Nick DelRoseFebruary 18, 2018

Keeping Time


Hourglasses, sundials, clocks, and calendars have all been methods we use to keep track of time. With a check of the watch (or smartphone) we can know whether we’re running late or we have time for a coffee stop. But timing things right isn’t always a conscious decision, or a trivial one. Organisms need to know when to hunt, migrate, hibernate, mate, molt, and flower, to list a few. The “time” that we are most familiar with is marked by earth’s rotation on its axis (days) and revolutions around the sun (years). Here we look at time through multiple lenses, because meaningful information that winds one organism’s “clock” may be extracted differently than that information which winds another’s.

We start off with Sarah Holts “The Making of the Fittest” and Sharon Shattuck’s and Flora Lichtman’s, “Flu: The Great Migration”, in order to orient ourselves across a landscape of time over which we observe genetic change. We then take a turn to Anna Massih’s film, “Flowering Time,” where we are given an example of how plants learn to detect the passage of time. In “The concept of time in biology, and the unity of life”, Dr. Brian Enquist gives a talk at University of Oxford on the relativity of biological time, where he presents that biological time is experienced differently by different sized organisms. We then touch on gas exchange with Danielle Parsons and Ravi Sheth’s colorful (and trippy) film, “EXCHANGE”. Finally, we end with a paper, “Control of body size by oxygen supply reveals size-dependent and size-independent mechanisms of molting and metamorphosis” (Callier V. et. al) where we find that gas exchange is not only the currency for energy production, but also acts as a measure and regulator of body size—and a time marker for metamorphosis.

The Making of the Fittest (By Sarah Holt)

The Making of the Fittest

Sarah Holt’s film, “The Making of the Fittest,” highlights the research of University of California, Berkeley’s Dr. Michael Nachman. Exploring a very clear example of evolution, Dr. Nachman is able to assign players in the food chain across the New Mexican Valley of Fire, where volcanic eruptions 1000-years past have left a challenge for the rock pocket mouse: how to elude their predators—most notably owls. Volcanic eruptions have left greater than 40 miles of hardened, dark lava rock, in a desert where animals like the rock pocket mouse previously relied on its light color for camouflage on the fair desert sands.

            Dr. Nachman uses live capture traps to collect mice from on and off dark lava flows, showing that over the past 1000 years the rock pocket mice have developed darker hides. Interestingly, the selective pressure for darker fur does not affect their underbellies, where the mice have remained white. Their predators, searching from above, will struggle to see the darker mice regardless of whether their underbellies remain light.

            Dr. Nachman’s team traces the color change to a series of mutations in the mice DNA: within the Mc1r gene that controls the pigment of the hair follicle. While the mutation itself is random, the selective pressures that favor dark mice on lava flows comes from the predators themselves—the drivers of this genetic timescape.

Flu:  The Great Migration (By Sharon Shattuck and Flora Lichtman)

Flu: The Great Migration           

Flu: The Great Migration,” by Sharon Shattuck and Flora Lichtman, gives us another genetic timeline. In it, Trevor Bedford describes his research to trace flu viruses back to their origins, which he finds to be Southeast Asia. Constructing a family tree using ~10,000 RNA samples, the genetic information coding material transcribed from DNA, Trevor reveals two flu timelines. While Influenza A (which includes the H3N2 strain) evolves quickly and thus escapes our immunity more easily, Influenza B evolves slower and more often infects children who haven’t yet been exposed to the flu. H3N2 also travels quickly across the globe, while Influenza B can remain in one location for years.  What’s the explanation for these differences?

            Trevor draws a link between whom the virus tends to affect and how the virus spreads. While H3N2 infects more adults that travel via airplane, spreading the virus across the world, children most vulnerable to Influenza B tend not to fly. Understanding how Influenza travels and how different strains develop is key in the developing of the flu vaccine each year—a necessity for a virus undergoing so much genetic change to dodge its host’s immunity.

Evolution need not keep time—it happens according to the rate of genetic mutation and reproduction of an organism. On the other hand, time is not merely a landscape across which we passively experience. We may be able to see genetic changes over the course of 1000s of years, but there are ways that organisms have adapted to keep time in order to survive and reproduce.

Flowering Plants - The Right Timing​ (By Anna Massih)

Flowering Time - Fluorescently tagged Flowering Time (FT) protein, shown traveling via the Phloem into the plant shoot. (Coupland Lab)

Anna Massih’s “Flowering Time” gives a prime example of how organisms sense time. This film explains how sessile plants use the length of sunlight in a day as an indicator of when to flower and produce seed. In agriculture, flowering too early or too late translates to a poor crop yield. At a time where the world’s population is booming, flowering time could be an important genetic access point to control crop yield and feed more people. These type of problems can be solved with research and development of various Genetically Modified Organisms (GMOs).

            Dr. George Coupland from the Max Planck Institute sought an answer for how this time-telling mechanism is controlled, using the plant model Arabidopsis thaliana. It’s known that when kept in dark, these plants will not flower. He and his team found that even in light, when the leaves are removed, no flowers form. This led Dr. Coupland and his team to ask: what signal is traveling from the leaves to the shoot? Through molecular techniques they discovered a protein that starts the process of flower formation, CONSTANS. When daylight is sufficiently long, CONSTANS builds up to adequate levels to turn on another gene, FT (Flowering Time). FT travels via the plant phloem (the vascular transport tissue), to the shoots where it turns on genetic pathways required for flowering. By relying on daylight length, the plant is thereby ensured that it flowers during the appropriate time of year.

We’ve moved from cases where genetic change happens over the course of years, to an instance where time must be detected across the period of the plant life cycle (in the case of Arabidopsis thaliana, merely months). But how does time differ across species?

Tree Branching Sketch by Leonardo Da Vinci

The concept of time in biology, and the unity of life with Prof Brian J. Enquist

Click here to watch film

Here, Professor Brian J. Enquist gives a talk about how we and other organisms perceive the passage of time. Biological time, he presents, is relative, yet has constants related to metabolic rate. He starts with a diagram developed following an observation by Max Kleiber comparing organism size and metabolic rate, the “Mouse to Elephant Curve”. As animals increase in size, so does their metabolic rate. However, if you look at the metabolic rate per cell, small animals have much faster metabolic rates per cell than larger animals.

Schmidt-Nielsen, K. Scaling, Why is Animal Size so Important?; Cambridge University Press: Cambridge, UK, 1984

Here’s how he goes on to explain it: Energy production requires oxygen in aerobic organisms— which we will touch upon in the following video— but how is oxygen transported? The answer is through networks. Oxygen-carrying blood travels through arteries and capillaries to provide every cell with that oxygen. Dr. Enquist presents that while an animal's size doubles, there’s a cost according to resistance and transport time of resources through these networks. This cost means that cells of a larger organism actually have to run with a decreased metabolic rate in order to allow for the changes in access to the vasculature.

            Here’s one experiment that brings light to the importance of vascular connection: isolate a (slow metabolic) cell from a large organism in the lab, and the cell will take on a much faster metabolic rate in the petri dish. Cancer cells, Dr. Enquist also notes, tend to rob nearby cells of their vascular connections and run metabolically unchecked, explaining their rapid growth.

All this adds up to a big statement: metabolic rate is a dictator of lifespan, and how we perceive time. The trends show that metabolically fast (small) organisms tend to have shorter life spans than the metabolically slow (large) organisms. Yet all of these organisms will expend around the same amount of energy per mass in their lifespan: ~8 x 10⁵ kJ/kg.

EXCHANGE (by Danielle Parsons and Ravi Sheth)


I bring us to “EXCHANGE” because as we’ve seen, metabolism has an important role in our perception of time. In this film we learn about how mitochondria produce Adenosine triphosphate (ATP), a molecule that chemically stores energy necessary for life and needed for the function of every cell. Energy in the form of electrons pass along an electron transport chain on the inner membrane of mitochondria, powering proton transporters that shuttle protons up their concentration gradient. This proton gradient then drives an ATP-generating motor. Oxygen plays a key role in this process, as it is needed to accept electrons at the end of the electron transport chain. This is why oxygen, in aerobic organisms, is necessary to every cell, and why every cell of our body must be connected to blood vessels.

Fixed tracheal network at beginning and end of 5th larval instar. (Nijhout Lab)

Control of body size by oxygen supply reveals size-dependent and size-independent mechanisms of molting and metamorphosis

Click here to read article

As touched on earlier, as organisms increase in size so too must their vascular systems. In Dr. Frederick Nijhout’s lab they ask how Manduca sexta caterpillars determine when they’ve reached the proper size prior to molting and metamorphosis. The answer lies in their fixed tracheal system— a system of tracheae that allows for gas exchange with the outside via holes called spiracles. When the caterpillars reach a certain mass, their fixed tracheal system, which does not grow, is stressed to supply oxygen to the organism, triggering the mechanism for molting. Dr. Nijhout and his lab observe that this is the main pathway of size-recognition, and consistent with that, caterpillars put in low oxygen conditions will molt at a smaller size.

Thus, gas exchange not only plays a major role in metabolic rate and lifespan, but also appears to control the timing of metamorphosis in caterpillars and likely in other insect larval molts. In fact, if you’ve wondered why insects in prehistoric times were so much larger than today, you might already have your answer. Atmospheric oxygen levels were much higher at this time, making a larger body size possible.

About the author


Nicholas DelRose is a plant biology PhD candidate at New York University, studying root regeneration in Arabidopsis thaliana. He is also the co-founder and art director of a new greeting cards company, Damaged Goods.  His art and biology interests began at an early age when he became well-practiced in papier mâché and fascinated by the metamorphosis of caterpillar to butterfly. He has continued interest in the intersection between art and biology, and in science communications through 3D illustration, animation, and writing.

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