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“Sea Anemones are Half-Plant, Half-Animal, Gene Study Finds.”
Ok, maybe calling it the worst headline in the world is a little hyperbolic, but it is a terrible headline. I have seen this headline over and over again, phrased exactly the same way, indicating that many, many sites do not bother even attempting to write their own versions, but simply cut and paste from other sources. But that is not the problem I have with it. The headline is woefully incorrect, seriously misleading, and damages all the hard work educators have spent trying to get people to understand genetics and how it affects our evolutionary understanding. The people who wrote this headline should really have known better and the people who wrote the articles should certainly have known better. For an example of a well written article that really explains what the research says, yet has this horrid title to it, try here. The information in the article is excellent if one can get past the horribly misleading title. In many cases, the author of the article is not to blame because the headlines are written by completely different people, who don’t necessarily either read nor understand what the article really says. That is a serious problem because many people, if not most, only read the title, or if they read the article, only remember the spin imposed by the title. Thus, titles matter (for more information on the effects of headlines, try here, here, here, here, and here).
The headline and many of the articles imply that a new study on the genetic code of the sea anemone revealed a mixture of animal and plant DNA. The research does not in fact say that. So I will attempt here to explain what it really DID say. To summarize, the genome of the sea anemone is very similar to other animals because it is, you know, an animal. However, there are certain key aspects of its gene regulation that are similar to plants. This is not as bizarre as it might sound though.
To begin with, let’s clarify what the article is referring to. Most of the time, when people talk about genetics, they are referring to the nucleic acid sequences, specifically Deoxyribonucleic Acid, or DNA, that code for genes. This is actually only a small part of the DNA. The rest is taken up with a variety of other things, including a variety of gene regulatory elements, junk DNA (broken genes, viral sequences, etc.), and chromosome structural sequences. The genome, or total genetic sequence, collected into a set of chromosomes, can be thought of as a book. The text includes all the gene sequences, but most of it has been marked out and written over ( what is often referred to collectively as “junk DNA”). The table of contents, page numbers, chapter headings, introductory publishing information, and index would be the regulatory bits; and the spine, cover, pages themselves, and everything holding it all together would be the structural elements. All of these parts are included in the complete DNA sequence, along with various proteins like histones that help package all the DNA.
Pretty much all of this DNA in the sea anemone, according to the study, is very similar to other animals, even vertebrates like us. The genes are similar, the regulatory sequences are similar, pretty much everything is similar. This is interesting because it speaks to the relative closeness of relationships between all animals. The genes used by sea anemones are simply variations of genes found within us. The regulatory sequences are variations of the same sequences we use.
However, not everything is the same. There are small sequences called micro-RNAs. Ribonucleic acid, more commonly just called RNA, is most commonly known as the molecules that help translate DNA gene sequences into working proteins. But that is not all they can do, Unlike DNA, RNA can do more than act as a codex of information. RNA can act as an enzyme at the same time. Enzymes are typically proteins that act on other proteins or on the DNA and RNA themselves. When micro-RNAs act on the DNA and RNA, they regulate expression of the genes, altering how much and what kind of proteins are created. This is where sea anemones differ from other animals. The micro-RNA of sea anemones is more like plants than animals. It had always been supposed that plants and animals evolved their versions of micro-RNAs separately, because they use different sequences and use different molecular pathways. They act differently. For instance, in animals, micro-RNAs bind to multiple proteins and inhibit their functions. Plant micro-RNAs are much more specific and slice up the protein, they don’t just inhibit them. Thus, it may be that sea anemones are telling us that the system developed before plants and animals split off from the ancestral organisms from which both plants and animals evolved. Not only that, but that the original pattern was kept by plants and substantially altered in animals.
The other part of this story that is not made clear is just what relationship sea anemones have with other animals, as well as plants for that matter, which in this case is fairly important. When looking at the early history of eukaryotic (with a nucleus containing DNA), multicellular animals, sea anemones are really, really early. Sea anemones are part of a group called cnidarians. Cnidarians, so named for cells called nematocysts, or stinging cells, also include what are generally called jellyfish, along with coral. On the tree of animal life, you can’t get much more primitive. The only animals thought to have evolved earlier than cnidarians are sponges and ctenophores, commonly known as comb jellies. They are so close to the base of the animal tree of life, one might say if they were lower, they would be only a step away from being fungi. Fungi, according to the genetic research, branched off from the animal lineage shortly after the split between animals and plants, which indicates just how closely related these early forms are.
In addition to being really close to the the plant/animal split, there is one last thing to consider. Sea anemones, like coral, depend on a mutualistic symbiosis with green algae, which, obviously, are plants. The algae collect sunlight to make sugar and oxygen, which gets shared with the sea anemone. The sea anemone in turn provides the algae a secure home, guarded by venomous tentacles. This relationship is similar to the well-known symbiosis with clownfish (remember Finding Nemo?), in which the clownfish gets protected from predators while providing food for the anemone. This is one case in which having messy tenants is actually a good thing.
Now, considering that the anemone relies on algae for its survival, linked as it is metabolically to the algae, and evolutionarily is not that far from being a plant itself, is it any surprise then to find that some of its metabolic regulation uses a system seen in plants? Sea anemones are not half animal/ half plant. They are extremely primitive animals that have their metabolisms linked directly to a plant, unlike the indirect link that other animals have (eating plants or animals that eat plants is a strong, but indirect link, wouldn’t you say?).
Were you able to solve Monday’s mystery fossil? They aren’t little poop balls, nor are they clams, although they are often mistaken for them.
This photo can be found at the Arkansas Geological Survey website under “Brachiopod.” They look a lot like clams. Brachiopods, often called lamp shells, have two shells and live in shallow marine environments just like clams and the occupy the same niche, feeding on organics filtered from the water. But unlike clams, which are molluscs, just like snails and squid, brachiopods are lophophorates, most closely related to bryozoans, the “moss animals.”.
So what is a lophophorate? Lophophorate means “crest or tuft bearer, so named for their feeding apparatus called a lophophore, which is shaped like a roughly circular or semi-circular ring of tentacles. These tentacles lazily wave through the water passing through the lophophore, catching small particles of food suspended in the currents. Thus, everything in this group are what is known as suspension feeders. These lophophores serve not only to collect food, but for gas exchange as well. In addition, the animals are headless, with the lophophore surrounding the mouth. The food enters the mouth and passes through the digestive tract, which makes a U-turn and dumps out what it can’t digest just outside the ring of tentacles. Clams do essentially the same thing, only they use an entirely different apparatus to do so.
Clams attach themselves to surfaces by secreting a collection of what are called byssal threads. Most brachiopods, on the other hand, form a pedicle, a stalk that holds them in place. Some do not make pedicles, instead just gluing themselves down directly onto the rock.
Another difference that can usually be seen between clams and brachiopods is the symmetry of their shells. Brachiopods are symmetrical from side to side, their left side is the same as their right side. Clams follow a different pattern. They usually have two identical shells, but the shells themselves are not symmetrical. This is not always true though. The Cretaceous oyster, Exogyra ponderosa, has an huge, thick shell on one side and a thin lid for a shell on the other. But as a general rule, this usually works. Another difference that is sometimes stated is that brachiopods use their muscles to close their shells, while clams use their muscles to open their shells, closing them by the use of ligaments; thus making brachiopods more susceptible to predators. This, however, is not true. In truth, brachiopods use their muscles to both open and close their shells. Clams have large adductor muscles that function to close the shells and they have ligaments that open them when the muscles relax.
Brachiopods are quite diverse, with many different types. They range in size from less than a dime to almost 40 cm (15″). There are two general groups, the Articulates, which have toothed hinges holding the shells together, and the Inarticulates, which do not have teeth, so they fall apart easily after death. Probably the most commonly found in Arkansas are spirifers, known for being somewhat wing-shaped , with a prominent sulcus, or depression in the center. Many brachiopods prefer solid substrates, like rock, others were adapted for softer substrates like sand or mud. Productids, like the ones in our mystery fossil, often grew spines, which helped secure them to muddy surfaces. Others, like strophomenid brachiopods, handled muddy substrates by developing large, very flat shells, which floated on the mud like a snowshoe. Still others, like the modern-day lingulids, developed long pedicles, allowing them to burrow down into the sediment.
Brachiopods have been around since at least the Cambrian, over 520 million years ago. They were most abundant in the Paleozoic Era, but suffered greatly during the Permo-triassic extinction event. They recovered to some extent, but never reached their previous abundance due to the appearance of clams, which began taking over some of the spaces they occupied. Nevertheless, there are still several different kinds in the modern ocean and can often be seen clinging to rocks near shore or buried in the sand. In Arkansas, you won’t find any living specimens, but you can find numerous fossil brachiopods in the Paleozoic rocks throughout the Ozarks and Boston Mountains, even in some places of the Arkansas Valley. Stop by any outcrop along Highway 65 between Conway and the north edge of the state, particularly limestone outcrops, and you are likely to find some. You can find a few in the Bigfork Chert in the Ouachitas, but they are not nearly so common as they are farther north.
It’s Monday! Time for a new mystery fossil. See if you can guess what this is. Don’t clam up, put your guess in the comments below.
Despite the snow, we didn’t get a chance to have any other posts this week other than the Monday Mystery fossil. We did, however, have three different school trips in the past couple of weeks to talk to kids about fossils, dinosaurs, and the skeletal system, as well as giving talks on the fossils telling us about the origins of crocodiles and dinosaurs, as well as attending a talk on the origins of birds. So a lot of paleo work, just not much showing up here. Fortunately, some of you had some time to examine our mystery fossil and congratulations to Laurenwritesscience for coming up with the correct answer.
It is indeed a stromatolite. Bruce Stinchcomb has a video on Youtube showing several examples of Ozark stromatolites and providing a good explanation of what they are.
Essentially, stromatolites are microbial ecosystems, built up of layer after layer of microbial mats. The general description is that of blue-green algae, which forms a sticky layer over the surface of a rocky surface in a shallow marine or coastal environment. Blue-green algae are not actually algae and are better referred to as cyanobacteria. These bacteria are photosynthetic, just like plants, so they need sunlight, thus limiting the depth at which they can be found. Actually, they are typically found right at the water’s edge in the tidal zone. This sticky substance, while maintaining their hold on the rock, also tends to collect sand, clay, and organic debris. Over time, all the stuff that sticks to the mat blocks the sunlight from the cyanobacteria and they migrate above the layer and build another mat, which collects more debris, which causes them to build another mat, etc. Stromatolites form much the same way as piles of laundry. By the time you finish washing one set, there is another pile forming in a neverending stream. The life of a cyanobacteria in a stromatolite is a depressing condition of always digging themselves out from under a pile just to get dumped on again. I am sure most people can empathize.
The sticky mucus (properly referred to as extrapolymeric substance, or EPS for short, but we can go with mucus here) forming the mat does more than just cause things to stick to it. The mat protects the bacteria in from ultraviolet radiation. It also allows the bacteria to control the microenvironment around them, keeping such things as pH levels in a good range. It also has an unfortunate aspect for the bacteria. The mucus allows the levels of calcium and carbonate ions to build up until they precipitate out of the water as calcium carbonate, also known as calcite (when referring to the mineral), or limestone (when referring to the rock). So not only are the poor bacteria constantly getting buried, they are getting turned to stone in their very own medusa nightmare. Life is hard as a cyanobacteria. But just wait, it gets worse.
These microbial mats are not just cyanobacteria, though. There are lots of other organisms that live in and on them. There are many other types of bacteria. There are sulfate reducing bacteria, which use sulfur like we use oxygen, only they release hydrogen sulfide instead of carbon dioxide, causing a nice rotten egg smell. There are purple sulfur bacteria that eat the hydrogen sulfide, as well as colorless sulfur bacteria that eat both the hydrogen sulfide and the oxygen released by the cyanobacteria, thus free-loading off of everyone. In addition to bacteria, there are plenty of prokaryotes (organisms without nuclei that holds their DNA) and eukaryotic (with nuclei) single-celled and multi-celled organisms living in the mat. Diatoms, single-celled photosynthetic organisms that grow their own shell, live on top, while nematodes burrow through the mat. In addition to all this, a wide variety of animals love to chow down on the mats. Everything from snails, sea urchins, crabs, crawfish, and just regular old fish happily eat them. As a result, there are not a lot of places left in the world you can find stromatolites growing. The Bahamas and Shark’s Bay, Australia are the best areas to find them.
They may be rare now, but at one time, they ruled the earth. As some of the oldest living communities in the world, they have been around for at least 3.5 billion years (that’s 3,500,000,000, or roughly 600,000 times the length of human civilization) and for more 2/3 of that time, they were the only game in town and in all probability served as the cradle for all eukaryotic and multi-cellular organism on the planet. These days, if you live in Arkansas, the only places you can find them are as fossils in the Cambrian age Cotter Formation and Ordovician age Everton Formation in the Ozark Plateau.
For further information (and the source of the images shown here), check out the stromatolite page at the Arkansas Geological Survey and the Microbe Wiki stromatolite page, as well as the Microbes.arc.nasa.gov site, which supplies a nice teacher’s guide to teaching all about microbial mats, designed for grades 5-8.
I don’t know where you may be, but where I am, ice is covering everything and all the schools are closed. It’s a great day to pull up the covers and stay under the blankets, maybe get a cup of hot chocolate and wait for warmer weather. That makes today’s Mystery Monday fossil particularly apropos. Yes, this really is a fossil, not just layers of sediment.
Many people have an issue with scientists, particularly those studying evolution and paleontology, for making statements they feel are pure speculation. I absolutely agree that people should be upfront about what is known and what is speculation. Most scientists ARE generally clear about that. If you ask most scientists, they will tell you what we know and don’t know. That is actually one of the biggest problems that scientists have with almost all of the shows and most of the books written for the public. Those outlets are not clear about what we really know and what we don’t, what is speculation. Most scientists I know work really hard at trying to clarify that sort of thing and get very frustrated when their words are twisted around. Many scientists have refused to work with film crews for precisely that reason. So please don’t blame the scientists. Write to the shows and demand they are clear about their speculations.
Sadly, I wish I could say all scientists act this way, but it is true, not all do. Scientists are only human after all. There are problems with some scientists. Believe me when I tell you that we recognize this and try to stop it. The lab I worked in to get my doctorate had a reputation for being spoilers, as it were, because a large portion of our research involved figuring out the limits of what the data really let us say and then telling others no, you can’t say that because the data do not extend that far. Our work was very much about separating speculation from reasonable interpretation and fact. But we were hardly alone in that regard, it is something most scientists work hard to do. Paleontology is admittedly one of those fields in which it is easy to take the fossils we have and in our excitement try to say too much about them. So we do our best to restrain ourselves and other workers from extrapolating too far. Go to a paleontology conference and you will see that on display in abundance.
Unfortunately, that rarely shows up in material done for the public. The film crews and honestly, most of the public, do not want to hear we don’t know. They want to hear the fanciful stories. Most people get annoyed with scientists when they equivocate and don’t give straight answers. We frequently hear from people, well which is it? Is it this way or that way? If you can’t say with absolute certainty one way or the other, you must not know ANYTHING, when in point of fact, there is a vast difference between not being sure and not knowing anything, I am sure most will agree. But most people don’t want to hear we don’t know with certainty, we can only say this much about it. I have even seen that in my college courses. Many students are uncomfortable with the material I cover in which there are no good answers everyone agrees on. They want definitive answers. A large part of that, I think, is that science is taught in schools very poorly, as a list of facts to memorize, not as a way of thinking and an expanding body of knowledge that is constantly re-examined, with large areas we don’t know yet. In fact, and what makes science fun and interesting for people doing it, is that science is more about what we don’t know than what we do. But happily, I can say that is changing in many areas, with the introduction of more hands-on, exploratory teaching methods.
One of the challenges though, is that many things the lay person thinks are pure speculation are not speculation at all, but are backed up by lots of evidence that there is simply not enough time to go into. Many computer programmers simply tell their clients what they do is magic because to answer their questions adequately would take months of training to even get them to the point they could understand the answer. Would you tell a computer programmer what they are doing is pure speculation simply because you don’t understand it? We aren’t trying to be elitest, there is just a lot of information we don’t have time to transmit. There is simply too much going on, too much data, too much research for anyone to keep track of it at all. Even professionals who try to keep up as part of their full-time job can’t do it. So it would be foolish to think anyone who doesn’t spend most of their time studying the research could possibly have a good grasp of the intricacies and quantity of data. It therefore becomes quite the annoyance when people say you can’t know something when they have no idea how much we do know. Many of those things people say we can’t know have been studied for decades by many people who have spent their lives figuring out how to go from speculation to concrete data and hard fact. Most people don’t realize the extreme levels of simplification it takes to get some concepts across because no one can provide all the data backing up those assertions without having their audience earn a graduate degree in the process.
Is all this me telling you to just trust whatever we say? Absolutely not. But don’t expect to come in on the ground floor and know what is going on at the top any more than you could expect to speak perfect French by catching someone speak a few words on TV. Understand that you are only getting the tip of the iceberg. What you see on TV is a seriously flawed transmission of a few grains of knowledge from a mountain range of data. Learn as much as you can from reliable sources. The more you know, the richer your interactions with professionals and the more in depth we can talk to you. We will be happy to share with you everything we know, that’s our job. But what we tell you is highly dependent on the level at which you come to us and the amount of time people are willing to spend. Also understand the quantity of data is more than any one person can understand, even those whose job it is to do so. That is why we have many people studying problems. No one can have all the answers. That is why we keep asking questions. Being open about what we know and what we don’t allows us the freedom to learn more and shows us the path about where to go next. Scientists don’t leave things at speculation, they try to figure out how can we go from speculation to understanding. But if you want to understand all the steps involved, may I suggest grad school?
Today we have a picture by Ronny Thomas of a very well-known animal, although it is quite rare in Arkansas. In fact, only one has ever been found in the state. So what do you think it is? Stay tuned for the answer on Friday.
I’m sorry, but I forgot to post the Mystery Monday fossil on the blog. I posted the fossil on the Facebook page, but somehow failed to get it posted here, for which I apologize. Here is the fossil I posted, including the identifying portion cropped from the original picture. This image was taken from trilobites.info, a great website for all things trilobite.
It was correctly identified as a trilobite, although this one is the species Irvingella, not Bristolia as was guessed. Irvingella is very similar, but lacks the tail spine and the second set of spines is a little farther down the body. They are both listed as “fast-moving low-level epifaunal” feeders by the Paleobiology Database, which means they scurried quickly about over the ocean floor. But whereas Bristolia is thought to have been a deposit feeder, much like a crawfish, Irvingella was a carnivore, preying on worms, bugs, and such. They both lived in offshore marine environments, but whereas Bristolia has been found mostly in shallower waters, Irvingella has been found widespread from offshore throughout the continental shelf and even deeper water. This may have more to do with Bristolia having only been found in a few places in the southwestern United States while Irvingella has a much broader range throughout much of North America and Asia. They both lived in the Cambrian Period, although Bristolia seems to have lived a little earlier than Irvingella (there are some discrepancies in the published records making it difficult to compare exactly, this is partly due to revisions of the time scale and refinements in age estimates over the decades making detailed comparisons problematic).
Since our last Forum Friday recap, we have started a new year. We have reviewed the Walking with Dinosaurs movie. We identified an Exogyra ponderosa oyster, Archimedes bryozoan, Aetobatus eagle ray, and this Irvingella trilobite.
Over on the Facebook page so far this year, we have seen some amazing animals, including sharks that glow in the dark, a fish that walks on land, and a caterpillar who’s tobacco breath repulses spiders. We even learned why sharks don’t make bone, but polygamous mice have big penis bones and an organism that changes its genetic structure seasonally.
We saw two articles on fighting dinosaurs. We learned how they took over the planet and discussed scaly dinosaurs for a change. We found out some ancient marine reptiles were black and Tiktaalik had legs.
A lot of articles hit the press on human evolution in 2013. We also found out (some) humans developed the ability to tolerate lactose to not starve and how we smell sickness in others. We also found a great book on Evolution & Medicine. We also saw evidence of how our actions affect the evolution of other animals and someone who thinks they can understand dog language.
We read that plants may have caused the Devonian extinction event, a genetic study saying placental mammals originated before the end-Cretaceous extinction event despite no fossils ever having been found, and that small mammals with flexible schedules handle climate change better than big mammals that keep a stricter schedule.
We found a great , concise explanation of evolution and three different short videos on the history of life on earth, two of them animated and set to music. We also heard Neal DeGrasse Tyson urge more scientists to do more science outreach (and how to cook a pizza in 3 seconds). Unfortunately, we also heard about the deplorable conditions during filming on Animal Planet and creationism in Texas public schools, as well as how the failure to take evolution into account can screw up conservation efforts.
So what did you like? Did you guess the fossil? Is there anything you want to see? Let us know.
It’s been a very busy weekend, so this will be a very short post. today I simply want to introduce the latest mystery fossil. This is a bizarre little fossil, measuring less than 2 cm across. It’s not the best picture, I admit, but there is enough resolution to identify it to at least the Order. I will post a clue a day until Friday, when I will reveal its identity. Good luck, take a guess, and have fun.
Tuesday’s clue: These teeth are used to eat animals much, much smaller than the animal it came from.
Wednesday’s clue: We are very popular at many aquariums.
Thursday’s clue: Some people say i have wings, but I do not fly. I may have a cold heart, but I don’t bite.
Welcome back! I hope everyone had a great holiday to mark the end of a great year. 2013 marked the inaugural year for Paleoaerie. Version 1 of the website was set up, providing links to a wealth of online resources on fossils, evolution, the challenges of teaching evolution and the techniques to do it well. The blog had 26 posts, in which we reviewed several books and websites, discussed Cambrian rocks in Arkansas and the dinosaur “Arkansaurus,” and went to the annual meeting of the Society of Vertebrate Paleontology. We looked at geologic time and started a series on dinosaur misconceptions. We also had several Forum Fridays, recapping the many news stories reported on the Facebook page. One of the recent things we’ve started is Mystery Monday, posting a fossil of the week for people to try to identify. Speaking of which, to start off the new year, the first mystery fossil will be posted early. look for it at the end of this post.
In the upcoming year, we hope to expand the site, providing many more resources, along with continuing posts on Arkansas geology and fossils, including many more mystery fossils. Stick with us and you will learn about the history of Arkansas in a way that few people know. The site will be revamped to be more user-friendly and enticing to visitors. If plans materialize, we will be adding interactive activities, animations, and videos, many of which will be created by users of the site. Materials from workshops and talks will be posted for people to view and use. More scientists will be posted that have offered their services to teachers and students. We encourage you to contact them. They are there as a resource.
Of course, all of this does not come free. it takes money to provide quality services. Thus, more avenues of funding will be pursued, including other grant opportunities and likely a Kickstarter proposal. You may soon see a small button on the side of the website for Paypal donations. Any money donated will go first towards site maintenance. Other funds will go towards a student award for website design, a 3D laser scanner to put fully interactive 3D fossil images on the site, and materials for review and teacher workshops. If grant funding becomes available, additional money will be spent on research into the effectiveness and reach of the project. But even if no more funding becomes available, you can still look forward to continuing essays on Arkansas fossils, reviews of good books and websites, and curation of online resources suitable for teachers, students, and anyone else interested in learning about the endlessly fascinating history of life on planet earth.
I mentioned at the beginning about the latest mystery fossil. Here’s the first hint: it is a very common fossil found in Arkansas and lived during the Mississippian period roughly 330 million years ago. More hints and photos to come. Leave your guesses in the comments section. Don’t worry about getting it wrong, every success has lots of failures behind it. Errors are only stepping stones to knowledge.
Clue number 2: Many people think I’m a coral, but I’m not.
Clue number 3: I am named after a famous Greek mathematician and inventor.
What am I?