Biology

Is Multicellular Life Common?

The day before the NASA team announced they found 7 planets around the Trappist-1 red dwarf star (three in the habitable zone)1, I went to the Duquesne University Darwin Day lecture by Dr. Nick Lane. If you want, you can watch Dr. Lane’s lecture online.

There are an amazing number of things I want to talk about from that lecture, but with the NASA announcement, I’d like to bring up one: Dr. Lane feels that bacterial-style life may be common, but multicellular life is exceedingly rare.

A quick summary goes like this: Life started on Earth 4.1-3.8 billion years ago. The big argument is whether life bothered to wait for the Late Heavy Bombardment (LHB) to end. The constant bombardment of space rubble doesn’t sound like the best time to start life, but there’s good evidence2 it either started before the LHB end or incredibly shortly thereafter.

A lot of interesting biochemistry went on in cells for the next 2.3 billion years, but it was all single-cell, with maybe a few mats or poorly separated colonies of single cells cooperating–but hardly differentiating into specialized tasks.

Then, something different happened. Multicellular life went hog-wild and became a dominant force. What happened?

According to the endosymbiosis theory of Dr. Dr. Lynn Margulis in 1967, an archaeal cell somehow grabbed a bacteria and didn’t destroy it. The two became symbiotic, and the bacteria became the powerhouse for the new cell–a primitive eukaryote. With this division of labor, the new cell took off, evolved, and became multicellular life.3

It took 2.3 billion years. It only happened once. Dr. Lane thinks that, while the odds are good we will find life somewhere–Mars or Europa or Titan4, or Trappist-1e–it will probably be bacterial or algal.

The step to mitochondria was too hard. It might be “The Great Barrier” that explains why the universe isn’t over-run by aliens. And once the step occurred, it might have been a long, difficult fight to survive it. Mitochondria lost most of their DNA to the cell nucleus, but not all. Reaching that balance must have been incredibly difficult. And mitochondria are dangerous. They’re very tiny, but the energy they produce is tremendous on a cellular scale. They keep those few genes to themselves to keep something “bad” from happening. When cells are programmed to die, the mitochondria are chief players in the destruction. And mitochondria leak out their free radicals, damaging the cell and causing aging. Mitochondria are playing with fire–or at least oxidation!

Dr. Lane may be right. He knows far more than I do. But I’d argue it might not be that bad.

First, life had to invent a lot of biochemistry. Most of the interesting biochemistry in humans and other eukaryotes can be found in yeast. The “last common ancestor” that grabbed a bacteria to become a eukaryote was extremely sophisticated biochemically. There may have been many steps necessary before a cell could even successfully grab the free-living precursor of mitochondria.

Second, a lot of bad things happened during that time. The creation of photosynthesis sucked the carbon dioxide out of the air, causing the Earth to freeze over. There’s a lot of debate as to how many times life was nearly killed off and earth became “Snowball Earth,” but it was at least once and probably a lot more. Any early eukaryotic-like cells with symbiont bacterial energy sources may have died off during those Snowball Earth periods. Survival may have favored the less energetic bacteria and archaeons.

Third, once the primitive eukaryotes got past the “let’s learn to cooperate with this thing I just swallowed” stage, they may have been very difficult to compete against. Mitochondria provide great efficiency and power. Bacteria can still survive as bacteria–and by preying on eukaryotes, but something trying to bridge the gap between them might be in a very precarious position, especially during the time when it’s learning to deal with the engulfed bacteria.

Fourth, it did happen more than once. Some bacterial cell grabbed a cell of algae and, in a process remarkably similar to what happened with the mitochondria, turned it into a chloroplast. So there were two cell lines–those with mitochondria and those with chloroplasts. Yet today, we see plants with chloroplasts and mitochondria. It turns out that mitochondria-containing cells and chloroplast-containing cells merged several times. This process is similar to the one that created chloroplasts and mitochondria. And finally, someone found a bacteria that has engulfed another bacteria. It’s a crude symbiosis, and may have happened “recently,” where “recent” is defined in something between biologically “recent” and geologically “recent.”

Dr. Lane is probably right. Multicellular life is difficult.

But it may not be hopeless.

Although….

If Dr. Lane is right, then the “Great Barrier” is behind us. If I’m right, then perhaps there are multiple Great Barriers instead of just one. Examples of these barriers might be, developing intelligence, developing technology, surviving technology, and becoming starfaring.

With the Doomsday Clock two and a half minutes to midnight, it might be more comforting to think the Great Barrier is behind us and statistically, we will survive the coming years.

1.5 billion years ago: Mitochondria

Dr. Lynn Margulis

  1. https://www.nasa.gov/press-release/nasa-telescope-reveals-largest-batch-of-earth-size-habitable-zone-planets-around []
  2. http://www.livescience.com/5426-life-survived-earth-early-bombardment.html []
  3. There’s no way I can footnote this, except to point to the link with Dr. Lane’s lecture or suggest you get his books, which are written for the general public. I’d suggest Power, Sex, Suicide as a good beginning, although you might want to read it on a Kindle or make a book cover if you are reading it on the bus. []
  4. OK, life on Titan might be weird. Lane, in the lecture, put the odds of something biochemically similar to Earth-life at 995/1000. Titan just might be different, if life exists there []

Why Would You Drain a Swamp?

Biologists think of swamps (and other wetlands) as wonderful places.1

Swamps control runoff from rain. Here in Pittsburgh, we’re actually working at constructing artificial swamps and wetlands. These swamplets will be far cheaper than the non-biological catch basins that were proposed. In a town focusing on tourism related to our riverlife, eliminating sewage discharge is a must.

Swamps purify water. The plants and microorganisms break down toxins, collect silt, and remove heavy metals from the water. Swamps purify water better than modern water treatment plants–and often cheaper as well.

Swamps protect against hurricanes. Besides acting as a buffer zone between human habitation and the ocean, swamps and other wetlands tend to rapidly suck energy out of hurricanes. Much of the increased hurricane damage costs is attributable to wetland destruction.

Swamps have great biodiversity. That means the environment people depend on for their survival is made stronger. Biodiversity means the web of interactions between organisms are complex–a great place to go “bioprospecting.” Very often, nature has already solved chemistry and biology questions of use to humans. Antibiotics and many drugs are modified versions of biological compounds. Enzymes catalyze reactions, requiring less energy and produce purer products. Swamps and wetlands hold new antibiotics and chemical pathways that, if we don’t kill them off, we might find and make money off of!

“Draining the swamp” is such a strange metaphor. If someone says that they are “draining the swamp,” they are actually saying they’re going to make the problems worse, make solutions harder, and endanger society.

I would be suspicious of that person. Maybe they just don’t know much about swamps.

Or maybe they do, and they’re hoping you don’t.

  1. WWF: The Value of Wetlands []

They Brought the Penguins Inside…and I Want to Cry

The National Aviary in Pittsburgh brought the African penguins in from their outdoor exhibit because the weather is too cold.

Normally, that would make me laugh.

But I looked up where African penguins live. They’re from around the part of Africa closest to Antarctica. The weather gets as bad—or even worse—than Pittsburgh.

In the wild, the penguins would ride out that cold. A few, mostly the weak and sick, might die. As Steve Irwin used to say, “That’s nature’s way.”

But at the beginning of the 19th century, nature had about 4 million African penguins. Since then, the numbers have been plunging. There are only 55,000 African penguins left in the wild. At the rate it’s going, there won’t be any African penguins living free in 15 years.

The National Aviary wants to take special care of their African penguins, not only because they want to do their best for the animals, but because zoos are the last realistic hope for their species.

Careful records are kept on the family history of the penguins. They do this to maximize the genetic diversity of the species. Some of the birds are over-represented in the world captive population and aren’t permitted to breed. They are traded between zoos to ensure genetic diversity.

And they’re brought in when it’s too cold.

Because of habitat loss and pollution and even global warming, it’s unlikely that the African penguins will ever be reintroduced if they go extinct in the wild. Reclaiming habitat from industry and beach houses and toxic spills is rare. There’s only so much money for reintroduction, and there are species that might be better to spend that limited money on.

The only examples of these beautiful African penguins will be in zoos. And we’ll bring them inside when it gets too cold, because we don’t dare lose one of these remaining few.

The Genetics of Convergent Evolution of Vocal Learning

Convergent evolution occurs when two unrelated species evolve similar results. The most famous example of convergent evolution is the eye of the octopus. The octopus, an invertebrate, has a “camera” eye, just like vertebrates do. A “camera eye” has a light-excluding orb like the box of a camera. It has, a lens to  focus light, like the lens of a camera. The iris  controls the amount of light entering like the iris of a camera controls the aperture. The retina on the far side of the orb from the lens and iris reacts to the light, like film or an image sensor. Shrimp, insects, and other creatures have different eyes that work in different ways. There are many ways to evolve an eye, but two widely separated groups reached similar results.

In “Convergent transcriptional specializations in the brains of humans and song learning birds1,” Pfenning et. al. took the full genetic sequences of several hominids, parrots, songbirds, hummingbirds and non-vocal learning birds and compared them using powerful and complex data analysis on computers. The researchers demonstrate that the area of the brain devoted to learning vocalizations evolved separately in primates and in birds. Among the birds (hummingbirds, songbirds, and parrots), the area for vocal learning evolved two or three separate times. That the same ability—the ability to learn and replicate vocalizations—evolved separately several times was to be expected. The ability to learn new patterns of vocalizations has many evolutionary advantages. But what the researchers found was the 50 or so genes used to control the development in this area were similar across the three groups of birds and primates. The last common ancestor of birds and humans was 310 million years ago. That’s a long time. Dinosaurs evolved about 230 million years ago, so the last common ancestor predates the dinosaurs by about 80 million years.

How did the different groups reach the same biochemical result?

Imagine you purchase a lot in a city. What you can build is determined by the size of the land, the geology, the surroundings, and any applicable zoning regulations. If the lot already has a foundation on it, your choices are more limited. You can destroy the foundation (expensive and time-consuming) or you can build based on the restrictions caused by the foundation. If the first floor has also been built, what you can build is much more limited unless you remove the additional work and start over.

In the same way, the structure of the brain of the last common ancestor of birds and primates imposed limits on how the brain could evolve.

Remember that evolution does not progress from simpler to more complicated or even from less fit to more fit. Evolution is random; it’s stupid, it doesn’t think and it doesn’t plan. The genes of the next generation are determined by chance: chance of mutations, chance in mating, and chance of survival. Even biologists have difficulty understanding this. We think of the first cells and then think of humans and mistakenly conclude evolution had a goal of creating intelligent creatures like us, but that isn’t a correct view of evolution. I find myself having to fight the incorrect urge to speak as if evolution had a goal. Anthropomorphizing evolution is an easy mistake to make, but very, very wrong.

If a bunch of organisms with a brain happen to evolve into creatures that can learn vocalizations, what’s the most likely way it can happen? Is it more probable that structures already in place will be used by chance, or is it more likely that those structures will be lost and then a new structure will happen to evolve? Now, actually calculating the odds on those possibilities is impossible, but you don’t have to run a Monte Carlo simulation to realize that more times than not, the existing brain structures will be used.

In the case of the vocal learning areas of the brains, apparently using certain genes is the most probable way to do it.

The finding that convergent neural circuits for vocal learning are accompanied by convergent molecular changes of multiple genes in species separated by millions of years from a common ancestor indicates that brain circuits for complex traits may have limited ways in which they could have evolved from that ancestor.2

Is it the only way to produce vocal learning? No one knows, but I doubt it. There could be some creature out there that evolved vocal learning a different way. If different gene patterns for vocal learning exist, one of the four groups examined (mammals, parrots, hummingbirds and songbirds) might have used it instead.  That the four groups all used a similar genes to perform the same function shows that alternate methods are likely rare.

Going back to the octopus, some species are capable of learning to mimic other creatures or their surroundings visually. Is this “display learning” a similar form of data analysis to vocal learning or is it hardwired mimicry? Do both systems use similar genes? The last common ancestor between vertebrates and invertebrates date back at least to the Cambrian. so that’s a very long time ago and in a totally different system in the brain. If the genes for display learning and vocal learning have similar properties (let alone similar genetic sequences), it would tell us there are severe restrictions on how brains learn.

  1. Pfenning, A. R. et al. “Convergent transcriptional specializations in the brains of humans and song learning birds.” Science 346 1256846 (2014) PDF downloaded 12 Dec. 2014. []
  2. Ibid []

Science in 80 Liters (20 Gallons)

In 1967, I was in third grade and got a book by Beverly Cleary titled “Henry Huggins.” In the book, Henry goes to a pet store and buys a pair of guppies. The two guppies had babies. Soon Henry’s room and life are over-run with jars of fish. This story disaster inspired me to ask my parents to let me have an aquarium. My parents agreed, and soon there were three aquariums in our new house.
Recently, I looked back on those experiences with tropical fish and realized just how much science I learned from them. Making the water safe for the fish taught me a lot of chemistry. Learning about the fish, keeping a balanced tank the fish could live in, and breeding them introduced me to topics in biology long before I had them in my classes. Even mathematics, physics and a touch of engineering came into play.

Today, scientists and educators are making a deliberate attempt to interest children in science, technology, engineering and mathematics—it’s abreviated STEM. In the past, such activities tended to be aimed mostly at boys. Now, the goal is to interest everyone, no matter their gender.

I learned through books. My first book on aquariums taught me how to set up a small 5 gallon tank. As I got bigger books, I got bigger tanks. My Dad was an engineer, but for the most part, he stuck to lifting heavy objects, curbing some of my excesses, and suggesting how to look up an answer. It worked for me.

Part of me would love to write a book for third through fifth graders explaining the science as they set up a modern aquarium. Unfortunately, my wife and I weren’t blessed with children. I’m not sure if I’d know how to write for third to fifth graders.

As I thought about it, I realized I don’t want to write for those third to fifth graders. I want to write for their parents. The parents can guide their children, pick and choose the topics that are appropriate, and interpret the lessons for their children’s level of understanding. With any luck, the parents and children have fun together with the tank.

And who knows? Maybe the parents will gain a little more understanding and appreciation for science.

As I see it now, I’ll write a lesson about once a week, focusing on the particular topic involved with that stage of the aquarium setup. That might seem slow, and, as I get a feel for it, perhaps the frequency of the posts will increase. But one of the tricks to setting up an aquarium is to take it slowly. If, in a single day, you purchase an aquarium, set it up, and put the fish in, there’s a high probability that you’ll waste a lot of money and kill the fish.

If anyone is going to follow along, I would appreciate getting feedback. What was clear? What wasn’t clear? What was too difficult for your child to understand? What was too simple? What was too expensive? What better ways are there to do this? A comment section is available at the end of each article. I’ll make every effort to answer questions and learn from any suggestions.

2nd Law of Thermodynamics Permits Evolution

2nd Law of Thermodynamics Permits Evolution

Creationists repeatedly claim that the Second Law of Thermodynamics prohibits evolution. Buzz. Wrong. False. Incorrect. This claim has been around at least back to when I was in college, back when disco was popular. It was wrong then and it’s still wrong.

Continue Reading…

Pittsburgh’s Day of Giving

Pittsburgh’s Day of Giving

Tomorrow, October 3, 2013 is Pittsburgh’s Day of Giving. This is the 5th year for the Day of Giving. As the PittsburghGives.Org website says,

PittsburghGives is an initiative of The Pittsburgh Foundation.  The aim of this initiative is to:

  • Increase the level of knowledge about nonprofits in our region
  • Leverage or increase individual funding or organizations or an issue in our community
  • Spotlight the charitable trends in our region.  Where are people giving?  What are your community’s nonprofits saying is vital and needed right now?

Continue Reading…

Water, Martian Dirt and Life

Water, Martian Dirt and Life

In a paper just released, “Mars soil contains a huge amount of water, reports NASA’s Curiosity rover.” (1) If you’re interested in making drinking water, check out this video: So Mars Has Water. Could We Drink It?

Unfortunately, getting potable water out of the soil will be difficult, especially with all the oxychlorine compounds (2). If you’re interested in making rocket fuel to get back to Earth, it’s a lot simpler, especially if you’re willing to deal with liquid oxygen and hydrogen. (3)

But what does this mean for life?

Continue Reading…

  1. The original paper is here, unfortunately behind a paywall: Volatile, Isotope, and Organic Analysis of Martian Fines with the Mars Curiosity Rover. []
  2. Possibly the oxychlorine compounds are perchlorate, which is a serious water pollutant here on Earth and the oxidizing agent in high power rocketry motors. Yeah, my hobbies sometimes come in conflict []
  3. The basic technique for creating oxygen and hydrogen out of the Martian soil is an exercise left to the reader. The actual chemical engineering involved in creating automated stations to create tanks of liquid oxygen and hydrogen on Mars to await human explorers is an exercise left to the people designing the Human Exploration of Mars Project–or second year Chem Es taking a sadistic final. []

@realscientists Features David Schiffman This Week

@realscientists Features David Schiffman This Week

Every week, @RealScientists on Twitter has a “real scientist” talk about what they’re doing as a way of showing the public what “real scientists” do. This week features David Schiffman (@WhySharksMatter), “a Ph.D. student at the Abess Center for Ecosystem Science and Policy at the University of Miami…“. David grew up in Pittsburgh. (1) He’s working toward his Ph.D. by studying the ecology and conservation of sharks.

I’m looking forward to following our native son on @realscientists this week as he explains his work and answers questions! (2)

 

  1. David’s not the only marine scientist I know from Pittsburgh. Maybe the Three Rivers give people a taste for even more water! 😉 The Pittsburgh Zoo and PPG Aquarium has a great shark exhibit, too. []
  2. (Maybe it will make up for the Discovery Channel’s disastrous Shark Week Megalodon fraud. My wife, Nancy, still hasn’t forgiven the Discovery Channel for that one. If it’s not Mythbusters, we’re not watching it, and she’s even annoyed at the Mythbusters promos which seem to offer new episodes of Mythbusters but are repeats. []

What Penguins Tell Us About Ocean Warming

What Penguins Tell Us About Ocean Warming

One of the featured attractions at the National Aviary is the Penguin Point exhibit. The African penguins on display are used to a warmer climate. (1) In the winter, the Pittsburgh National Aviary provides them with heated areas. The penguins hate having to walk across any snow that accumulates in their enclosure.

While African (and many other species of) penguins are used to warmer climates, they all live in areas where cold water flows near land, and it’s because of chemistry. That little quirk–that penguins live near currents of cold ocean water–is a clue to something profound about the ocean and warns us of a danger of global warming. Continue Reading…

  1. This is one reason African penguins are popular in zoos–you don’t have to keep them refrigerated all year! []