So You Want a Fish Tank: Fresh or Salt Water?

It’s important to choose whether you are going to go with freshwater or saltwater before you cycle your filtration, so it’s a decision that needs to be made early. It’s also important to choose because you can’t mix freshwater and saltwater fish in one tank.

Why Can’t We Just Mix Fish?

Everyone, and I mean everyone, seems to want “a Nemo”. I’ve been asked about a tank for “a Nemo” (a clownfish) half a dozen times in the last year. Problem is, clownfish are saltwater fish. You can’t just throw them in with your goldfish (for multiple reasons) and expect anything good to come of it.

The reason you can’t mix saltwater and freshwater fish has to do with osmosis. Osmosis is related to diffusion, where molecules move from high concentration to low concentration. If you drop food coloring in a glass of water the food coloring spreads out. This is diffusion. If you blocked the food coloring from moving with some sort of membrane that allowed water to move through it the water would move instead. That would be osmosis. Instead of the food coloring spreading out into the water the water would come to the food coloring.

Now imagine a fish. At a cellular level all a fish is is a bunch of bags of slightly salty water. It’s not all salts, but there’s stuff dissolved in the fish. There’s less stuff dissolved in freshwater and more stuff dissolved in saltwater. So when a fish is placed in freshwater there’s more stuff dissolved in the fish than the surrounding water and water tries to move into the fish. A fish in saltwater faces the opposite problem. Somewhat bizarrely it actually loses water to the surrounding ocean.

Most of this water loss or gain takes place in a fish’s gills. Gills are, at their most basic, thin blood vessels that are surrounded by water. Under the gill cover of a bony fish (the operculum) the gills look like red feathers, each filament of the “feather” being a blood vessel. This works wonderfully for fish because fish blood is normally lower in oxygen than the water (since the fish used oxygen in its cells), higher in carbon dioxide (since the cells produced CO2 in the same process that used oxygen), and higher in ammonia (which we discussed last article). This means that, without the fish doing anything but pumping blood through the gills, oxygen enters the fish’s blood and CO2 and ammonia leave. However, there’s no way to allow these things to diffuse across the blood vessel and not let water through, and so the fish also deals with the loss and gain of some things it would rather not have moving in and out of its body.

However, fish are well-adapted to live in the water. Freshwater fish are adapted to deal with a constant influx of water by having ways to constantly push it back out. Saltwater fish do the opposite. A few fish are euryhaline, meaning they can deal with a wide range of salinities, and these fish can generally change their physiological strategy based on the water they find themselves in. (I still wouldn’t recommend moving a euryhaline fish directly from freshwater to saltwater. It might require hours, days, or even months to switch over.) (A few fish deal with this issue in an entirely different way, where they match the salinity of the water around them, but these aren’t fish you tend to keep in aquaria.)

Now imagine taking a freshwater fish, like an oscar, and dumping it into saltwater. The oscar is pumping water out of its body because it normally has water flowing in. Now water is flowing out, and the oscar is just making it worse. In short order the oscar will be dead. If we move our clownfish into the oscar tank the opposite thing will happen with identical results. The clownfish will pull water in even though water is now rushing into its cells. Its cells will begin to lyse (explode) and it will die.

This grid shows a freshwater fish (an oscar, Astronotus ocellatus) and a saltwater fish (an ocellaris clownfish, Amphiprion ocellaris) in both fresh and salt water. The depth of the blue indicates the salinity of the fish and the surrounding water. The black arrows indicate the direction that water travels by osmosis (towards the saltier area) and the purple arrows indicate the direction the fish moves water to compensate. As you can see, when a fish is in the correct environment the arrows are in opposite directions, which keeps the water level inside the fish constant. When the fish is in the wrong environment the arrows are in the same direction, and so the fish’s own physiology exacerbates the osmotic problem, leading to the fish’s death.
This work by Eric Butler is licensed under a Creative Commons Attribution 4.0 International License.

So don’t mix freshwater and saltwater fish.

Ok, So How Do I Decide?

If you have your heart set on a particular species then you need to go with that water type. But if you’re flexible on exact fish here are a few basic rules.

Saltwater gives you a greater variety of non-fish things to put into a tank. Saltwater gives you the opportunity to go for a reef tank, which is full of corals, crabs, shrimp, tube worms, clams, and perhaps echinoderms like starfish or sea urchins (although be aware that starfish often die rapidly in tanks – at least rapidly for starfish). For some people this is a big draw, and reef fish are very pretty fish. I run a small saltwater tank that is nothing but some easy corals, snails, and crabs. I like it a lot, and the small animals make up for some of the big disadvantages of saltwater tanks. The flip side of this is that some of the odder animals sold for saltwater tanks are so poorly understood that it’s almost impossible to even get accurate advice for keeping them alive.

Saltwater is much more expensive. Not every item and every fish is going to be more expensive, but I have paid between $1-$14 per fish for freshwater fish and between $6-$25 for saltwater fish. I’ve never seen a freshwater fish that I wanted that I thought was too expensive (which is to say I’ve seen expensive fish, they just aren’t frequently seen or interesting to me). I’ve skipped on buying dozens of saltwater fish because of price. Now, maybe I’m just cheap, but this is something to consider. This price difference is due to some of what follows.

Saltwater fish are much harder to keep. One really obvious difference between the ocean and freshwater is size. Oceans make up about 66% of the planet’s surface and freshwater makes up about 0.02%. Saltwater fish live in enormous bodies of water while freshwater fish normally don’t. A lot of the freshwater fish popular in tropical fishkeeping come from small creeks or pools (although, contrary to often-repeated opinion, wild betta fish do not actually live in puddles [although some killifish have been reported breeding in puddles]).

Imagine a small creek running through a tropical area in which there is a distinct wet season and a dry season. In the dry season the water becomes hot, more polluted with fish waste (because there’s less water per fish), and because the water isn’t being replaced it ends up with more of whatever it picks up from the creek bed (which may make it more acidic if the bottom is mostly dead plants, or harder if the bottom is certain sorts of stone). When the rains come the water volume may triple in a day. The new water is colder, cleaner, neutral to slightly acidic in pH, and has nothing dissolved in it. If the fish can’t survive these huge changes in the water they live in they’ll die out as a species. Now imagine the ocean. It doesn’t rain for six months. Nothing changes. It rains for a month straight. Fish right at the surface notice the influx of cold, fresh water, but fish ten or twenty feet down probably don’t even know anything is happening. And so, as a direct result of their environments, freshwater fish tend to be much more tolerant of temperature change, pH changes, water hardness change, and those nitrogenous wastes I talked about in the filtration article. Saltwater fish, on the other hand, are much more likely to die when anything changes. This not only makes the fish more expensive, it also means you need a lot more equipment to keep saltwater fish alive.

You should think about a bigger tank for saltwater. Actually, bigger tanks are easier in many ways (which I’ll discuss in another article), but since saltwater fish come from such large environments the advantages of a larger tank are all magnified for them.

You are also much less likely to be able to breed saltwater fish at home. Maybe you don’t care about this, but if you ever want to try to breed fish freshwater fish are much easier. With guppies the challenge is to prevent them from breeding. A few saltwater fish (like some cardinalfish) have been successfully bred in the aquarium, but most can’t be. (This also means that if you’d like to avoid buying fish that have been caught in the wild, perhaps in ways that aren’t very good for the environment, you have more choices in freshwater.) The reason for this is that the ocean has a very different current system than freshwater. Freshwater basically all flows to the ocean. The ocean, however, has loop currents. A number of oceanic species lay eggs that float on these giant currents, hatch out into larvae that look very different from their parents (and live a drifting life far above the bottom), and eventually circle back home (or another suitable area) where they become “normal looking” and start acting more like the adults. Freshwater fish tend not to do this, since having your eggs blown constantly downstream isn’t such a good idea. This means that plenty of freshwater fish will lay their eggs on the ground or on plants and a fish keeper can take care of them, whereas many saltwater fish lay eggs that just go straight into the filter with all the other floating debris.

My quick advice would be not to go for saltwater unless you really, really want a particular fish (or are rich and retired). Saltwater tanks are more expensive and much more work.

What if you had gills?

Recently one of my friends asked me about a device, about the size of a gas-mask filter, that claims to extract enough oxygen from water to allow you to breathe while submerged. He had some thoughts about the mechanical details and whether this device could outperform gills, but what he asked me was, essentially, this: if you had gills how big would they need to be? This is an interesting question1 and so I thought I’d share a detailed, sourced answer.

Let’s start with some basic fish biology drawn from Bone and Moore’s 2008 general ichthyology text, Biology of Fishes. A typical 1 kg fish has 18,000 square centimeters of gill lamellae. These gills extract 70-80% of the oxygen available in the water. This is such a big task that around 30% of the blood resistance in a fish’s circulatory system is in the gills2.

If we simply scaled this up to a 70 kg human3 we’d get 126 square meters of gill lamellae. This isn’t the number we want, though, since approximating a 70 kg human with a pile of seventy 1 kg fish isn’t accurate4. There are issues both of scaling efficiency (larger animals tend to need less oxygen per kilogram) and metabolic rate (humans are much more energy-hungry than fish on a kilo-per-kilo basis). What we actually want is a metabolic rate for our 1 kg average fish and a human metabolic rate5 so we can scale from there.

Clarke and Johnson (1999) estimated the metabolic scaling equation for teleost fish overall. Since teleost fish encompass more than 90% of all fish species a teleost fish equation is probably pretty close to a generalized fish equation. The equation from Clarke and Johnson is ln(metabolic rate as mmol of oxygen per hour) = 0.8(ln(body mass in grams)) – 5.43. A 1 kg fish would then need 1.101 mmol of oxygen per hour.

Ravussin et al. (1982) measured subjects of varying obesity and determined that non-obese subjects used 6,118 kJ a day for their resting metabolism. Leonard (2010) states that in humans 1 liter of oxygen is equal to 5 kcal of energy. Working through a lot of conversions (1 mol of oxygen is 1,000 mmol and is 22.4 liters at standard temperature and pressure, so that’s 44.64 mmol/liter, 5 kcal is 20.92 kJ so that’s 2.13 mmol/kJ, 6,118 kJ/day is 254.9 kJ/hr) we get 543.98 mmol of oxygen/hr. So, if an average, non-obese human needed to get by with gills we’d be looking at 889.4 square meters of gill lamellae just to meet basal metabolic needs.

Now, if you’re following all of this you may see a problem: that gill area/mass ratio is for a fish in total, not a fish that only rests. But we’ve calculated this for a human that only rests. Surely fish have some built-in safety factor which will help us out here. However, we exercise using mostly aerobic muscle activity, and fish exercise using mostly anaerobic muscular activity. Fish also use about 10% as much energy as land mammals in locomotion (both of these facts come from Bone & Moore, 2008). So whatever the safety factor a fish has to let it engage in fast movement that safety factor is going to be far too low for a human.

So what would 889.5 square meters of gill lamellae look like? This is hard to figure out. Gill lamellae are very small and tightly-packed, and so a lot of surface can fit in a small area. However, our average human now has gills 494 times larger than our 1 kg fish. Imagine a medium sized trout. Now imagine the gills – the full, feathery, red structures behind the operculum (gill cover). Now imagine basically 500 of those. If the trout had a mere cubic inch of gill our hypothetical human would need 0.29 cubic feet of gills. Of course, that much gill tissue would change the water flow through it in ways that would force changes in the gill dimensions as well, and so an actual cube of gill tissue would have dead spaces in it and would need even more tissue. Instead, the best design would probably be more like stacked wings of tissue, probably about the size of a person’s head. Remember, that’s a minimal gill that will let you breathe underwater but not really move around (or panic). If you were planning on living underwater, instead of just hopping into the water and drifting with the current, you’d need gills probably at least twenty times that size, since activity can easily use twenty times as much oxygen per minute as resting.

Sanity Check

These numbers appear strangely large. Would you really need gills twice the size of your torso to sustain you swimming around underwater? And it is possible I made an mathematical error. However, the sanity check suggests that this is probably about right.

First, that oxygen use rate is about 8 times higher for our hypothetical human than our fish on a kg-for-kg basis. (We’d need the exact weight of Ravussin et al.’s subjects to do better.) Since endotherms, like humans, tend to have metabolisms about ten times faster than ectotherms (like the vast majority of fish) we’re running clearly in the sanity zone on that one, perhaps even lowballing human oxygen needs (although large animals, like humans, are more efficient per kilogram than small ones, like our 1 kg fish).

Second, what’s a comparable animal? A great white shark is a large, endothermic fish. Its gills take up an area behind its head about as long as the head length. Great white sharks are also have lower body temperatures than humans (which reduces energy use) and are very streamlined, hydrodynamic swimmers, which means they use far less energy moving than humans do. (Humans, and all walking animals, use lots of energy in their limbs just holding themselves off the ground, while swimming animals can use all or almost all their energy moving themselves forward.)

Thirdly, what are swimming mammals doing? Not using gills. Water, under good conditions, only holds about 3% as much oxygen as air does. This means that gills should be larger than lungs for a given oxygen demand. If we ran the numbers based off of this we’d get gills that were 33 times larger than lungs. However, gills are more efficient than mammalian lungs (see the 70-80% oxygen capture rate quoted above) and so we can probably reduce the gill size by a factor of three. That would give us gills 11 times larger than lungs.

All in all, the gill sizes we’ve estimated seem reasonable, if extremely large.


Bone, Quentin;, and Richard H.; Moore. Biology of Fishes. Third Edit. New York, New York: Taylor & Francis, 2008.

Clarke, Andrew, and Nadine M. Johnston. “Scaling of Metabolic Rate with Body Mass and Temperature in Teleost Fish.” Journal of Animal Ecology 68, no. 5 (September 1, 1999): 893–905. https://doi.org/10.1046/j.1365-2656.1999.00337.x.

Leonard, William R. “Measuring Human Energy Expenditure and Metabolic Function: Basic Principles and Methods,” Journal of Anthropological Sciences 88, (2010): 221-230.

Ravussin, E., B. Burnand, Y. Schutz, and E. Jéquier. “Twenty-Four-Hour Energy Expenditure and Resting Metabolic Rate in Obese, Moderately Obese, and Control Subjects.” The American Journal of Clinical Nutrition 35, no. 3 (March 1, 1982): 566–73. https://doi.org/10.1093/ajcn/35.3.566.


Extinct or Alive…. is actually pretty good

Yesterday evening I watched the premiere episode of “Extinct or Alive”, Animal Planet’s latest entry into the genre of cryptid1-hunting TV shows. I have a love/hate relationship with these shows, in that I love watching them so I can hate them. Most of them are excellent demonstrations of the vast gap between what laypeople think wildlife science looks like and what actual scientists do. Animal Planet, especially, has been a repeat offender with these sorts of shows, putting out lots of shows in which people search for cryptids but, in the process, make outrageous claims, demonstrate a lack of basic information about science, or just do stupid things that make no sense. “Extinct or Alive” is much, much better.

I have long believed that a good cryptid-hunting show could help explain science to people. Why doesn’t your eyewitness account of a Bigfoot establish it for science? Well, let’s see what a proper investigation which would meet scientific standards would look like. This would demonstrate the difference between “I am saying that I saw” and “we have evidence other people can examine”. “Extinct or Alive” is basically this show, although it’s not perfect.

Let’s start with the bad. I expected lots of bad (hence the title) but my actual complaints are few.

First, there’s not a lot of clarity on how different the Zanzibar leopard (the subject of the first show) is from mainland leopards. It would be easy to believe that most scientists believe it to be a separate species, when the range of opinions seems to range from “subspecies” to “very mildly different African leopard”.

Second, there’s the constant mention of the coelacanth. Admittedly, the host (Forrest Galante) has a personal connection to the story of the coelacanth’s rediscovery, but the coelacanth is a pretty odd case. Whether a deep-sea fish can make it millions of years without being recorded as a fossil is pretty different than the question of whether a big cat species can survive on a heavily-populated island.

Third, Forrest has a tendency to talk about himself as a lone wolf maverick, and yet in the first episode he is in contact with two other people working on this issue! Forrest seems to bring some real expertise to the table (unlike many other cryptid-hunter hosts) but it’s clear that it didn’t take Forrest to get people interested in the issue of species that may not really be extinct. Forrest also has the unfortunate habit of talking about the species he is looking for as if they are alive and need our help to stay this way, when this is only hopefully true of them.

But what about the good?

First, this is a cryptid-hunting show, not a monster-hunting show. The Zanzibar leopard is treated as a real cat. Nobody claims that it is the most dangerous animal on Zanzibar or that people lived in constant terror of it. Oddly, this is sort of true in Zanzibar – it was the largest big predator (aside from humans) and its reputation as a witch’s familiar did make people view it with real suspicion. However, Forrest treats this as an animal whose persistence into the present needs to be verified for conservation issues. This is in marked contrast to a show I once watched about the potential for thylacines to still be alive, which spent every spare minute trying to convince you that what was effectively a marsupial coyote was a deadly killer.

Second, the creature under investigation skews towards the plausible end of the spectrum. Zanzibar is under-studied enough that since the Zanzibar leopard’s supposed extinction date a subspecies of servaline genet was discovered there, and in the 22 years between that discovery and the filming of this episode of “Extinct or Alive” only two photos of that genet had ever been taken. (As it turns out, “Extinct or Alive” managed to improve that number. This only reinforces how easy it is to miss animals in Zanzibar.) Moreover, the leopard was known to have been there (it’s a known species, not an entirely new one) and the gap between now and its disappearance is only a matter of decades, not centuries or (in some of the crazier cryptid cases, millions of years).

Third, Forrest appears to know about animals. In my coelacanth article (referenced above) I made fun of “Expedition Mungo”, a show that lives on in infamy for several reason, one of which is the show’s host picking up a very human-like (although also clearly non-human), but very small, skull off the forest floor in Africa and asking someone what it was2. A monkey. Seriously, what other options were there? Forrest, on the other hand, seems to be a decent naturalist, and shares his love of animals with the viewer. Again, this reinforces the “looking for poorly-known creatures” angle against the “looking for monsters” angle so many other shows have.

Fourth, alternative hypotheses are made on-camera. Alternative hypotheses are extremely important in science, but many cryptid-hunters seem convinced that every small sign of a cryptid is proof positive. Forrest gets footage of something spotted very, very close to his trail camera and proceeds to explain that while this could be a Zanzibar leopard it could also be a servaline genet. In fact, after working you up about how this could be a leopard he pops your bubble with the second hypothesis. This isn’t just correct, it’s a good pedagogy, since people who were convinced that they were looking at a leopard will suddenly lose confidence and, hopefully, be more careful about such confidence in the future.

Fifth, the show spends time on actual science. Forrest gets a good, uninterrupted chunk of time to talk about sampling protocols and the importance of collecting as much data as possible. I think they cut the scene before he finishes actually writing the date on the sample container, but you understand why he is doing this, and frankly I don’t need to watch him write it out, I liked the fact that he explained to the audience why you always write the date, the time, and the location on your sampling containers (along with marking the point in your GPS, even if you’re pretty sure this sample isn’t the species of interest – all of this was mentioned by Forrest on camera).

Sixth, the show got what are really impressive results for such a short time frame. (Yes, I could complain about doing science as a travel show where the main scientist hops from continent to continent, but if it funds some actual science I’ll live with it.) This isn’t the good thing. The good thing is that the show gets results that would send many other shows over the moon and then Forrest says that it isn’t enough. The burden of scientific evidence hasn’t been met, and explains what else he will need and starts working on collecting that data. So, by the end of the show you have good reason to believe that the Zanzibar leopard is not extinct but you are also aware that Forrest believes that he needs DNA evidence to absolutely prove that this particular type of leopard is really present. Moreover, you know from the end credits that there is continuing work on that front – Forrest coming in with some cameras wasn’t the end, it was the preliminary work to a longer project.

So, what could ruin this for me? Well, if the problems I mentioned get larger and the good points get smaller that could make the show worse. What I really want to see, though, is how the show handles definitively poor evidence. What happens when they go somewhere and literally every lead is a dud, and it becomes apparent to us at home that there never was anything to this story except hoaxers or mistakes? Will Forrest say on-camera that he thinks there isn’t anything there, that the species he targeted really is extinct? Or will we get the all-too-typical hand waving and the promise that there’s always missed evidence?

However, for now, I think this show teaches some good science in an interesting way. Let’s hope that continues.

UPDATE: Also SPOILER. In the second episode Forrest does not find what he’s looking for. However, he does find something else which matches the descriptions he was given of the mystery creature fairly well. He’s pretty up-front that he thinks the villagers are not describing the extinct species he was looking for but this other rare, but known to be extant, species. Good job, Forrest!

Introducing ReactionTimer

ReactionTimer, released today (although in secret beta on this site for several months), is exactly what it sounds like: a reaction timer. However, it also provides a number of challenges that are designed to time your reaction time plus the time required to perform some mental task. This program is deliberately smartphone-friendly.

Basic usage consists of these steps:

  1. Select a challenge from the list of yellow options. (Your current selection will be white text on a black background.)
  2. Click “Start Challenge”. You will have a brief window of time to move your cursor/finger over the large button that says “Click on go”.
  3. The the dots (…) above “Click on go” will change and some sort of signal will appear.
  4. If the signal is correct click “Click on go”. Otherwise wait for the correct signal.
  5. Once you click (correctly) your time will appear and will be logged on the screen below the buttons.

The image above shows a screenshot of the program as it might appear on a smartphone1. The tail end of the list of challenge options can be seen at the top, followed by a black-bordered block containing the instructions for this challenge type. Below this is the word “GO!”, the signal for this challenge, and under “Start trial” is my time for this challenge. Below “Click on go” is a chronologically-ordered list of my times, with the most recent at the bottom.

In this case we can also see the use of ReactionTimer. The change from “Countdown” to “RandomGo” has added 189 milliseconds to my reaction time. By trying different challenges one can actually measure the time required to mentally process the signal.

Challenge Options

Countdown is the simplest challenge. After a brief moment to allow the user to prepare the screen shows a countdown –  3, 2, 1, GO!. The timing is the same at each transition which allows the user to click “Click on go” when “GO!” should be appearing and not actually wait for the signal to be processed by the brain.

Random Start is perhaps the best measure of actual reaction time. The signal area remains as the starting three dots (…) until, at random, it changes to the word “GO!”. The signal is clear and unambiguous, the only challenge is waiting for the visual processing of the signal.

When Word is Go draws randomly from a list of words. These are all sorts of words, but all are capitalized only on the first letter, except for “GO!”. The transitions between words occur at regular intervals, but the user must still identify what the word is.

When Word is Go (Annoying) also uses a random list of words, but unlike normal When Word is Go all of the words are two letters, capitalized, and followed by an exclamation mark. This makes them less visually distinct from “GO!”.

When Word is Animal lists random words, some of which are the names of animals. If the random word is the name of an animal the user should tap “Click on go”. Unlike the previous challenges this challenge incorporates multiple correct answers, which makes it noticeably harder, as the user’s brain has to process what the word is, not just whether it is or isn’t one specific word.

When Word is Not Animal is the opposite of When Word is Animal. Is it harder to parse a negative than a positive? Now you can see!

When Word is Adjective lists random words, and the go-signal is when the word is an adjective. Care has been taken to supply the list only with words that are clearly adjectives or clearly not. However, this one requires a great deal more mental processing than the previous ones.

When Addition Problem is Right supplies the user with a simple addition problem (two numbers, both under 10, and their sum). Most of the time the sum is not correct. (Under the hood ReactionTimer adds up the numbers correctly and then normally adds or subtracts a small, non-zero, random number.) When the numbers actually add to the displayed sum the user should click. This one gives the user more time between transitions than the previous ones.

When Colors Match presents the user with a colored square and the colored word “Text” (see below). When the colors of both items are the same the user should click. This one largely lays the groundwork for later challenges involving color and allows the user to get a baseline reading for recognizing color matches.

When Color is Right involves the Stroop Effect. Instead of a colored block and colored text that says nothing useful the colored text is also the name of a color. When the name of the color and the color of the text match (e.g., the word “Green” in green) the user should click. Honestly, this one drove me nuts every time I tested it.

When List Ascending presents the user with a list of four numbers (e.g., 8, 10, 21, 31). If the list is ordered so that each number is larger than the number to its left the user should click. (So, for instance, the user should click if presented with my example list, but not if it had read 10, 8, 21, 31.) This forces the user to make multiple evaluations (three, specifically) to solve the problem.

When Word is Not Animal + Color Match combines two previous challenges. This is meant to allow a user to see if evaluating two different challenges is harder than evaluating just one, and if the difficulty is additive. This one can be used alongside When List Ascending to see the difference between the same evaluation multiple times (“is this number larger than the one on its left?”) and multiple types of evaluations. In this case, in case this is unclear, a colored square and some text will appear as in When Colors Match. However, unlike When Colors Match the text will be a word. When this word is not the name of an animal and is also the same color as the colored square then the user should click.

All of these challenges together are meant to allow a user to evaluate the time required to perform a whole suite of mental tasks as well as to evaluate how combining tasks affects processing time. There are definitely other options that could be added, although this set seemed to me to capture most of the main comparisons I was interested in. However, I welcome feedback if there are additional challenges that could be added to capture new dimensions of mental processing.

So You Want a Fish Tank: Filtration

The reason I am writing this series of articles is because it turns out that one of the things I get asked about most is keeping fish. Sure, I could talk about what biogeography tells us about the evolution of Siluriformes, but people seem to want to know why their guppies are dying. So here’s a series of articles on setting up and maintaining a fish tank and the science behind it. If you want a quick, simple, here’s-how-to-own-some-fish guide this isn’t for you. This is a science blog, so I’m going to tell you not just what to do but why. That way if you can’t use my favored approach you’ll be able to make an appropriate substitute, or at least you’ll know why your guppies are dying (and then hopefully stop buying more and condemning them to death).

This article series is also aimed primarily at people who want relatively unfussy tanks. This is partly a demand issue, where there are far more people who want a low-maintenance tank with some pretty fish in the living room than people who want to breed rare Central American fish in a basement fishroom. This is also partly an issue of knowledge: people running their own complicated set-ups are likely to already know this stuff, and I am also less knowledgeable about complicated set-ups. I have a lot of fish tanks in my teaching and research labs but most of them are deliberately set up so that if I miss a water change during finals week nothing bad happens.

Our first article is about filtration because filtration is how you are most likely to kill your fish. If you are saying, “I don’t have a filtration issue because my water looks clean,” then this is you for sure.

The short take-home, for people who really wanted a different sort of article, is:

  1. Filtration is mostly about getting rid of invisible fish waste.
  2. Biological filtration is where it’s at.
  3. Biological filtration requires you to cycle your tank BEFORE you add fish.
  4. Ultimately, filtration can only save your fish for so long, so you’ll need to change the water periodically as well.

Fish are Toxic Waste Machines

Fish are little toxic waste machines. Filtration is generally divided into three different varieties (mechanical, chemical, and biological) but the first and most important thing to understand about filtration is that a perfectly healthy fish in perfectly clean water will, as a direct product of its metabolism, produce toxic waste which needs to be filtered out. Time and time again I see people asking for help on fish-keeping forums who are sure that their fish caught a disease and need medicine when their fish have merely, but largely literally, peed until their water became toxic. And, instead of changing the water to remove this dangerous waste, these people often spend money buying treatments that, at best, treat the wrong problem and at worst kill the very organisms that will help them solve that problem.

The central issue here is that a fish tank is not a closed ecosystem. Fish tanks are not closed ecosystems because, most importantly, you feed the fish. While there are lots of things fish may eat all fish eat products that were once alive (other animals, plants, or single-celled organisms). What is most important here is that all living things contain at least trace elements of protein. Even plant food, which is generally considered to be protein-poor, has small amounts of plant enzymes in it, and those enzymes are proteins. Moreover, many fish eat relatively protein-rich animal food, and all fish need to eat protein to build their own protein-rich bodies. The problem with this is that protein contains nitrogen, and lots of it. When protein is used to build more protein (i.e., a fish eats a worm and converts some worm-proteins into fish-proteins) that isn’t an issue. However, when protein is used for energy, which is also very common (and impossible to prevent, before you ask if you can feed a special diet that will stop this), the nitrogen in the protein just becomes waste. What it becomes as part of the metabolic process is ammonia (NH3).

This sealed ecosystem requires no filtration because: 1) it’s sealed, with no added food 2) it supports nothing larger than the tiny dots swimming in the water. (And it does have the biological elements of biological filtration, just no pump driving water through.)

 

This is where the problem starts. If you’ve ever used ammonia as a cleaning product you are probably familiar with its toxicity (and with the fact that it looks just like water). Even smelling ammonia can make your nose and eyes burn. Ammonia is so toxic that in land vertebrates energy is expended to transform ammonia into something less toxic (either urea or uric acid, depending on what sort of land vertebrate you are1). Fish2 have the luxury of being surrounded by water and so instead of storing urea or uric acid for later excretion they simply dump the ammonia into the water. This actually happens largely through the gills. While fish do urinate like land vertebrates they also have a large area in the gills where blood is a thin membrane away from the surrounding water (if this weren’t true they wouldn’t be able to extract oxygen from the water) and ammonia simply diffuses out of the bloodstream. In the wild this ammonia would be dispersed across gallons and gallons of water. In a fish tank the ammonia can’t go anywhere and so it can rapidly accumulate to dangerous levels.

Fish waste isn’t the only source of ammonia in a fish tank. Dead animals also produce ammonia as they decay, since bacteria causing a body to rot are just eating it, and dead animals are full of protein. These dead animals may be a fish that died while you were gone for the weekend, or a snail that you didn’t realize came in on a plant and which has now died, or the bits of dead animals in the food your fish didn’t eat.

Filtration

Filtration is commonly divided into three categories, and so I’ll go through them under the normal titles.

Mechanical Filtration Mechanical filtration is what people who just got their first fish tank tend to worry about most. Mechanical filtration is about removing the “bits” that make the water look dirty. It normally involves some sort of pad or grating that catches these bits and has to be cleaned off or changed out on a regular basis.  Two important things to note about mechanical filtration are:

1) The fish mostly don’t care. Sure, getting rid of bits that will rot reduces ammonia, and that’s good, but fish live in water that is muddy, full of sticks, or stained with tannins all the time. Some fish do like or maybe even need crystal-clear water but other fish actually prefer water that is hard to see through. I have some fish in my lab that live in water the color of weak coffee. Originally their tank was clear water, but after some reading I discovered that these were fish from blackwater environments where tannins leaching from dead plants turn the water brown or black. I added these chemicals and the fish are much more active now. Mechnical filtration is largely something you do to make your fish tank look nice to you.

2) You should be doing water changes, and when you do this you should be using a siphon. It’s a lot easier to get rid of visible fish feces and old food by siphoning it out than it is to rely on a filter to do this. With a siphon you can also stir up your gravel to get out things that have become trapped between the pieces. (If you have a sand bottom everything will collect on the top.) I have largely abandoned mechanical filtration except for this siphoning in my tanks.

Chemical Filtration

Sometimes you have weird chemicals in your tank. Chemical filtration deals with these. These can come from a variety of sources – something you put in the tank as a decoration, something your water treatment company put into the water, or some off-kilter biological process. The most common chemical filtration you will see is activated carbon (charcoal) filtration. These filters use either loose activated carbon or bags of activated carbon to remove harmful chemicals from the water. This is exactly what most drinking water filters for home use use. A few important notes about chemical filtration:

This is loose activated carbon. It is often sold in a white cloth bag instead.

 

  1. The most worrisome chemical, unless you (or your child) throw random things into the fish tank, is the chlorine or chloramine your water treatment company probably adds to your water. This stuff kills bacteria quite nicely, which is a problem in your tank (biological filtration depends on a colony of beneficial bacteria to work) and also burns fish gills. I have a friend who changed water in their tank and didn’t remove the chlorine first. Within two hours all of her fish had died of suffocation. You can trickle water through activated carbon to remove this but a better strategy is to get a bottle of water conditioner and add some to the water you are about to put in the fish tank. The only time I have ever run chemical filtration on a tank was when I once had a problem with wood staining the water in a tank that was supposed to stay clear. I added some activated carbon to the filter and within a week the problem was solved.
  2. All chemical filtration runs out over time and has to be changed. Activated carbon filters eventually stop working and may even begin to shed previously-trapped toxins back into the water. Unlike biological filtration, which tends to improve over time, chemical filtration works best straight out of the box and gets worse over time.

I have an ambivalent relationship with chemical filtration. One thing I see far too much of is tiny plastic tanks sold with a “filter” that isn’t anything more than a way to suck water through a bag of activated carbon. These probably do save some fish from owners who dump water into the tank straight out of the tap without adding a dechlorinator or (shudder) use cleaning products to clean out the tank and leave chemicals behind. They also probably make a killing for the companies that make them, since the carbon bag will be regularly replaced, and my guess is that a lot of fish will also be getting replaced. On the other hand, a bit of activated carbon in a filter can save you from all sorts of chemical weirdness. I always keep some in lab for the day when someone knocks a strange chemical over into a fish tank. It hasn’t happened yet, but when it does I’ll be dumping that carbon in the filter.

This extremely tiny all-in-one tank was sold for betta fish (it’s suitable for shrimp). The filter consisted of nothing but a bag of activated carbon and a pump to pump water across it. I’ve helped this tank out by adding plants and putting a sponge over the filter intake (which serves as a place for biological filtration bacteria to colonize).

 

Biological Filtration

Biological filtration is your right-hand man, your best weapon, in the fight against ammonia. Far too often it seems that people go to a pet store and say that their fish are doing poorly. The store may ask to test the tank water (most places that sell pet fish will test your water for you, which is good to know) and they determine that the person in question has too much ammonia in their tank. So they sell them something like AmmoLock and the person goes home, treats the tank, and in a few weeks their fish are dead. I’m not saying that short-term ammonia-detoxifiers aren’t any good. However, they are short-term solutions. When you realize that you’ve got 2 ppm of ammonia (which is REALLY bad) something like AmmoLock will save your fish now. But what keeps you from having that 2 ppm next week again? Biological filtration.

I’m sitting about six feet from a fish tank that I built all the filtration for myself. It has no chemical filtration. It has mechanical filtration only by accident. What it does have is about 100 times as much biological filtration as a “normal” store-bought filter for a tank that size would have. (It also has live plants, which serve as backup biological filtration.) Biological filtration is filtration3 and everything else is making the tank look pretty.

The concept behind biological filtration is to make ammonia less toxic. One way to remove ammonia would just be to change the water in the tank constantly. In fact, some large aquariums “filter” their tanks exactly like that, pumping water out of the ocean constantly and sending the old water back. (It’s one reason so many aquariums are right on the waterfront.) However, if you can’t do that maybe you can make the ammonia less toxic so that it doesn’t cause a problem until the water does get changed. This involves converting ammonia into less-toxic nitrite and then converting nitrite into less-toxic nitrate. I said above that 2 ppm of ammonia would be very bad. 2 ppm of nitrate is nothing. I’ve had fish survive short periods in which the nitrates spiked above 100 ppm.

So how do you convert ammonia to nitrate? Several different kinds of bacteria do this4 to get energy. So, in effect, all you need to do is provide these bacteria with somewhere to live and then send them water with ammonia to “eat”. These bacteria also need oxygen. Hopefully, your water has enough of this, but a wet/dry filter design (which is a design in which the biological filter stays wet but isn’t submerged) really maximizes this.

This sump tank serves as the main filter for a 110-gallon salt water tank on the stand just above it. Water pours in through the hoses at the top, trickles through the filter media visible inside, and is pumped back to the tank. By trickling the water through the media in a shower-head fashion the media is exposed to both water and high levels of oxygen, increasing its effectiveness.

 

CYCLE YOUR TANK. Biological filtration depends on an entire mini-ecosystem in which fish produce ammonia which some bacteria use for food, producing nitrites, which another group of bacteria use for food and produce nitrates. There are no “out of the box” mini-ecosystems. You have to grow one in your filter before you can safely add fish. There are a few ways to do this.

  1. There are directions for fishless cycling online. That’s what it will be called. It involves adding ammonia directly to a tank with no fish and monitoring the levels of nitrites and nitrates. Once the ammonia is reliably converted to nitrates in a timely fashion the tank is cycled.
  2. You can feed the tank like there were fish in it. The rotting food will produce ammonia just like it would going through a fish. This doesn’t always work perfectly, since you may get the amount wrong, but it’s worked well for me. Mind you, I also follow all the extreme safety tips I give later about adding fish.
  3. If you’ve got a large enough tank you can cycle it with some hardy fish (or invertebrates). Guppies work well for freshwater. The idea is simple: a 55-gallon tank can hold far more than a few guppies. If you add a few guppies the sheer volume of water will keep the ammonia concentrations low for a while and give the bacteria in the filter time to start growing. Once that seems to be working well you can (slowly) add other fish.

Cycling takes time. A lot of fish stores (that admit that you need to cycle tanks – some will pretend that you can just plug the filter in and go, probably because that way you’ll be back to buy more fish really soon) will say that it takes a week to cycle a tank. Cycling isn’t binary. A tank can be more or less cycled, and cycling probably continues for months or years, as ecological communities become more complex and shift in composition. I generally cycle for several weeks, and in one case a rather-accidental four months.

So can you cut down on the time to cycle a tank? Yes! And no.

  1. You can buy a lot of products that claim to do this. I’ve heard that there is one refrigerated bacterial infusion that may or may not be available in the US that works well. However, most of these are just ways to pay money for something that is free. There are no products that can instantly cycle a tank and you don’t need to buy any products to cycle a tank. One of the major barriers here is that you need live bacteria of the right sort, and keeping bacteria alive in storage with no ammonia for food is hard. Another barrier is that I’m not sure we really know exactly what bacteria are involved in cycling a tank. Nitrosomonas and Nitrobacter are obviously important but there’s reason to suspect that this is a complicated story with a lot of ancillary characters.
  2. However, you may know people who have live, complete bacterial communities available. These are people with working fish tanks. People such as myself, who have more than enough biological filtration, can often pull a sponge or some media out of a working filter and either drop it in your filter (or tank) or squeeze it out into the tank. This will look like someone just squeezed disgustingly dirty water in a nice clean tank but that “dirt” is the bacteria you need. This can cut cycling time by a lot. You do want to match water type as much as possible. Putting filter material from a saltwater tank into a freshwater tank is probably unhelpful. If your tank is tropical you will probably get better results from a tropical tank, and so on (but any freshwater tank should help some with any other freshwater tank).
  3. It is possible to start a tank already cycled. It’s the filter that cycles, not the tank (mostly), so if you take a filter off a working tank and put it on a new tank it’s already cycled. This is most useful if you are moving small fish to a larger tank where they will grow larger. Imagine that you have a 10 gallon tank and just realized that the fish you bought will grow a lot larger than the fish store told you. You want to switch them to your new 40 gallon tank now before they grow larger and let them grow up in that tank. However, you don’t have a cycled 40 gallon filter. No problem! You only have 10 gallons worth of fish right now, so you can move the filter for the 10 gallon tank to the 40 gallon tank and start both filters. In a month both filters will be full of bacteria (the small filter will “seed” the big one) and the small filter will have carried you through the danger period. You can take the small filter off.

This homemade sponge filter is effectively filtering the water in a shrimp breeding tank. It does extremely poor mechanical filtration (despite some people claiming that sponge filters are mechanical-only) which saves the lives of the small shrimp, who can’t get sucked in anywhere. It does excellent biological filtration as water is drawn into the chunks of filter foam and expelled at the top. My sponge filters are uglier than many commercial ones, but also have a lot more sponge, which is probably why mine seem to work better. I could also easily pull one sponge block off and transfer it to a new tank to kick-start the cycle.

 

As always, a few more important notes about biological filtration:

  1. Biological filters get better over time. “Cleaning” a biological filter makes it worse. You’re cleaning off the bacteria that do the work. Yes, they look like sludge (“biofilm” is what a bacterial sludge layer is termed by experts) but they are what makes this all work. Now, sometimes you do need to clean the biological filter because it’s jammed up and water doesn’t move through it but try to do two things. First, clean it in tank water, not chlorinated water. Remember, as far as aquatic organisms are concerned, chlorine is murder. Second, if at all possible clean only part of the filter so the bacteria from the other part can rapidly re-colonize the post-apocalyptic landscape of the cleaned filter. I like filters than have things like two different sponges in the biological filtration section so you can clean one and leave the other alone. (Admittedly, custom filtration is easy when you build your own filters.) I sometimes see people on fish forums say they think their tank has a fish disease when it has ammonia poisoning and so they clean everything really well to kill the germs. This just kills their fish faster.
  2. Biological filters are alive. Things like fish medicines can kill parts of them. The wrong temperature or the wrong pH can kill them. If you have a filter go bad that can make a bad day a lethal day for a fish, so if things seem to be going crazy consider that maybe the first problem (temperature, pH, medicine) caused a filter problem.
  3. The key to a biological filter is the conversion of ammonia to nitrite and nitrite to nitrate. You can buy a test kit for these chemicals at most fish supply stores. This can help you troubleshoot a lot. If, for instance, you see an ammonia spike but no nitrite or nitrate spike the biological filtration isn’t working because lots of ammonia should rapidly become lots of nitrite and so on. If you see a nitrate spike but the other numbers are staying low something bad may have happened but the biological filtration isn’t the problem. The day I wrote this I found a dead fish in a tank in lab. It had probably actually died the day before and been rotting the whole day. I had a bad nitrate spike but the biological filter (homemade out of two pieces of PVC and some high-grade filtration sponge from SwissTropicals) had converted a deadly ammonia spike into an unpleasant nitrate spike.

Change Your Water

All this filtration is great, but even with the best biological filtration in the world your nitrate levels will gradually creep up. There’s no way around that, and the very expensive devices you can buy to hold back the inevitable are not worth it. What is easy is to change the water regularly. I generally aim for changing 50% of the water in a tank every week. I sometimes don’t manage this, but I also test my tanks for ammonia, nitrite, and nitrate, and so I know exactly which tanks need water changes. Changing the water is simple: turn off the filter and heaters if they will get dry during this process. Dry filters tend to burn their motors out and dry heaters can sometimes explode. Remove 50% of the water (don’t remove all the water). Dechlorinate more water. Let it sit for a bit to get to room temperature. Add it into the tank. Turn the filter and heaters back on.

Bioload

Your tank plus your water changes plus your biological filtration define your maximum bioload. Bioload is the “load” your animals place on the system. Above a certain amount of living animal tissue5 in a tank (be it fish, shrimp, snails, or whatever) and the level of nitrates in the tank will get too high before you change the water. More water dilutes the nitrate, more biological filtration prevents ammonia from staying as ammonia, and more water changes gets rid of all the fish waste faster. I advise you (if you are a beginner) to under-load your tank.

Imagine that your tank can hold 2 pounds of live fish without going toxic. (I’ll discuss how to determine what load you can support in another article.) The temptation is to put 2 lbs of fish in it and have the tank look “alive” with lots of fish, or maybe a really large centerpiece fish. The problem with this it that you have no room for error. I mentioned earlier that I found a dead fish in a tank today. I probably missed that fish yesterday (it had been looking poorly two days ago and yesterday was crazy). That fish went from producing ammonia like a live fish to producing much, much more ammonia as it rotted. If I had that tank stocked at 100% bioload I would have gone over 100% and I probably would have killed all the fish in the tank. Instead, I have that tank understocked. I might be at 40-50% bioload. When a single zebra danio died in the tank that might have temporarily pushed me up closer to 100%, but it didn’t push me over. I did a big water change today and it’s all taken care of.

A lot of my lab tanks do not get optimal maintenance. I under-load them and I don’t ever have issues with them. Meanwhile, I know lots of fish hobbyists who always pack their tanks and have to stay on top of everything. It’s possible to do (I know people who do it) but if you want a casual, low maintenance fish tank avoid the temptation to cram it chock full of fish.

I Wish I’d Known That, But Now It’s an Emergency

So, what if you didn’t read any of this until after you put fish in your tank? You didn’t cycle the tank, you maybe don’t have any kind of filter, and now the fish are acting funny.

  1. Get a filter. The right sort, which means one that has biological filtration (it may say this, or it may have a “biowheel”, or it may have sponges that water go through, or it may have media bags that look like broken pottery).
  2. When in doubt, water change. Just make sure to dechlorinate.
  3. If you need to use an emergency anti-ammonia product go ahead.
  4. If you can get filter-gunk from someone with a working tank do it. This will kick-start your cycle.
  5. Start testing the water, or getting it tested. What you want to see is the ammonia levels drop and the nitrate levels rise. Once your ammonia is getting converted into nitrates reliably you have a working biological filter and your tank is cycled. This can take a while, especially since you’ll need to be removing ammonia from the tank to keep the fish alive rather than leaving it in to feed the bacteria.

In the next article I’ll discuss choosing tanks, for those who haven’t already committed themselves.

Welcome SciREN folks!

Hello to everyone coming here via the SciREN event! This post will direct you to the some of the things you might be looking for. Always feel free to comment as well if you need help or want to share feedback.

The online simulators are here. If you are particularly interested in the niche partitioning simulator that I demoed at SciREN that simulator is the one called 100 Places.

Blog articles explaining each simulator are here.

There are some known bugs in some of these programs! Check here for those.

If you can’t find something drop me a comment.

 

RapidModel is Here

RapidModel is one of the original in-browser programs. This may be an odd thing to say since it’s only just appearing now, as the fourth project (or fifth, or sixth, depending on how you count the projects in beta) but it’s actually the second in-browser program I wrote. Much like the original version of CamoEvolve it needed some serious fixes. Unlike CamoEvolve it needed so many fixes that it really wasn’t workable, and so I took it down, re-wrote the code effectively from scratch (I kept a few drawing functions), and have now put it back up (having, in the meantime, re-written the whole site).

RapidModel is based on something I did in college. In one of our classes (probably Conservation Biology) we played around with a program where we could link items together and then play with sliders on them and see how they affected other items. I assume we built population models with this system, but I don’t really remember. RapidModel is similarly generic (but also free and does not require downloading).

At its most basic, RapidModel is a bunch of nodes that hold numbers with connections that cause the numbers in one node to influence the numbers in other nodes. The numbers in a node may represent anything – number of caribou, GDP, cans of beets – and the connections can take almost any form. So, without further ado, a brief explanation of the objects in RapidModel.

Nodes

Nodes are just number containers. To create a node select Add/Edit Nodes and click on the black part of the screen. A new node will appear where you click and you’ll be asked to name the node. You’ll also be asked for:

Number: The number the node starts with. When you hit “Reset” the node will remember this number and reset to it as well.

Maximum: The number in the node will not exceed this number. In some cases the maximum is based on a real world constraint and in others it exists just to keep the model in some sane range.

Minimum: The number in the node will not drop below this number. For many real objects zero is a natural choice.

If you edit a node (which you do by selecting the radio button with the node’s name after creating a node) you can also choose to check Round to Integer. In this case the node will never display non-integer numbers. However, it does keep track of non-integer effects. So, for instance, if an integer node held a 2 and you subtracted 0.1 from it ten times in a round the node would drop to 1. If you subtracted 0.1 from it once a round nothing would happen for ten rounds, and then it would drop to 0. For many real-world items rounding to integers makes sense. There are no 0.3 whales or 0.71 consumers out there.

Connections

Connections can only be created in the sidebar. Create some nodes, selected Add/Edit Connections, and select Add New. Connections name themselves in a way that describes exactly what they do (for instance, a recent model of mine had a connection called “Seals-Sharks”) so you won’t be asked for a name but you will be asked for a start node and an end node. Circular connectors are fine. Calculators (which we’ll discuss next) can only be starting nodes. Here’s the important thing to remember: start nodes do something to end nodes. This is easy to think about with additive nodes. You take the number from the start node, go over to the end node, and add that start node number to the end node. What a start node does to the end node is determined by the node type, which is just a mathematical operator. Connection weights can be used modify how much of the start node is used to modify the end node. For instance, to grow a node by 50% a turn connect a node to itself with an additive connection of weight 0.5. You could do exactly the same thing by setting up a node that just held the number 1.5 and using it as the start node for a multiplicative connector of weight 1.

Calculators

You create calculators much like nodes, which calculators are (technically) a subclass of. However, unlike nodes the important things that go on in calculators have to be done from the sidebar menu. Calculators have a set of arguments with exactly the same name as in nodes and these arguments (maximum, etc) function exactly the same way so I won’t re-describe them.

However, while calculators are programatically nodes they are ideologically very fancy connections. Unlike nodes they don’t retain a number for multiple turns, modifying it. Instead they calculate a value fresh every turn. Originally this was done by using dozens of connections and dummy nodes but calculators work much better. It’s the addition of calculators that made RapidModel usable. To use a calculator you must give it an equation. Equations can contains the names of nodes, numbers, and a small set of mathematical operators. Equations are written in a pretty straightforward manner: Squirrels/Trees gives you the number of squirrels per tree this turn. If you type an equation correctly you will see “No errors” when you hit enter. Otherwise you’ll be told what part of the equation was an issue. Calculators will also identify nodes that they draw numbers from and create yellow connections to them automatically.

The equation reader can only handle the following operators: +, -, * (multiplication), / (division), ^ (exponentials). It cannot handle order of operations. All equations are read left to right. So Squirrels/Trees/10+1 is equivalent to ((Squirrels/Trees)/10)+1.

Calculators can also be used to delay effects in a model. The delay time simply puts the calculator X turns behind the rest of the model. At the very simplest a calculator could simply take the value from another node a hold it for a certain number of turns (for instance, price responds to the demand of two turns ago). Because of the delay function the initial number of the calculator can be important. Perhaps you are multiplying by the output of a delayed calculator. If you start with 0 in the calculator you’ll zero out your next node as well, whereas if you started with 1 in the calculator nothing would happen for the turns before the calculator showed its first calculation.

So what does this look like?

Here’s a silly example. I want trees to grow slowly. I also want the squirrel population to grow but to be capped at 2 squirrels per tree. I made this model.

Trees and Squirrels are just nodes, set to round to integers. SquirrelsPerTree is a calculator with the equation Squirrels/2/Trees, which hits 1 when there are two squirrels per tree and stays under 1 when there are less than two squirrels per tree (as in this screenshot). Trees connects to trees with an additive connector of strength 0.1 which causes the population to grow by 10% per turn. (Again, while trees are integers, the accumulation of partial trees still eventually triggers the addition of a tree.) SquirrelsPerTree creates dummy connections (in yellow) that can’t be edited but which show that it uses both Trees and Squirrels for its calculations. Squirrels is divided by SquirrelsPerTree, so when there is extra space around the population expands. The minimum cap on SquirrelsPerTree can be used to lock the squirrel growth rate at some maximum and the maximum cap can be used to prevent the squirrel population from crashing violently.

I have no idea what you’ll use RapidModel for. I’ll definitely use it for population models in ecology this semester, but I deliberately made it extremely open-ended. If you do something fun with it leave me a comment.

Spiders Eating Bats and Fish

In honor of a recent presentation that I made at the North Carolina Museum of Natural Sciences Bugfest event I thought I would highlight two interesting articles relating to spiders. Both are from the open access journal PLoS ONE and so both are freely available to read to anyone with a working internet connection.

The first article is Bat Predation by Spiders by Martin Nyffeler and Mirjam Knörnschild. This topic is perhaps best introduced by the set of photos that accompanies the article.

Spider species that were found to have killed bats included both web-building and hunting spiders (which do not make webs). Most of the hunting spiders recorded eating bats were tarantulas. In several cases the predator appears to have been a member of the genus Avicularia, an arboreal tarantula genus that could easily access locations in trees where bats sleep during the day. In India one of the arboreal Poecilotheria species was recorded eating a bat. In other cases the tarantulas were ground-pounders, such as a large Lasiodora, a genus that includes the Brazilian salmon pink bird-eater. Other hunting spiders also got in on the action. A huntsman spider in India was recorded killing a bat and a fishing spider was recorded stalking a bat pup in Indiana. In both of these latter cases the predation event appears to have be interrupted by the observer.

Obviously, since spiders don’t fly, it’s much easier for web-building spiders to eat a delicious bat. The main culprits were members of the genus Nephila, the golden silk orb-weavers, whose webs can span 1.5 meters (roughly five feet) and whose bodies are the largest of all the web-spinning spiders. Other web weavers included other nephilids and members of the Araneidae, another orb-weaving family. Most of these spiders spin large webs and are themselves large spiders. North American readers may be familiar with the genus Argiope, of which one species, A. aurantia, the black and yellow writing spider, is found across a large section of the continent. These spiders represent some of the smaller species known to catch bats in their webs.

The bats caught in webs also tended to be small, with small microbats (often subadult) being the most common. Larger bats are likely to break through a web when they hit it, which would prevent them from being captured by web-building spiders. The heaviest bat reported captured in this study was an adult that probably weighed 11g, while another specimen could have weighed somewhat more.

The question of whether bats are actively preyed upon by spiders is also raised in this study. In some cases a bat may run into a spider web and become entangled and die of dehydration, exhaustion, or exposure without any active attempts at predation by the spider that made the web. In some of the cases cited here the full predation sequence was observed (attack, kill, feeding) whereas in other cases only the feeding end of the sequence was involved, and in some of the web spider instances only entanglement was observed. Oddly, this includes all the Nephila clavipes records, which may mean that even smaller Nephila kill bats entirely incidentally, and gain nothing by capturing such large animals in their webs. Larger Nephila species were observed to actively kill and eat bats.

Overall, this study concludes that bat predation by spiders is probably infrequent. A bat must fail at multiple steps to be killed by a spider. First, it must fail to avoid the web, and bats appear to be pretty good at avoiding webs. Second, the bat must become entangled in the web, when a large majority of bat-web impacts probably result in a destroyed web and a bat with some spider silk stuck to it. Third, the bat must fail to escape from the web. Since bats can struggle against the web and potentially break free this may result in some number of very brief bat captures. Obviously, active predation by the spider can prevent the successful escape of the bat, as the bat can be envenomated and crippled beyond its ability to break free even before it dies.

Many of the bats captured in this study were young, which may suggest that inexperience (and lower body weight) play an important role in leading to bat capture by spiders. The authors also suggest that echolocation frequency and nearness to home may play a role, as some bats are thought to rely on memory, and not echolocation, when close to their roost.

Finally, the authors ask whether bats are at all important to spiders as prey. For some spider species, they conclude, bats are so large that a single rare bat capture can sustain the spider for an extended period of time.

The second article is Fish Predation by Semi-Aquatic Spiders: A Global Pattern by Martin Nyffeler and Bradley J. Pusey. Clearly Martin Nyffeler is as interested in spiders killing vertebrate prey as I am. Again, a photo montage of spider-induced carnage seems appropriate.

As with bat predation, spiders were more likely to engage in fish predation in warm areas of the world, although in this case “warm areas” included a much wider band around the equator, with the largest number of records of fish predation coming from the United States. Again, the only continent without records of spider predation on fish is Antarctica. The authors note that, for instance, a long study in Canada observing Dolomedes triton never observed this species catching fish, whereas a smaller amount of observation time in Florida observed this same species capturing fish multiple times. This may be biased by the greater presence of small fish in warmer areas.

The family Psiauridae was responsible for most of the fish captures by a wide margin – roughly 80% of all fish captures came from this family. The genus Dolomedes (common in North America) was one of the primary culprits, with Dolomedes triton (five out of six of the images above) being one of the species with the most records. This group of spiders hunts at the water’s surface, and attacks fish through the surface of the water after directly touching the fish. Fish are then dragged out of the water to be consumed, which the authors note is necessary for the spiders’ method of feeding to work and also gives the spider an advantage in holding on to potentially-struggling prey.

The size of the fish captured was usually quite small. However, the spider was usually smaller. Fish were on average 2.2 times longer than the spider (unsurprising, given that fishes tend to possess longer body plans) and up to 4.5 times as heavy. Given my interest in catfish I do wish to note that one very small Ictalurus punctatus was reported as a prey item. Fish may also be made vulnerable by low oxygen levels (which drive fish towards the surface) and a tendency towards surface-feeding. The Gambusia mosquitofish seem especially vulnerable to being eaten by spiders.

Unlike spider predation on bats, spider predation on fish seems to be a normal (if often unobserved) behavior. Like predation on bats, a spider that successfully kills a fish can be expected to derive quite a lot of benefit from this kill.

Both of these papers noted something that should be, but isn’t always, obvious: many spiders are generalist predators with very simple means of determining whether something is prey or not. Prey specificity in spiders is probably normally quite low. For web-spinning spiders the rule is probably something like “what struggles without escaping is lunch”. Fish-eating spiders may have slightly more complex rules by which they determine that they can haul a struggling fish to shore but again things like estimated size are probably more important than taxonomic placement of potential prey.

Possibly more interesting in a general context, all of these events involve a smaller predator bringing down larger prey. Most predators do the opposite (a house cat, for instance, hunts mostly mouse-sized animals). The advantage that webs and venom give spiders is apparently sufficient to allow them to break the “rules” governing predator-prey size relationships. I’ll probably write more on that eventually but that will have to wait until I get time to do a full write up on what we know about Harpagornis moorei.

 

Catfish and the Lazarus Taxon Problem

Some time ago I mentioned the phenomenon of Lazarus taxa. For those who don’t remember, Lazarus taxa are taxa that are known from fossils that appear to disappear from the fossil record and then re-emerge (“from the dead”) significantly later. The concept gets tossed around a lot when discussing the possibility that groups thought to be extinct might still persist. One of the central questions in evaluating the odds of Lazarus taxa occurring is the completeness of the fossil record. Now, nothing I’m going to say is going to be surprising to a paleontologist, but the fossil record is, as far as completeness goes, pretty terrible. I’ve sometimes heard the fossil record compared to a TV show that is missing chunks. It’s probably more like five non-consecutive frames from an hour long show.

One of the clades that demonstrates this well, and that I happen to know about, is catfish. By catfish I mean the Siluriformes, a quite large group of mostly freshwater fish, some of whom don’t look very much like the “classic” catfish. Catfishes often have a heavy-duty first fin ray in their pectoral fins which happens to preserve well and is identifiable to major group. (This fin spine is meant to stab potential predators, as more than a few recreational anglers have found out.) Because of this catfish fossils are sometimes identifiable even in a severely fragmented state. This is good because fish bones are pretty lightweight compared to tetrapods and fish skeletons are easily scattered and the bones broken.

Diogo (2004) discusses a fossil from the catfish genus Corydoras dated to the Paleocene. Corydoras is a common modern genus, found not only as many species in South America but also as the “cory catfish” in pet stores across the world. The Paleocene period is just past the massive extinction event that brought the Mesozoic1 to a cataclysmic end. To give an idea how unlike our modern world the Paleocene was consider that mice, bears, and cats had not yet evolved, and that the ancestors of whales were walking on land at this time. And yet here’s a modern genus, Corydoras. Moreover, Corydoras is endowed with bony, armored plates that wrap around its body, making it potentially much more fossilizable than other fish (although it is a small fish). Given the success of the modern genus we might expect to find that the world is littered with Corydoras fossils. Instead, Diogo (and I have seen nothing more recent to suggest that new discoveries have changed the picture) notes that there are no other Corydoras fossils until, perhaps, recent sub-fossils. There’s a 56 million year fossil lacuna for this genus.

However, the story gets more interesting. Diogo was arguing for what now seems to be a seriously minority position about the age of the Siluriformes but what makes this an argument is that everyone is sure that we do not have the earliest Siluriformes in the fossil record. A short digression into geologic timelines (really just what I needed to teach myself to follow the arguments I was reading) is needed here. We live in a large era called the Cenozoic. The prior large era is the Mesozoic, known for dinosaurs. The Mesozoic is coarsely divided into three pieces: the Triassic (oldest), Jurassic (middle), and Cretaceous (most recent2). The Cretaceous is divided more finely into a number of periods which I can’t remember because only two have catfish fossils, the last two, the Campanian and the Maastrichtian. The Maastrichtian is the very last sliver of time before the disaster that closes out the whole Mesozoic.

The very earliest catfish fossil comes from the Campanian in Argentina but skip forward just briefly in time to the Maastrichtian and catfish fossils are found in Bolivia (de Muizon et al., 1983; Gayet et al., 2001), India (Cione & Prasad, 2002), Niger (possibly, I cannot find the original description, just a mention in Cione & Prasad [2002]), the western United States (possibly, the species Vorhisia is not unanimously agreed to be a siluriform, Frizzel & Koenig, 1973), and Spain (Pena & Soler-Gijon, 1996, possibly not actually Maastrichtian but just beyond, the authors place the fossil on the border between the Maastrichtian and the following era). Also importantly, even within just the undisputed (as far as I know) Bolivian finds at least two major catfish clades are present. de Muizon et al. identify these two clades as the families Ictaluridae and Ariidae. Even if these exact assignments were to be disputed it seems unlikely that the total diversity of catfish at this site will be reduced. What this means is that the snapshot we have of early catfish is a diverse, widespread clade. Clades don’t start this way. Clades start as small, localized groups with low diversity. They then spread and diversify. It’s a bit like looking through a photo album and finding that the earliest photo you have of someone who you are researching is a photo of them holding their first child. You know they are not a child themselves but you also don’t know quite how old this makes them. All you know is that the beginning is further back.

I won’t get into the (long, complex) debate about when the first catfish swam the rivers of Earth (and the first catfish probably did swim in rivers, not lakes) but what we know is that the Siluriformes have a significant ghost lineage, the name for a lineage that is unrepresented in the fossil record. When we discuss things like Lazarus taxa we should be aware just how many creatures we know existed during times in which they did not leave fossil records.

Perhaps fittingly, since the last Lazarus taxa article discussed the coelacanth, there are particular biases against bony fish in the fossil record. Becker et al. (2009) discuss our friend Vorhisia and the other osteichthyan fish found in that time and region. They also discuss why the fossil record for Cretaceous fish is so poor. They list four things that bias the fossil record against bony fish.

  1. Fish skeletons are lightly built and fall apart easily. Many are from small animals. The bones can be destroyed easily and what is collected are frequently only a few more durable parts of the skeleton (like teeth).
  2. Fish bones are often hard to identify because a lot of basic work remains to be done. Perhaps someone has already found a Jurassic catfish, which would be a major find, but can’t identify it as such because the work comparing catfish skeletons to other fish skeletons hasn’t been done and so this person can’t determine what they have.
  3. Bias in collection and research. Basically, nobody cares about fish. People grab the big stuff and prioritize that when they do research. Fish bones may get left in the ground or in a file drawer instead of being described.
  4. In the specific area Becker et al. described the rock type was also not a good one for preserving fish.

Now, there are examples where it would be hard to claim that the fossil record is simply too patchy to show the continued existence of a taxon. For instance, the (unfortunately frequent) claims that pterosaurs or plesiosaurs have made it into the modern era require that entire lineages of large creatures with very distinctive bones have made it millions of years without leaving fossils. However, individual species seem quite capable of dodging fossilization for extensive periods of time.

 

Becker, M. A., Chamberlain Jr., J. A., Robb, A. J., Terry Jr., D. O., & Garb, M. P. (2009). Osteichthyans from the Fairpoint Member of the Fox Hills Formation (Maastrichtian), Meade County, South Dakota, USA. Cretaceous Research, 30(4), 1031–1040. http://doi.org/http://dx.doi.org/10.1016/j.cretres.2009.03.006

Cione, A. L., & Prasad, G. V. R. (2002). The Oldest Known Catfish (Teleostei:Siluriformes) from Asia (India, Late Cretaceous). Journal of Paleontology, 76(1), 190–193. http://doi.org/10.2307/1307189

Diogo, R. (2004). Phylogeny, origin and biogeography of catfishes: support for a Pangean origin of “modern teleosts” and reexamination of some Mesozoic Pangean connections between the Gondwanan and Laurasian supercontinents. Animal Biology, 54(4), 331–351.

Frizzell, D. L., & Koenig, J. W. (1973). Upper Cretaceous Ostariophysine (Vorhisia) Redescribed from Unique Association of Utricular and Lagenar Otoliths (Lapillus and Asteriscus). Copeia, 1973(4), 692–698. http://doi.org/10.2307/1443069

Gayet, Mireille; Marshall, Larry G.; Sempere, Thierry; Meunier, François J.; Cappetta, Henri; Rage, J.-C. (2001). Middle Maastrichtian vertebrates (fishes, amphibians, dinosaurs and other reptiles, mammals) from Pajcha Pata (Bolivia). Biostratigraphic, palaeoecologic and palaeobiogeographic implications. Palaeogeography, Palaeoclimatology, Palaeoecology, 169(1–2), 39–68.

de Muizon, C., Gayet, M., Lavenu, A., Marshall, L. G., Sigé, B., & Villaroel, C. (1983). Late Cretaceous vertebrates, including mammals,from Tiupampa, Southcentral Bolivia. Geobios, 16(6), 747–753. http://doi.org/http://dx.doi.org/10.1016/S0016-6995(83)80091-6

Pena, A. D. E. L. A., & Soler-Gijon, R. (1996). The first siluriform fish from the Cretaceous-Tertiary interval of Eurasia. Lethaia, 29(1), 85–86. http://doi.org/10.1111/j.1502-3931.1996.tb01841.x