babcock, L.E., compilers, 2012, Geologic Time Scale v. 4.0: Geological Society of America, doi: 10.1130/2012.CTS004R3C. Marine oxygen isotope records are from Lisiecki, L. E., and M. E. Raymo, 2005. A Pliocene-Pleistocene stack of 57 globally distributed benthic d18O records, Paleoceanography, 20, PA1003 (doi:10.1029/2004PA001071).