A Fast-Forwarded Look at How Our Oceans Might Be in a Few More Decades

This is scary stuff, when you get right down to it: With atmospheric CO₂ concentrations rising, where does it all go? Well, lots of it goes into the ocean. There, it's estimated to have caused a 30% increase in hydrogen ion concentration since the beginning of the last century. An increase in H⁺ levels means a drop in pH as the ocean becomes more and more acidic.

Our oceans are turning into vats of acid.

Does that scare you?

It should scare calcareous organisms more, since they're the ones who will be bearing the immediate brunt of ocean acidification: as acidity increases, their calcium carbonate shells disintegrate. Many, if not most of, the ocean's coral reefs, clams, snails, etc are threatened by this. And of course, not only them, but the ecosystems--and economies--based around them. Detailed discussion of the mechanisms and effects of ocean acidification has been made before, you can find one at wikipedia.

We might be able to visualize some of the effects that ocean acidification will have in our children's lifetime right now, according to a new letter in the journal Nature. [454:96-99] Hall-Spencer et al. use marine CO₂ vents in the Mediterranean as a natural experiment to see the correlation between high carbon dioxide levels and marine life community structure. The vents they monitor flux in CO₂ output normally throughout their existence, and they chose vents that emit only CO₂, without poisonous sulphur compounds or heat. Thus, they were able to limit confounding effects other than CO₂, and come to stronger conclusions about the association of CO₂ and reduced numbers of calcifers in the ocean.

They found a 30% reduction in species numbers (mostly calcifiers) near the vents versus the control sites. Coral reef cover (from Family Corallinaceae, the red algae corals) was 60% outside of the vent areas but only 0% within it. (*poof* Gone.) As if to take these Corallinaceae's place, a number of algal genera grew fantastically within the CO₂-rich regions near the vents. These algae include some of the most invasive algae species in the world, like sargassum, which forms thick, floating mats, and Caulerpa, which is already threatening the Mediterranean with its ability to crowd out all other species.

Sea urchin numbers were also significantly lower around the vents, juvenile gastropods were nowhere to be found, and adult gastropods' shells were flimsy. Barnacles seemingly were able to close themselves off to protect themselves from the acidic water, except for the lowest-pH sites, where they, too, were decreased in number.

The results of this study by Hall-Spencer and his team corroborate theory as well as earlier experimental studies of a more limited nature that couldn't take into account ecosystem-scale effects as well as this study could. The authors acknowledged that their work with vents could not perfectly model world-wide ocean acidification due to temporal variation in pH at the vents, the patchiness of the high CO₂ regions in the ocean landscape due to the nature of the vents, and other abiotic factors that may have had some effect. And of course, it's correlational and not causational. Nevertheless, this study provides valuable insight into the drastic effect that anthropogenic sources of CO₂ may have on ocean ecosystems if greenhouse gases continue to be emitted at the present rate.

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note: 15 minutes after posting this, I realized with a big, forehead-slapping "duh" that in this post I was committing the very same error I was deriding in my earlier post about the incorrect inference of causation from observational studies. I had to go back and edit myself. How embarrassing...

Susan's Snazzy Arthropod of the Day: Zonocerus elegans

This is Zonocerus elegans, or the "elegant grasshopper." Native to southern Africa, it was commonly found in the area in Mozambique where I used to live. Its species name, though, refers only to its coloration, not to its locomotion: it has got to be the most ungraceful, clumsy excuse for a grasshopper I've ever seen. When it hops, it rarely ever seems to land how one might expect it wanted to; instead of hopping in a manner that would allow it to proceed in a straight, efficient path, it tends to sort of slowly flop, landing sideways or backwards or sometimes not even on its feet. Maladaptive? Nah, you don't have to be an effective escape artist if you're as nasty-tasting as these guys are. They have a predilection for eating poisonous plants and sequestering the toxins as a predator defense. Additionally, they secrete a foul-smelling yellow goo when handled, and taste accordingly. Most things won't touch them, and they often can be a pest in agricultural settings.
Unfortunately for Z. elegans, though, some humans like funny-tasting stuff. The Pedi people of South Africa, for example, traditionally enjoyed them as a relish with porridge. I'm not certain how they dealt with the sequestered poisons; perhaps the concentrations are generally too low to affect humans, or the poisonous substances (generally cardiac glycosides or pyrrolizadine alkaloids, even cannabinoids) are degraded upon cooking.
In any case, other than their zesty flavor, I'm sure the Pedi also enjoyed how darn easy they are to catch. I would have liked to have been shown the proper way to catch them and cook them up. Nowadays, though, Z. elegans doesn't have as much to worry about. With entomophagy and other traditional diets on the wane in southern Africa, this pretty insect must be breathing a little grasshopper sigh of relief as it flounders off into the sunset, uneaten.


Photo by Lambert Smith, from insecta.co.za. Used with permission.

Kneeling at the pipes: a poem by Marge Piercy (dedicated to Amy W. and her roommates)

Princely cockroach, inheritor,
I used to stain the kitchen wall with your brothers,
flood you right down the basin.
I squashed you underfoot, making faces.
I repent.
I am relieved to hear somebody
will survive our noises.
Thoughtlessly I judged you dirty
while dropping poisons and freeways and bombs
on the melted landscape.
I want to bribe you
to memorize certain poems.
My generation too craves posterity.
Accept this dish of well aged meat.
In the warrens of our rotting citites
where those small eggs
round as earth wait,
spread the Word.

Score One More for Evolution--Magical Disappearing Fish Eyes

OK PEOPLE. Evolution is a fact. The details are up for grabs--that's how science goes. The book of Genesis, the seven days, the whole shebang, is an allegory, ok?
Now, can we just get over it and stop being stupid jerks and ruining kids' science educations? Really.

So we all know that deep down in dark caves lives oodles of weird animals without eyes. You've got your blind shrimp, your blind isopod, your blind salamander, and your blind fishy friend, the charismatic Astyanax jordani, the subject of a big huffy fit courtesy Casey Luskin at the Discovery Institute.

Luskin's argument is that loss-of-function mutations--i.e. mutations which occur randomly, screwing up a functioning gene so it "breaks"--are not contrary to the idea of intelligent design. The idea seems to be that God created something a certain way, and then something in our imperfect, corrupted world caused some oops to happen in the DNA that messed up God's perfect design. Ignoring the flaws in that argument for a moment (If that were so, and loss-of-function mutations were just unfortunate mistakes, how would they get fixed in a population? Could it be--gasp! natural selection??), let's examine Luskin's claim briefly.

He claims that the only thing that "Darwinism" (what a bad, incorrect term) cannot explain is gain-of-function, when an organism actually acquires a new trait.

Unfortunately for him, this loss-of-function in Astyanax jordani is actually a GAIN-of-function: a developmental gene called sonic hedgehog is actually upregulated, which increases skin sensitivity (beneficial to cave life, no?) while having the side-effect of disrupting eye development. PZ Myers has a great discussion of the flaws in Luskin's "argument" and the details of how A. jordani lost its eyes over at the Panda's Thumb.

Take that, Discovery Institute.

Educational Support in Mozambique

When I was in the Peace Corps, I served as a secondary school biology teacher in rural Mozambique. There, I encountered a whole lotta kids and a whole nottalotta teachers, crammed into school buildings with few supplies. In some cases roofs were even threatening to fall down on students' heads; they had never been replaced after being bombed out by RENAMO during the civil war, the contractor having absconded with the donated repair funds. The kids were like kids everywhere, sometimes curious, sometimes bored, sometimes awesome, sometimes little shits. There were a number of generally undereducated yet dedicated teachers, working from 7am with the beginning of 1st period of the first school shift, until past 10pm when the sixth period of the 3rd shift ended, five days a week, three trimesters a year. And then there were a whole bunch of corrupt jerks who were only still there because there was such a desperate teacher shortage. I read now about how the Mozambican government is putting in place a new program to support and supervise teachers and schools. I hope it stops those corrupt jerks I knew from deliberately lowering students' grades after barely teaching at all for a whole trimester in order to extort money and sex from them to pass. I can't wait to see the day when Mozambique has enough trained teachers to kick the predators and the thieves out of their school system.

Stats 101 for Journalists--Correlation vs. Causation

While perusing your favorite newspaper, you may have run across an all-caps, bold-print headline with a title something like this: EATING SPINACH EVERY DAY WILL PREVENT CANCER, DOCS SAY. Generally, these articles will include speculation from researchers on how exactly this miracle food will keep you cancer-free; perhaps its those antioxidants, perhaps its high fiber content. Whatever the reasoning, the implication is that you should run out immediately to the grocery store and commence a daily diet reminiscent of a rabbit’s.

Not that there’s anything wrong with spinach. Your mom and popeye were right, spinach is very good for you, in fact. And hey, maybe it is a key part of a diet that will aid in preventing cancer.

The problem is, in fact, a statistical one. A common statistical error that perennially causes stats profs to tear out their hair in frustration, or perhaps, if they’re old and jaded, to merely roll their eyes and shrug.

The problem is the inference of causality from correlation.

Most likely, the study had a design something like this: hundreds of people were followed throughout a number of years, and periodic surveys were sent to them asking them about their diets. They filled out the form stating how many times a week they ate certain foods, and sent it into the study center. Or maybe they got phone calls from research assistants, asking the same questions. But regardless, it was not an experimental study—that is, nobody put these hundreds of people in cages and gave them different kinds of diets, each with different amounts of certain foods. It was observational, meaning that the researchers worked with what they could get—the pre-existing diets of their study volunteers, over which they had no control. Instead of creating and administering different conditions to them, they scientists just watched the subjects and saw what happened. Their data allowed them to correlate a factor with an outcome, but not prove causation.

This may seem like an academic difference but it has far-reaching implications. In experimental conditions—say, working with mice in a laboratory—all of the conditions are carefully controlled, in order that any effects can be attributed exactly to a cause. Say that ethics regulations allowed scientists to put people in cages and experiment on them to see the effects of spinach on cancer. Every person would receive the exact same cage conditions: exact same lighting, medical treatment, air temperature, amount and type of exercise, etc etc etc. And they would receive the exact same diet—except for one key difference. Half of the caged experimental humans would receive a diet that had more spinach than the other group’s. Then, after many years of monitoring under these same conditions, if there were any difference in cancer rates between the two groups, this could be attributed exactly to the one difference that existed between the groups—that of spinach consumption. The only way to infer causality is through experimentation—manipulating conditions in a controlled manner to see what affects these differences have between groups.

Obviously, because of ethical and monetary restrictions, this kind of study design with humans is impossible. So why can’t you infer causality from observational studies—the type of survey study that was carried out to create the flashy newspaper headline? The problem is that nothing is controlled in the research subjects—you don’t know if they have the same conditions at home, the same income level, the same amount of exercise, the same anything. What if it is not the spinach that is causing some people to have lower rates of cancer, but something else, that happens to be associated somehow, coincidentally, with spinach consumption? Fresh vegetables are expensive. They also require more time, generally to prepare—to wash, cut, etc. What if its not the fact that the cancer-less people are eating spinach, it’s that they can afford to have more fresh vegetables in their diet because they are wealthier, and maybe their extra wealth allows them to see the doctor more frequently? Or what if the extra little bit of time they have in their day that allows them the time to prepare fresh vegetables like spinach also happens to be enough extra time to go jogging as well? Any number of other, hidden, things could be the actual cause, or one of many causes of the lowered cancer rates in these people. The spinach may have nothing to do with it; it may just have been associated somehow with the actual, unrecorded cause.

Experimental studies, which allow true inference of causality, are impossible in many cases when the study animals are human beings. The best correlational studies looking at human habits and disease outcome over many years have huge numbers of people and try to get as much information about their participants as possible—background health info, income, marital status, exercise habits, etc, in order to take all these factors into account. And they often find very interesting and useful results, linking certain types of diets, lifestyles, or exercise habits to long-term rates of disease. But no matter how well these studies are designed and carried out, no newspaper can ever report on their findings using the word “cause.” Even if they record as many different variables as they can think of from their study participants—exercise, religious beliefs, geneology, length of their little toe, etc, it’s impossible to know whether or not they recorded any information about the factor that is truly causing the differences seen in the study. The conditions and the participants themselves are just too variable. To talk about causation in this context is simply incorrect, and perhaps even false.

What’s then the use of these large-scale observational survey studies? These studies are useful in finding links to diseases, which can then be studied directly in an controlled experiment using mice—which are 80-some-percent genetically related to us. Once this same connection is found in a controlled, experimental environment, one can finally come to some conclusion about causation.

I had a stats prof who had written his master’s thesis on biologists’ understanding of statistics. He found that over 70% of research published over several years in a peer-reviewed biological journal had statistical errors. It’s no surprise then, that newspaper writers are prone to the same kinds of statistical mistakes. It’s then up to the discerning reader to look beyond the headline, dig a little deeper, and figure out if the research was carried out in such a way as to merit the flashy headline. Dramatic words like “causes” and “leads to” and even just “will” sell newspapers. But they may not be statistically and scientifically accurate—be smart and judge for yourself.

A Bold Foray onto the Internet

I'm a little behind on this whole "internet" thing. Not because of any purposeful luddism, just because of--oddly enough--the timing of my Peace Corps service. Turns out I happened to be gone just as blogging, social networking, and the like were just picking up their swing, and so I kind of missed the trend. It took me a year to find Facebook to be less than completely creepy, and now almost another for me to get used to the idea that I might post something online that anyone and their trollish mother might read. I like to think of this as "charmingly antiquated," as opposed to the more not-nice "hopelessly backward."

In the meantime, I'm still a terrible nerd, and blogging seems to be the best way for me to get out my enthusiasm for science, public health, music, and interesting miscellany, as well as my general irritation with the world's occasional imbecility.

Enjoy!