Marine Conservation: The Coral Reef

Submitted as the third writing assignment in the Marine Megafauna course at this month.

How Might Ocean Acidification Affect the Coral Reef?

One might think that the coral reef ecosystem, as a warm water ecology confined by requirements for warmer water temperatures to mostly tropical and semi-tropical waters between 30 degrees north and south of the equator, might see little negative impact from global warming.  Indeed, one might optimistically expect that Atlantic and Pacific coral reefs might extend their overall habitat, if shallow enough waters permitted, perhaps to 35 or even 40 degrees north and south, as the subtropical seas warm.

Yet there are more pessimistic concerns which moderate optimism about global warming’s relation to coral reef ecosystem health.  First, some regional endemic coral species, especially in warmer equatorial waters, may not adapt readily to rapid rises in water temperature, so a decline in local species diversity might occur. Second, thermal stressors might alter disease susceptibility, which has already been suggested to be leading to loss of coral health in the Great Barrier Reef. Third and perhaps more importantly, global warming is occurring in association with a slow but steady increase in atmospheric carbon dioxide, likely from human burning of fossil fuels. When atmospheric carbon dioxide dissolves in the oceans, it does so as the weak acid, carbonic acid, which lowers the alkaline ocean pH. Because the primary structural mineral of the reef (calcium carbonate in the form of crystalline aragonite) is more soluble in an acid environment and so tends to dissolve in more acid watery environments, global ocean acidification creates a problem which may threaten the structural integrity of all coral ocean reef habitats. The Intergovernmental Panel on Climate Change has projected that all of our oceans’ pH will potentially fall by 0.3 to 0.4 pH units over the next century. This report will focus on the conservation issue of ocean acidification and its potential implications for coral reef species.

Coral species are very diverse, and there are soft as well as hard species of coral. Even soft-bodied corals contain a calcite skeleton which, cemented by successive generations of organisms, forms over time a layered stony structure underlying even soft-coral-predominant reefs.  For the purposes of this article, we will focus on a single hard coral species, the commonly named “hood” or “smooth cauliflower” coral Stylophora pistillata, which is listed in conservation status by the IUCN as Near Threatened. This coral species has a wide distribution in the tropical and semitropical regions of the Indian and Pacific oceans as well as the Red Sea, but is not generally found in Atlantic or Caribbean reefs. S. pistillata spreads readily within a given ocean basin by larval attachment and colony formation on the under-surface of driftwood or floating pumice. Its polyps tend to be about 1 mm in diameter and several cm long, and though its colonies can be confluent to meters in diameter, they are typically just centimeters in size, sometimes much smaller when seen as young colonies on smaller floating structures. Because it can thus form easily lab-transportable intact colonies, S. pistillata has been a favorite for laboratory studies of coral organism metabolism. Like all hard corals, its coral polyps secrete a calcium carbonate exoskeleton which forms the body of the coral colony and ultimately contributes to the stony base habitat of the reef itself. It is this calcium carbonate (aragonite) mineral exoskeleton which may be threatened by the conservation issue of ocean acidification.

I will focus on the paper “Live tissue imaging shows reef corals elevate pH under their calcifying tissue relative to seawater,” written by Alexander Venn, Eric Tambutté, Michael Holcomb, Denis Allemand, and Sylvie Tambutté and published in PLoS One on May 27, 2011 (online This article reports a research study designed to probe the chemical micro-environment at the polyp-mineral reef interface, where the polyp attaches to the rock of the reef.  There, the polyp has a specialized outer layer called the calicoblastic epithelium. This layer of cells secretes the mineral deposits which cause the rock of the reef to slowly grow by accretion.

The researchers collected microscopic photographs of the cell-aragonite crystal boundary and measured the micro-environmental pH at this polyp-mineral interface.  In particular, the study microscopically sampled both intracellular and extracellular fluid pH at this interface. The study showed that, even in the midst of flowing seawater, the polyp actively created and maintained a more alkaline pH at its active aragonite crystallization region just under the polyp. This crystallization area, which was always in intimate contact with the calicoblastic cells, was kept more alkaline than surrounding seawater pH of 8.15 by about 0.5 pH units in sunlight and 0.2 pH units in darkness. Thus, the article suggests that coral can and does compensate for a more acid ambient seawater pH than is ideal for calcium mineral deposition by actively maintaining a more alkaline pH locally in the region where alkaline pH is most critical for precipitation of aragonite calcium carbonate crystals.

The researchers kept ambient seawater pH at 8.15 and did not assess pH differences in a more acid environment. Nevertheless, this result seems reassuring, since it supports the hypothesis that, as long as a smooth cauliflower coral Stylophora pistillata colony remains healthy in other respects, it should be able to compensate (especially during daylight and with some small additional metabolic energy costs) for the predicted rises in pCO2 and drops in ocean pH over the next hundred years. Thus, tropical reef building may well continue beyond the year 2100 despite predicted increases in atmospheric carbon dioxide. Note that unmitigated optimism is not warranted by this study. We do not expect metabolic flexibility and pH tolerance to be the same across all species of coral, and furthermore, much of the lower supporting portions of today’s barrier reefs are composed of older, less live-populated, deep ocean aragonite rock walls, which might still tend more toward dissolution with drops in ocean pH.

Brief biography of a conservation biologist who is studying the consequences of ocean acidification on reef ecosystems: Jean-Pierre Gattuso.
Jean-Pierre Gattuso is a senior research scientist at the Laboratoire d'Oceanographie de Villefranche, in France. Dr. Gattuso is the editor of the journal Biogeosciences and has been active on several American and European expert panels on climate change, serving as an expert regarding the potential effects of future ocean acidification. His research interests include the cycles of carbon and carbonate in coastal ecosystems and the responses of ocean organisms and ecosystems to changes in the overall environment, including ocean acidification.

Further Readings:
Projecting coral reef futures under global warming and ocean acidification. Pandolfi JM, Connolly SR, Marshall DJ, Cohen AL. Science. 2011 Jul 22; 333(6041):418-22 (subscription-only accessible at
Major cellular and physiological impacts of ocean acidification on a reef building coral. Kaniewska P, Campbell PR, Kline DI, Rodriguez-Lanetty M, Miller DJ, Dove S, Hoegh-Guldberg O. PLoS One. 2012; 7(4):e34659. Epub 2012 Apr 11.
End of the century pCO₂ levels do not impact calcification in Mediterranean cold-water corals. Maier C, Schubert A, Berzunza Sànchez MM, Weinbauer MG, Watremez P, Gattuso JP. PLoS One. 2013; 8(4):e62655. Epub 2013 Apr 30.
Intergovenmental Panel on Climate Change. Climate Change 2013: The Physical Science Basis. IPCC web site, (accessed March 12, 2014).

Olfactory discrimination: the Nose Knows.

One TRILLION different smells?  Seems impossible to test and less likely prove, but then note that COMBINATIONS of base smells were used.  This is a little like generating lots of different shapes and colors and combinations of the same, and calculating the different color plates one could make.  By that measure, vision discrimination would be much, much higher.

Vol. 343 no. 6177 pp. 1370-1372 
DOI: 10.1126/science.1249168

Humans Can Discriminate More than 1 Trillion Olfactory Stimuli

Humans can discriminate several million different colors and almost half a million different tones, but the number of discriminable olfactory stimuli remains unknown. The lay and scientific literature typically claims that humans can discriminate 10,000 odors, but this number has never been empirically validated. We determined the resolution of the human sense of smell by testing the capacity of humans to discriminate odor mixtures with varying numbers of shared components. On the basis of the results of psychophysical testing, we calculated that humans can discriminate at least 1 trillion olfactory stimuli. This is far more than previous estimates of distinguishable olfactory stimuli. It demonstrates that the human olfactory system, with its hundreds of different olfactory receptors, far outperforms the other senses in the number of physically different stimuli it can discriminate.


Religion / Spirituality Correlates with Healthier Cortical Thickness.

Researchers have long known that there are robust correlations between spirituality and mental health in the US population. Now we have a report of a further correlation, between healthier brain tissues and spirituality, at least with regard to cortical thickness. 

Maybe there is a literal sense in Jesus' words, quoted in the New Testament, about spiritual bread. 


Neuroanatomical Correlates of Religiosity and SpiritualityA Study in Adults at High and Low Familial Risk for Depression

Lisa Miller, PhD; Ravi Bansal, PhD; Priya Wickramaratne, PhD; Xuejun Hao, PhD; Craig E. Tenke, PhD; Myrna M. Weissman, PhD; Bradley S. Peterson, MD

JAMA Psychiatry. 2014;71(2):128-135. doi:10.1001/jamapsychiatry.2013.3067.
Importance  We previously reported a 90% decreased risk in major depression, assessed prospectively, in adult offspring of depressed probands who reported that religion or spirituality was highly important to them. Frequency of church attendance was not significantly related to depression risk. Our previous brain imaging findings in adult offspring in these high-risk families also revealed large expanses of cortical thinning across the lateral surface of the right cerebral hemisphere.Objective  To determine whether high-risk adults who reported high importance of religion or spirituality had thicker cortices than those who reported moderate or low importance of religion or spirituality and whether this effect varied by family risk status.Design, Setting, and Participants  Longitudinal, retrospective cohort, familial study of 103 adults (aged 18-54 years) who were the second- or third-generation offspring of depressed (high familial risk) or nondepressed (low familiar risk) probands (first generation). Religious or spiritual importance and church attendance were assessed at 2 time points during 5 years, and cortical thickness was measured on anatomical images of the brain acquired with magnetic resonance imaging at the second time point.Main Outcomes and Measures  Cortical thickness in the parietal regions by risk status.Results  Importance of religion or spirituality, but not frequency of attendance, was associated with thicker cortices in the left and right parietal and occipital regions, the mesial frontal lobe of the right hemisphere, and the cuneus and precuneus in the left hemisphere, independent of familial risk. In addition, the effects of importance on cortical thickness were significantly stronger in the high-risk than in the low-risk group, particularly along the mesial wall of the left hemisphere, in the same region where we previously reported a significant thinner cortex associated with a familial risk of developing depressive illness. We note that these findings are correlational and therefore do not prove a causal association between importance and cortical thickness.Conclusions and Relevance  A thicker cortex associated with a high importance of religion or spirituality may confer resilience to the development of depressive illness in individuals at high familial risk for major depression, possibly by expanding a cortical reserve that counters to some extent the vulnerability that cortical thinning poses for developing familial depressive illness.

On the Tiger Shark (Coursera Course Writing Assignment #2)

Submitted as part of work in the Cousera course on Marine Megafauna last week:

The tiger shark sits atop the ocean food chain as an apex predator.  As a striped shark and a potential man-eater, it easily earns the name of ”sea tiger.” Cool facts: Tiger sharks hatch from eggs, yet are live born! Tiger sharks are voracious! They are known to eat anything that swims and many things, like crustaceans, that live on the sea bottom and don’t swim. Like their furry namesake, tiger sharks have a reflective layer in their eyes behind the retina to help them see in the dark.

As a shark, the tiger shark (Galeocerdo cuvier, Hawaiian name mano nihui) falls under the class Chondrichthyes, which are the cartilagenous fishes. Tiger sharks are in the taxonomic family of the requiem sharks (family Carcharhinidae), which are migratory, live-bearing warm water sharks which generally live in shallower waters at least part of the time. As so-called ground sharks, requiem sharks possess nictitating membranes, which are special, thin, moveable eyelid-like surfaces which allow the tiger shark to blink to remove the debris often present in brackish or shallow waters. The tiger shark’s order, the ground sharks or Carcharhiniformes, differs from the order Lamniformes, which includes the great white sharks and thresher sharks, because those related species, in the different order Lamniformes, lack nictitating membranes. Tiger sharks have their own subfamily, Galeocerdinae, and genus, Galeocerdo, as the only ovoviviparous (that is, its eggs hatch internally and the young are born live when fully developed) species in the family of the requiem sharks.  The requiem shark family also includes related species such as the bull shark and blacktip reef shark.
Tiger sharks are large sharks, reaching an average of about 400 cm, or 13 feet in length. Mature female sharks are usually about 10% larger than males of similar age. Body mass at maturity is around 600 kg, with exceptionally large females over 550 cm length and 1000 kg in mass. The tiger shark has a torpedo-shaped body thicker in mid portion than at its front and back, an elongated and broad nose, one dorsal and two pectoral fins, a barrel-shaped chest, and a narrower than average for sharks caudal keel area at the base of its tail fin. Tiger shark pups are born spotted, and these spots change to stripes as they mature. Juvenile tiger sharks have dark stripes on their sides as well as back, but these side stripes eventually tend to fade in older mature sharks, which then usually have visible stripes on the back but a more even dark coloration on the sides. Like most sharks, tiger sharks show a typical fish body countershading coloration, with darker bluish or greenish gray coloration on their top and sides and a paler white or yellow underbelly. Tiger sharks range throughout tropical and subtropical ocean waters. They are found mostly in coastal habitats rather than mid ocean regions of the Atlantic and Indian oceans, but are more widely distributed in the tropical and subtropical Pacific within both coastal and mid ocean regions, in association with the more widely distributed land of the islands in the tropical Pacific ocean. As generalist predators, they are likely more populous than shark species which are more restricted in their prey types, but as with most fish species, accurate population numbers are not available because we lack accurate census methods.  Estimates based on fishery data (tiger sharks caught per year) suggest to me a population of very roughly 5 to 10 million.
Tiger sharks use a wide variety of coastal and oceanic habitats during their 30 to 40 year lifespan.   They breed about every 3 years, with a period of gestation of 14-16 months.  Litter size ranges from 10 and 80 offspring. Mated females tend to move from more oceanic areas to larger island and coastal areas to give birth.  As stated above, this is ovoviviparous live birth, with eggs hatching internally. Pups may then possibly spend more time in warmer coastal regions, and then as juveniles the sharks will spend more and more of their time in less sheltered, more oceanic and colder environments. Sexual maturity is reached around age 6 to 8 years.
Adult tiger sharks may swim long distances for foraging daily, moving to patrol shallow coastal waters and then deeper areas up to 1200 meters depth, alternating sometimes many times daily in “yo-yo” style. When cruising in a foraging area, they may move slowly and stealthily, but they are capable of a sudden rush of high speed to seize prey in their sharp teeth and strong jaws. They are solitary hunters, but are able to cooperate without conflict when groups are seen scavenging large carcasses. A recent study in the Coral Sea concluded that tiger sharks which forage in shallow waters along the coast may later dive to depths of over 1000 m, covering a volume of over 2300 cubic km of ocean in a year. Tiger sharks eat a wide variety of fish, shellfish, seabirds, snakes, and turtles. They also eat mammals including dugongs, seals and dolphins. They are even known to eat other sharks, including other tiger sharks. Their “yo-yo” alternate movement, foraging from deep to shallow waters and back, may be a strategy to help them keep prey species from becoming wary of the shark’s presence, since the shark will not remain in any given spot for long.
Tiger sharks are the second most common (just behind the great white sharks) cause of shark attacks on humans. A recently published study (Papastamatiou 2014)  suggests that 25% of mature female tiger sharks in the Hawaiian islands region migrate per year from the region around the remote French Frigate Shoals atoll to the main Hawaiian islands, such as Maui, during late summer/early fall, perhaps to give birth. This migration coincides historically with an increase in tiger shark attacks in Hawaii during that season of year.
Conservation concerns:  Tiger sharks adapt readily to the presence of human structures and ships and can eat a varied diet in response to changes in types of prey, such as those caused by human over-fishing of other fish species. They are not currently considered endangered. Like most large sharks, they are threatened by commercial fishing pressures, such as those caused by commercial fishing for shark fins to supply culinary preferences in eastern Asia. Overall fishing catch rates for this species have been in continual decline over the past 25 years, so it seems that human fishing has adversely affected the size of the population.  There are few measures in place to protect the tiger shark population, and indeed culling to decrease local populations near shores used by human swimmers has been recently practiced in some locales. The World Conservation Union (IUCN) presently lists the tiger shark as "Near Threatened" throughout its range. One weak movement toward increasing the chances of the species' survival has been that quotas for shark fishing have been created to limit commercial fishing in the Atlantic, where tiger sharks are included in the large coastal group quota, which has an annual quota of 1,285 tons of several types of large sharks.

A tiger shark expert’s biography:
Carl Meyer, PhD, FIBiol
Dr. Carl Meyer is an assistant researcher at the Hawai'i Institute of Marine Biology.  His  current research focuses on the ecology and management of sharks and reef fishes. He has interests in the movement patterns, habitat use and trophic ecology of sharks and fishes, and the navigational abilities of sharks. His research addresses a variety of issues of management concern including impacts of shark ecotourism, shark predation on critically endangered species, effectiveness of Marine Protected Areas (MPAs) and impacts of human recreational activities in MPAs. 

Yannis P. Papastamatiou, Carl G. Meyer, Felipe Carvalho, Jonathon J. Dale, Melanie R. Hutchinson, and Kim N. Holland (2013) Telemetry and random-walk models reveal complex patterns of partial migration in a large marine predator. Ecology 94:2595–2606.
Meyer CG, O'Malley JM, Papastamatiou YP, Dale JJ, Hutchinson MR, Anderson JM, Royer MA, Holland KN. (2014) Growth and maximum size of tiger sharks (Galeocerdo cuvier) in Hawaii. PLoS One. Jan 8;9(1):e84799.
Werry J, Planes S, Berumen M, Lee K, Braun C, Clua E (2014). "Reef-Fidelity and Migration of Tiger Sharks, Galeocerdo cuvier, across the Coral Sea". PLOS ONE.  2014 Jan 8;9(1): e83249.
Fitzpatrick R, Thums M, Bell I, Meekan MG, Stevens JD, et al. (2013) A comparison of the seasonal movements of tiger sharks and green turtles provides insight into their predator-prey relationship. PLoS ONE 7(12): e51927. doi: 10.1371/journal.pone.0051927.

The pathetic fallacy in neuroscience, part 1: is it a help or a hindrance?

Why shouldn't neurons firing feel of something?
--Consciousness Explained, 1991

In his autobiography, Recollections of my Life (1937), Santiago Ramon y Cajal wrote of his studies of brain growth and development:

"What mysterious forces precede the appearance of the processes, promote their growth and ramification, stimulate the corresponding migration of the cells and fibers in predetermined directions, as if in obedience to a skillfully arranged architectural plan, and finally establish those protoplasmic kisses which seem to constitute the final ecstasy of an epic love story?"

This is an exquisite (as Ruskin would have put it) example of the pathetic fallacy, which in science is a term usually used in criticism of some scientific writing's false tendency to use poetic but technically incorrect language as a way of attributing emotion or cognitive features to nature. In the study of the nervous system, we see this when we attribute high level features of the organism, like thought, to lower level parts of the organism.

Let's look at another poetic quote, from English writer Thomas Hardy:

"The purl of a runlet that never ceases
In stir of kingdoms, in wars, in peaces;
With a hollow, boiling voice it speaks
And has spoken since hills were turfless peaks."

When attributing speech to a waterfall, it's clear poet Hardy does not mean his metaphor scientifically, and I'm sure neither did Nobel winner Cajal in his autobiography quoted above. Yet there is a danger in such attributions when untrained enthusiasts use imprecise language to shortcut the hard work of understanding cognition, ignoring the parts we cannot explain about the mind in a blur of sciento-poetic metaphor.

Let's look at a few examples from recent neuroscience texts:

"The frontal cortex is an organ of civilization..."
--Neuronal Man, 1985

...the brain's reward system:  a complex circuit of neurons which evolved to make us feel "flush" after eating or sex..."
--Key Studies in Psychology, 2007

mirror neurons...give the observer a direct feeling of what the others feel.
--Handbook of Neuroscience for the Behavioral Sciences, 2009

What might be an advantage of such loose language?

First, it might allow us to bridge the explanatory gap more explicitly than we otherwise do, and thus help us teach the correlates of consciousness without constantly mentioning the gap.  This might make descriptions of brain function more concise.

Second, it might facilitate student memorization by making neuroscience facts more important in explaining features of human life. If we are taught that your amygdala is where you feel afraid, this kind of teaching is much simpler than explaining the fear as a potentially nuanced cognitive and emotional feature which is complexly and probably irreducibly related to much more of the brain than we can teach a typical freshman undergraduate, which is related to the whole body's endocrine status, its social and physical environment past and present, and which can be modulated by memory integration which is itself modulated via activity in the amygdala.  Or, if pain is just C fibers firing, we don't have to inquire where or how we feel any further, and we might remember better about C fibers and their pain related transmission function.

Third, it might be correct linguistically to use brain region personifications, the way it might be correct to say the sun rises and sets, just because it conveniently fits the data from a certain point of view. Unlike sunrise, though, brain localization is not a common datum of the people who read the books above.  This leads to exaggeration and oversimplification by the readers.

There is a potential threat to future views of current neuroscience in our metaphors when they are inaccurate or misleading. There is a risk of creating a false optimism about where we are in our understanding of the links between our brains and ourselves, and of a backlash of drops in respect and/or funding against neuroscience when the media reports turn out to be just of misinterpreted, empty promises.

Finally, if there is something to be discovered about cognition that is as yet far outside our theories and technical means to find-- which I strongly suspect to be the case-- why should we dawdle with metaphors when we could be looking for the reality?

On the reports of human CRISPR research.

What He Jiankui et al., 2018 said was an important ethical principle. What He Jiankui claims he did by usi...