Frozen in time – lives, the universe, and everything

21 March 2014 by Malcolm Campbell, posted in Biology, Evolution, Science

If I could save time in a bottle, the first thing that I'd like to do, is to save every day, ‘til eternity passes away, just to spend them with you.” from Time in a Bottle by Jim Croce (1943-1973)

If you catch the light just right, you can see the waves.

Ripples in snow. Literally frozen in time.

As the snow fell, the conditions were ideal for creating the ripples. The ideal consistency of snow – fine enough to blow, thick enough to fall and adhere. The ideal consistency of wind – breezy enough to create waves on the surface of the snowscape, gentle enough to prevent banks from forming. The ideal consistency of temperature – warm enough to create damp snow, cold enough to freeze it in place. Snow, breeze and temperature worked together to shape a natural relief sculpture – ripples etched like tiny dunes on a white-blanketed desert. snowripples1

The frozen ripples captured a slice of time. The captured moment resides in, and above, and below their glistening undulations. A moment in life. A moment in the universe.

Beneath the ripples, in the icy soil below, life has been put on pause. The dynamic interplay of soil microbes, the single-celled organisms in their subterranean home, has been placed in stasis.

In less frigid times, in the earthy soil, microbes would go about the business of gathering nutrients. They would convert those nutrients to cellular energy, cellular machinery or cellular architecture – using those components to grow and divide. With each cell division, a new microbial cell is added to the population. Some microbial cells will senesce and die, but together the different microbes – bacteria, archaea, and fungi alike – will form a dense ecosystem of interacting organisms.

Bacteria dominate this ecosystem. There are tens of millions of bacterial cells in a single gram of soil. Here they grow. Here they divide. Here they evolve.

Changes, mutations, in the genetic code of some of the soil-borne bacteria would arise. Accidental mis-copying of the DNA code would result in a new letter of the code being substituted in one bacterium, a different letter being missed out in another.  Such small alterations would arise every now and then in different bacteria scattered throughout the soil.

One over here.

Another over there. snowripples2

Normally, nature would sift through the possessors of these small changes – favouring those that confer an advantage, eliminating those that create disadvantage.

Bacteria harbouring benign mutations might persist as a matter of happenstance – slowly emerging as new variants in the population.

Other mutations might cause the bacterium to falter – make it less suited to their soil-bound life. Such individuals will divide slowly, if they divide at all, and will eventually find themselves swamped out of existence by competing microbes.

Still other mutations might confer an advantage on their holder – the capacity to make use of a nutrient source better than neighbouring bacteria, for example. A bacterium with such a mutation would be are favoured in their environment. They would convert nutrients to energy and building materials faster. They would divide at a greater rate. They would, in time, begin to dominate their little patch of soil.

All of this would normally play itself out beneath the soil. But under the frozen ripples, in the soil beneath, these activities have been frozen in time. The winter freeze captures a snapshot of an evolutionary trajectory.

We know this because such snapshots have been captured in the laboratory. They’ve been captured through the Long-Term Evolution Experiment (LTEE) by the evolutionary biologist, Richard Lenski, and his colleagues.

On February 24, 1988, Lenski began an incredible experiment that is elegant in its simplicity, and remarkable for the discoveries that have emerged from it. On that day, Lenski inoculated 6 different flasks of broth from a single colony of the common bacterium Escherichia coli. At the same time, he also inoculated another 6 different flasks of broth from a different single colony of E. coli. The two different colonies of E. coli that were used to establish each group of 6 bacterial cultures varied only in their ability to use the sugar arabinose as a carbon source. One colony was able to grow using arabinose for carbon. The other was not. snowripples3

Each of the original twelve 50 mL flasks contained 10 mL of liquid broth. Over the subsequent days, the flasks were swirled to aerate the broth, and thereby enable the bacteria to grow. Once the E. coli reached a critical density, a small amount of the bacteria was transferred to fresh broth so as to dilute it 1:100. These “subcultures” were then allowed to grow again as before. The subcultures are then re-grown to the same density as before, diluted as before, and allowed to re-grow again.

Lenski and his colleagues have continued this cycle of subculture propagation for over 25 years now. More than 50000 generations of bacteria have passed since the original colonies were used to inoculate the first batches of broth in 1988. Each round of subculture carries each of the twelve cultures along its own line of inheritance – each culture is like a separate lineage in a pedigree.

Importantly, every 75 days – the time equivalent to the passing of 500 E. coli generations – a sample of the subculture is removed. Glycerol is added to this sample as a thermoprotectant. The sample is then frozen at -80C. The frozen sample captures a moment in time in the lineage for each of the twelve E. coli cultures. Lenski and his colleagues are able to return to these frozen samples, thaw them, and make comparisons between the ancestral bacteria and different generations. More so than anything else referred to as a “living fossil”, Richard Lenski’s frozen samples are truly living fossils. They are the “missing links” that have not gone missing. They literally hold the secrets of the past.

The overall story that has emerged from these snapshots in time is stunning.

The bacteria are clearly evolving.

Even in the relatively homogeneous environment of a swirled broth, E. coli evolves. By 2000 generations, cell shape differences could be seen between the ancestral bacteria and the different culture lineages. What’s more, by competing the growth of the derived lineages against their founding ancestor, and using this as a measure of fitness, E. coli fitness could be seen to increase within the lineages over time. Remarkably, it appears that this fitness can continue indefinitely – well, at least out to 50000 generations! snowripples4

What is perhaps even more remarkable is the way in which evolution has proceeded in the different lineages. There are marked examples of parallel evolution – the lineages are all increasing in fitness (albeit at different rates), and all show an increase in cell size to some extent. Strikingly, the way in which the independent lineages use their genes – the extent to which the instructions encoded within the genes are read out – is highly similar as well. For some lineages, this is due to mutations in a single gene, spoT, which controls the extent to which other genes are read out. It is striking that independent lineages all have mutations in the same gene – the individual letter changes are different across the lineages, but it is the same gene that is affected.

Of course, there are differences between the lineages as well. The most marked of these is that one lineage has evolved the capacity to grow on citrate. This capability emerged after 30000 generations in just one lineage. The citrate-utilising innovation has not been “discovered” by any of the other eleven lineages…yet.

While only one lineage has evolved citrate-utilising capability, several lineages have lost the ability to utilise maltose as a carbon source. Intriguingly, these same lineages have acquired the ability to resist infection by a virus that infects E. coli – despite the fact that the cultures have never been exposed to the virus!

While 25 years is relatively long in a human lifespan, in terms of evolutionary time, the Long-Term Evolution Experiment (LTEE) is less than a blink of the eye. And yet, even the frozen snapshots provided at 500-generation intervals reveal the constant pulse of evolution – the emergence of mutations and their selection, even in a homogeneous environment.

Imagine what is taking place beneath the soil. As opposed to merely one bacterial species, there are many. Each has its own evolutionary trajectory – a trajectory that is, importantly, shaped, in part, by the trajectories of those with which it shares the ecosystem. Within the soil, even though evolution is taking place with microscopic organisms, it is playing out on a very grand scale. snowripples5

Beneath the frozen ripples of a snowfall, this grand evolutionary scheme is momentarily paused. Like Richard Lenski’s freezer samples, the frozen soil holds a record of many different lineages at a particularly point in their evolutionary trajectory. The frozen ripples are a reminder that the ripples of evolution continue to make their mark in our ever-changing world – even if they are not visible to us.

The frozen ripples hold another imperceptible connection to the passage of time.

The ripples are seen by holding our heads just so. The light must glance off of them at the right angle. The ripples are only visible when the snow reflects the right amount of light, and when shadows fall to reveal the rise and fall of the waves. It’s what we see, and what is shaded by obscurity that reveals the picture in its entirety.

The vast majority of the light that is cast on the frozen ripples is from our Sun. Photons have made the 8 minute journey from our Sun to Earth to illuminate the snowy surface. Simultaneously, smaller amounts of light from the distant past are also case upon the frozen ripples. Notably, the “fossil remains” of light from 13.8 billion years ago very subtly strike the recently solidified undulations of snow.

These “fossil remains” are actually photons that were pushed to microwave wavelengths by the rapid expansion of the universe aeons ago. They are no longer visible to us, but they wash over us all of the time.

In the approximately 380000 years after the Big Bang, our universe continued to expand by orders of magnitude. As it expanded it cooled, allowing   collisions between electrons and protons, generating new atoms that populated the expanding space. Over this time period, and the years that followed, photon were stretched to those microwave wavelengths. It has taken 13.8 billion years for those photon fossils to reach us. On Earth, we detect this original microwave radiation as the cosmic microwave background (CMB) – a remnant of the origins of the universe. The universe is awash in these remnants of the earliest light – a giant pond of light in which we all bathe.

The record of the dawn of time should be imprinted in this pond – as ripples. snowripples6

At the very dawn of time, the universe underwent its first major, exceedingly rapid expansion, known as inflation. Inflation took place 10–35 seconds after the Big Bang. At this time the volume of the universe increased by a factor of up to 1080 in a fraction of a second. Inflation should have created huge distortions in gravity – so-called gravitational waves. These are waves that should resonate and echo like the ringing of a bell. So strong were these waves that they should also have left their mark on the CMB – like ripples in the pond of light. These ripples can be seen as alterations in the way in which the radiation is transmitted, and therefore observed. The impact of inflation should create what is known as primordial B-mode polarisation of the CMB. The best way to think of this is that it is like of a different quality – like shadows and brightness seen in the snow ripples.

At the farthest reaches of our planet, at the South Pole, scientists have been looking for these ripples. Using the Background Imaging of Cosmic Extragalactic Polarization (BICEP2) telescope, they believe they have found what they are looking for. The BICEP2 telescope is a 26 cm aperture telescope that monitors wavelengths at 150 GHz. By collecting transmissions from the CMB between 2010 and 2012, astrophysicists have detected statistically robust fluctuations that support the hypothesis that they were created by primordial gravitational waves from the dawn of time.

While there is some scepticism regarding the precise interpretation of the BICEP2 data, there is still something extraordinary about observable fields of distortion in radiation that is 13.8 billion years old. As this radiation has traversed the universe, making its way from galaxy to galaxy, to finally arrive at this planet, to be detected by a species born a mere 200000 years ago, it retained an 13.8 billion-year-old imprint of ripples in space. We can see that imprint as a living fossil – it brings the past of our universe to light – literally and figuratively. It is a record of the deep past, frozen in time, travelling the universe for us to decipher. snowripples8

The snowy ripples are a tangible reminder of the connectivity between the deep past and the distant future. They reflect an image of what was, in the most distant moments of our universe. They enrobe the most recent record of the evolutionary trajectory of the millions of organisms. They hold in preparedness the raw materials for building evolutionary diversity to come. Something so simple – frozen ripples – they reflect the astonishing history of all that was, and hold the great potential for everything that will be. Our lives are like this.  Each moment we live is a frozen instant in time – a reflection of all that we have been, holding the great promise of all that we might be.

Images: All photographs by Malcolm M. Campbell.

References:

BICEP2 Collaboration (2014) Detection of B-mode Polarization at Degree Angular Scales. (pre-publication)

Blount ZD, Barrick JE, Davidson CJ, & Lenski RE (2012) Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 489: 513-518

Cooper TF, Rozen DE, & Lenski RE (2003) Parallel changes in gene expression after 20,000 generations of evolution in Escherichia coli. Proceedings of the National Academy of Sciences 100: 1072-1077

Lenski RE & Travisano M (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proceedings of the National Academy Sciences USA 91: 6808-6814

Meyer JR, Agrawal AA, Quick RT, Dobias DT, Schneider D, & Lenski RE (2010) Parallel changes in host resistance to viral infection during 45,000 generations of relaxed selection. Evolution 64: 3024-3034

Wiser M.J, Ribeck N & Lenski RE (2013) Long-term dynamics of adaptation in asexual populations. Science 342: 1364-1367
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snowripples9


4 Responses to “Frozen in time – lives, the universe, and everything”

  1. Maddie Reply | Permalink

    The emerging field of resurrection ecology- resuscitating ancient, cryogenically preserved microbes and plants, and experimenting with them in the lab to understand evolution- is absolutely fascinating. I've written a few blog posts on the subject recently if you're interested...the second one is about psychrophiles that can actually repair their DNA at subzero temperatures, perhaps avoiding becoming "frozen" in evolutionary time!

    http://lonelyspore.com/2014/03/26/resurrecting-ancient-microbes-to-understand-evolution/

    http://lonelyspore.com/2014/02/03/frozen-bacteria-repair-their-dna-at-15oc/

  2. Maddie Reply | Permalink

    Thanks for sharing these! That's a chilling (no pun intended) running story, something I've also experienced. And who knew an animal as complex as a frog could freeze solid and survive? Fascinating stuff.

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