Category Archives: Evolution

Biological fight: the case of artificial stimuli in behavior research

by Piter Kehoma Boll The study of animal behavior is an important approach to understand several aspects on the ecology and the evolution of living beings, both from the analyzed animals themselves and the species with which they interact. For example, understanding how a bee recognizes a flower as a food source and how it approaches it may explain a lot about the physiology and the evolution of the flower and vice-versa, thus clarifying why such a combination of characters is the one that is found in the current population.

As with virtually any type of study in biology, a research may be done with sampling or experiments. By sampling you obtain non-manipulated information directly from the environment. You collect or observe a small sample of the whole and infer the general situation of the population based on it. On the other hand, in an experiment you manipulate the environment and watches how the organisms will react to the different stimuli presented to them and, from this, you develop your conclusion.

For example, if you want to know what a species of frog eats, you may find out by sampling, observing some frogs in the wild while they feed or capturing some and examining their stomach contents. You may also offer them different kinds of food, either in the environment or in the lab, and observe how the frogs reacts to each one.

Thus, in experiments you control the stimuli the species receives from the environment. This is the point where things start to get nasty. May the stimuli have artificial elements, i.e., elements that cannot be found by the animal in its habitat?

The opinions about it are divergent and recently led to a “formal fight” published in the journal Ethology:

On one side is a group of researchers from several universities around the world (Hauber et al., 2015) that defends the use of artificial stimuli to analyze behavior. They use as a model the studies on the rejection of eggs of parasitic birds by parasitized birds, a well-studied phenomenon.

First, let us contextualize this phenomenon briefly:

Several bird species, mainly cuckoos, do not incubate their own eggs. Instead of doing it, they lay them in the nests of birds of other species and hope that the poor creatures incubate and later feed the chicks as if they were their own. As a result, natural selection favors cuckoos whose eggs are more similar to the ones of the parasitized bird and also favors the parasitized birds that better distinguish their eggs from the ones of the intruders. It is a typical evolutionary race.

Find the intruder. The similarity between the egg of the parasite and the parasitized can vary greatly. Photos by wikipedia user Galawebdesign (left)* and by Grüner Flip (right).

Find the intruder. The similarity between the egg of the parasite and the parasitized can vary greatly. Photos by wikipedia user Galawebdesign (left)* and by Grüner Flip (right).

In experimental studies on egg rejection by parasitized birds, it is common to use artificial eggs that exaggerate features of natural eggs. This includes, for example, changing color and size in order to understand which is the most relevant for the bird to recognize the eggs as being yours or not. However, can we trust the results of such experiments using artificial elements?

Haubert et al. (2015) think that we can. Their arguments in favor of the use of such artificial stimuli are the following:

  1. Real eggs of the studied species are difficult to get in large quantities and could cause significant impacts over the populations if used. So, artificial eggs ensure the integrity of populations.
  2. It is difficult to get a set of natural eggs similar enough to allow the necessary repetitions to validate the test. After all, a result is only considered valid if it is recorded several times in face of the same stimulus. Artificial eggs allow identical copies and, thus, true repetitions.
  3. Natural eggs vary in several aspects at the same time, such as color, size, form, texture… In artificial eggs it is possible to control these aspects and allow only one to show free variation, so isolating the influence of each one during the recognition by the bird.
  4. A variation beyond the ones found in the wild may help to find populations with different degrees of perception of strange eggs and consequently where are the sites of higher selective pressure.
Original eggs of the parasitized species painted to exaggerate color features. Photos by István Zsoldos. Extracted from Moskát et al. 2010.

Original eggs of the parasitized species painted to exaggerate color features. Photos by István Zsoldos. Extracted from Moskát et al. 2010.

Not everyone looks so favorably to such an unrestrained use of artificial stimuli. Soon after the opinion of Hauber et al. we find the reply of David C. Lahti (2015) who faces all by himself the “artificialist” army. Lahti shows some aversion to such exaggerate use of artificial elements that many times are not used in a responsible manner.

Suggesting a more restrict use of artificial elements, he argues the following:

  1. Our perception of the environment is different from the one of the species we are studying. For instance, a bird sees a much wider range of colors than we do. When we paint an artificial egg black and white in order to simulate a natural black and white egg, we don’t know whether the bird really sees both eggs with the same colors. So, while we suppose that the eggs look similar by our perception, the reality from the bird’s point of view can be very different.
  2. When we try to create a set of artificial eggs that vary in only one aspect, such as the size of the spots on the shell, for instance, in order to control the influence of this stimulus only, we always end up including secondary stimuli that are not measured, such as the paint used to make the spots. If the birds shows a different response to eggs with small spots (natural ones) when compared to eggs with large spots (artificial ones), how can we know that the difference was not caused by the perception of the paint, either chemically or visually, by the animal? It would be necessary to perform tests that would discard this possibility, but it does not happen usually.
  3. Exaggerated artificial stimuli may go beyond the species’ range of recognition. An egg with a color too different from any color variation found in the environment could cause the bird not to see it as an egg, which would lead to problems in the interpretation of the results.

Concerning this last argument, Hauber et al. emphasize that is important to take care on a priori interpretations on the species behavior. That is to say, we cannot guess what the bird is thinking. The fact that the bird removes the parasite’s eggs from the nest or not does not mean that it is capable of recognize the egg as an intruder, or even as an egg. The way the bird interprets the stimulus is not as important as its response to it.

Therefore, we can conclude that artificial stimuli can be advantageous and in several circumstances they are the only available alternative. It is important, however, to take care with their use and try to be sure that secondary features, generally neglected, are not considered important by the animal.

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Hauber, M.; Tong, L.; Bán, M.; Croston, R.; Grim, T.; Waterhouse, G.; Shawkey, M.; Barron, A.; & Moskát, C. 2015. The Value of Artificial Stimuli in Behavioral Research: Making the Case for Egg Rejection Studies in Avian Brood Parasitism Ethology, 121 (6), 521-528 DOI: 10.1111/eth.12359

Lahti, D. 2015. The Limits of Artificial Stimuli in Behavioral Research: The Umwelt Gamble Ethology, 121 (6), 529-537 DOI: 10.1111/eth.12361

Moskat, C.; Ban, M.; Szekely, T.; Komdeur, J.; Lucassen, R.; van Boheemen, L.; & Hauber, M. 2010. Discordancy or template-based recognition? Dissecting the cognitive basis of the rejection of foreign eggs in hosts of avian brood parasites Journal of Experimental Biology, 213 (11), 1976-1983 DOI: 10.1242/​jeb.040394

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Filed under Behavior, Ecology, Evolution, Ornithology, Zoology

Pooping to evolve: how feces allowed us to exist

by Piter Kehoma Boll

ResearchBlogging.orgBillions of years ago, when the first lifeforms appeared on Earth, our planet was very different from what it is today. Oxygen, so essential for our survival, was not present in the atmosphere.

Thanks to the appearance of the first photosynthetic bacteria, the so-called Cyanobacteria or blue-green algae, our atmosphere started to accumulate oxygen. As you may know, photosynthesis is a process by which plants and other photosynthetic organisms convert water and carbon dioxide into oxygen and organic compounds.

Oxygen is a very reactive element, so it can easily interact with other compounds and is great to burn organic matter to release energy. Without oxygen, heterotrophic life, such as animals, would not be able to use large quantities of energy and therefore would have never been able to achieve large size.

As you may also know, animals most likely appeared in the oceans and only much later conquered the land. However, oxygen produced by photosynthesis accumulates mainly in the atmosphere and not in the oceans. Today, only 1% of the global oxygen is found in the oceans, and it was even worse during the first million years of multicellular life. Do you know why?

The most primitive animals alive today are sponges, which are quite different from other animals. They usually have a hollow body with several pores, which function as tiny mouths through which water carrying small planktonic organisms and other organic matter is pulled inwards and later released by a large opening on the top of the body. So the main thing sponges do is mixing water and extracting a small amount of organic matter from the water column. Their feces, when returning to the water, are not very different in size from the organic matter they initially ingested.

Sponges ingest organic particles and release organic particles. They are not very efficient in removing organic matter from water.

Sponges ingest organic particles and release organic particles. They are not very efficient in removing organic matter from water.

Thus, in a sponge-only world, the water column was possibly always crowded with dissolved organic matter. This was a feast for bacteria, which are always eager to decompose organic matter and, while doing so, they consume large amounts of oxygen. Therefore, water with high amounts of organic matter increases bacterial activity and turns the environment anoxic, i.e., without oxygen. As a result, there was no oxygen available to allow animals to become large.

Despite not growing very much, animals were still evolving, of course, and eventually the bilaterian animals appeared. Bilaterian animals have a bilateral symmetry and, the most important feature in this story, a gut. It means they ingest food, digest it, process it and later eliminate the rests as… poop! In the gut, feces become compact as fecal pellets and sink much quickly to the bottom of the ocean, cleaning the water column from organic matter and drastically reducing bacterial activity. With no bacteria decomposing in the water column, the oxygen levels rapidly started to increase, allowing animals to grow and things like fish to evolve.

Bilaterian animals produce compact fecal pellets which sink to the bottom, cleaning the water column.

Bilaterian animals produce compact fecal pellets which sink to the bottom, cleaning the water column.

If animals had never started to poop, we most likely would have never been able to arise in this world. Long live the poop!

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Holland, H. (2006). The oxygenation of the atmosphere and oceans. Philosophical Transactions of the Royal Society B: Biological Sciences, 361 (1470), 903-915 DOI: 10.1098/rstb.2006.1838

Turner, J. T. (2002). Zooplankton fecal pellets, marine snow and
sinking phytoplankton blooms. Aquatic Microbial Ecology, 27, 57-102

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Acoelomorpha: A Phylogenetic Headache

ResearchBlogging.orgby Piter Kehoma Boll

Take a look at these guys:

The green worm Symsagittifera roscoffensis (Graff, 1891). Photograph by Vincent Maran. Extracted from

Green worms Symsagittifera roscoffensis (Graff, 1891). Photograph by Vincent Maran. Extracted from

It’s a member of the group Acoelomorpha, animals which are still a puzzle in phylogeny. That means no one knows for sure where in the animals’ evolutionary tree they are exactly.

But first, let’s take a look about what makes an acoelomorph.

Those little guys are small worms, usually measuring less than 1 mm in length and living in marine or brackish waters or as symbionts. There are two groups of acoelomorphs: Acoela and Nemertodermatida. Acoels are the simplest ones; they have a mouth, but lack a gut, so that the food ingested goes directly to the internal tissues. In Nemertodermatida, there is a blind gut, i.e., with only one opening, like in the primitive cnidarians or in flatworms. In fact, they were initially classified as flatworms, but several features later challenged their position inside this phylum. The main differences are:

  • Acoelomorphs have an epidermis (“skin”) with cilia whose roots are interconnected in a hexagonal pattern, while other flatworms have independent cilia.
  • Acoelomorphs lack protonephridia (primitive kidney-like organs) and all other groups of animals have at least one of those or more complex organs with similar function.
  • While flatworms and all other protostomes (arthropods, annelids, mollusks, nematodes…) have ventral nerve cords and deuterostomes (chordates, echinoderms…) have dorsal ones, in acoelomorphs there are several nerve cords distributed radially along the body length.
Distribution of nerve chords in Acoelomorpha, Protostomia and Deuterostomia. Picture by myself, Piter K. Boll.

Distribution of nerve chords in Acoelomorpha, Protostomia and Deuterostomia. Picture by myself, Piter K. Boll.

Analyzing such features, it seems obvious that Acoelomorpha is a basal group of bilateral animals and may be the reminiscent of a primitive group of animals later almost completely extinct by their most complex descendants, the true protostomes and deuterostomes. The original radially-distributed nerve cords were simplified in dorsal or ventral ones in higher groups, but remained radial in Acoelomorpha.

Several phylogenetic studies indicate that Acoelomorpha is indeed a basal group of bilateral animals. They also lack several important Hox genes (responsible for determining body plan and organs’ distribution in animals) and it is quite unlikely that they would have lost most of them by secondary simplification.

Another group of simple animals, the Xenoturubellida, was sometimes proposed as a sister group for Acoelomorpha. Their proximity would be explained by several shared features, mainly the simple nervous system, the lack of a stomatogastric (mouth-gut) system, the structure of the epidermal cilia and the unusual fact that, in both groups, epidermal degenerated cells as resorbed in the gastrodermis.

A Xenoturbella worm. Photograph extracted from

A Xenoturbella worm. Photograph extracted from Hiroaki_Nakano_eng/

The group Xenoturbellida, however, has been placed in Deuterostomia in some molecular studies and recently Philippe et al. 2011 proposed that Acoelomorpha would also belong to the the Deuterostomia! But how could such a thing be possible when they obviously have primitive and unique features, like the radially placed nerve cords? The group’s explanation is that Acoelomorpha, as well as Xenoturbellida, have a sequence of microRNA (miR-103/107/2013) which is exclusive to Deuterostomia, so they would also be deuterostomes.

But wait a minute! What do they mean by “exclusive to Deuterostomia”? It means that that microRNA sequence is found in deuterostomes, but not in protostomes. Now think with me. We have 4 bilateral groups here: Acoelomorpha, Xenoturbellida, Deuterostomiaa and Protostomia. If you look at them this way, we can see that the statement “miR-103/107/2013 is exclusive to Deuterostomia” is false. The truth is that this sequence is absent in Protostomia, but present in all other groups. Wouldn’t it be more logical to think that, instead of deuterostomes acquiring this sequence, what really happened is that it was a primitive microRNA and protostomes have lost it?

If you consider Xenoturbellida and Acoelomorpha inside Deuterostomia, you have to assume that they passed through a huge simplification, and you maintain the radial nerve cords unexplained. Now if you think of them as primitive groups, the only thing necessary is to analyze protostomes as having lost a microRNA sequence. Quite a simpler explanation which doesn’t let open gaps.

Phylogenetic position of Acoelomorpha and Xenoturbellida according to Philippe et al. 2011. It means that (1) the bilaterians' ancestor had a complex set of Hox Genes; (2) miR-103/107/2013 appeared in an ancestor of true Deuterostomes+Xenacoelomorpha (Xenoturbellida + Acoelomorpha); (3) Xenacoelomorpha passed through a huge loss of Hox genes, loss of most internal organs and a mysterious set of radial nerve cords appear. Very complicated.

Phylogenetic position of Acoelomorpha and Xenoturbellida according to Philippe et al. 2011. It means that (1) the bilaterians’ ancestor had a complex set of Hox genes, being a complex animal; (2) miR-103/107/2013 appeared in an ancestor of true Deuterostomes+Xenacoelomorpha (Xenoturbellida + Acoelomorpha); (3) Xenacoelomorpha passed through a huge loss of Hox genes, loss of most internal organs and a mysterious set of radial nerve cords appear. Very complicated.

Position of Xenacoelomorpha as a basal group. It means that (1)

Phylogenetic position of Acoelomorpha and Xenoturbellida according to Boll et al. 2013 (that’s me!) based on a review of previous studies, as a basal group. It means that (1) the bilaterian’s ancestor was a simple animal, with a simple set of Hox genes, having miR-103/107/2013 and radial nerve cords; (2) the set of Hox genes became more complex and the nerve cords where simplified to either dorsal or ventral; (3) miR-103/107/2013 is lost in Protostomia. Way simpler.

You can read more in the references listed below.

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Boll, P., Rossi, I., Amaral, S., Oliveira, S., Müller, E., Lemos, V., & Leal-Zanchet, A. (2013). Platyhelminthes ou apenas semelhantes a Platyhelminthes? Relações filogenéticas dos principais grupos de turbelários. Neotropical Biology and Conservation, 8 (1), 41-52 DOI: 10.4013/nbc.2013.81.06

Egger, B., Steinke, D., Tarui, H., De Mulder, K., Arendt, D., Borgonie, G., Funayama, N., Gschwentner, R., Hartenstein, V., Hobmayer, B., Hooge, M., Hrouda, M., Ishida, S., Kobayashi, C., Kuales, G., Nishimura, O., Pfister, D., Rieger, R., Salvenmoser, W., Smith, J., Technau, U., Tyler, S., Agata, K., Salzburger, W., & Ladurner, P. (2009). To Be or Not to Be a Flatworm: The Acoel Controversy. PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005502

Hejnol, A., Obst, M., Stamatakis, A., Ott, M., Rouse, G., Edgecombe, G., Martinez, P., Baguna, J., Bailly, X., Jondelius, U., Wiens, M., Muller, W., Seaver, E., Wheeler, W., Martindale, M., Giribet, G., & Dunn, C. (2009). Assessing the root of bilaterian animals with scalable phylogenomic methods. Proceedings of the Royal Society B: Biological Sciences, 276 (1677), 4261-4270 DOI: 10.1098/rspb.2009.0896

Moreno, E., Nadal, M., Baguñà, J., & Martínez, P. (2009). Tracking the origins of the bilaterian
patterning system: insights from the acoel flatworm. Evolution & Development, 11 (5), 574-581 DOI: 10.1111/j.1525-142X.2009.00363.x

Mwinyi, A., Bailly, X., Bourlat, S., Jondelius, U., Littlewood, D., & Podsiadlowski, L. (2010). The phylogenetic position of Acoela as revealed by the complete mitochondrial genome of Symsagittifera roscoffensis. BMC Evolutionary Biology, 10 (1) DOI: 10.1186/1471-2148-10-309

Philippe, H., Brinkmann, H., Copley, R., Moroz, L., Nakano, H., Poustka, A., Wallberg, A., Peterson, K., & Telford, M. (2011). Acoelomorph flatworms are deuterostomes related to Xenoturbella. Nature, 470 (7333), 255-258 DOI: 10.1038/nature09676


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Where did milk come from? The mysterious origin of lactation in mammals.

by Piter Kehoma Boll In previous posts, I talked about two scientists who introduced “revolutionary” ideas to explain certain aspects in evolution, contradicting what other specialists use to say. But they come up with such unlikely explanations and use to ignore anything that says something contrary to their ideas that no one takes them seriously. You can read about them here and here.

Today, however, I will talk about another scientist who had interesting and innovative ideas, but much more likely and based on many more evidences. His name is Olav T. Oftedal and the topic is the origin of lactation.

As everybody knows, mammals are characterized mainly by the fact that females nourish their young through mammary secretions, the thing we know as “milk”. But how did this trace evolved in the mammalian lineage?

A cat (Nani) with her babies. Photo by Piter Kehoma Boll

A cat (Nani) with her babies. Photo by Piter Kehoma Boll*

Charles Darwin was one of the first ones to think of an explanation. Based on marsupials, Darwin concluded that mammals evolved from animals which carried eggs in a pouch and nourished them by cutaneous secretions. His idea was also inspired by seahorses, were eggs are carried in an abdominal pouch by the male and it was though that they might be nourished by cutaneous secretions too. However the subsequent discovery that the platypus, one the most primitive mammals, lays shelled eggs and have no pouch marked the ruin of Darwin’s theory on the origin of lactation. But… did it indeed?

In a paper published in 2002 in the Journal of Mammary Gland Biology and Neoplasia, Olav T. Oftendal raised some interesting questions and proposed an explanation to the origin of lactation very similar to the one proposed by Darwin one and a half century  before.

As it is known, mammals evolved from a lineage of amniotes called synapsids, from which they are the only extant group, so that everything about their ancestors must be assumed through fossil record.

Mammals’ ancestors are usually called “mammal-like reptiles”, but such a comparison is far away from what they really were. The animals we call reptiles – turtles, snakes, lizards and crocodiles – are sauropsids, so as birds, and they diverged from synapsids soon after the origin of amniotes and were probably very different creatures after some million years.

Let’s start thinking about what’s an amniote. The clade “Amniota” comprises all extant tetrapods other than amphibians, and they are characterized by the presence of a set of membranes surrounding the embryo which assisted in nutrient mobilization, gas exchange and storage of embryonic waste products, as well as in protecting it from the environment in a fluid-filled sac. But how were the eggs of those early amniotes?

When we think of an egg, we use to think of a bird’s egg, with a calcified shell, but this was probably not the case in early amniotes. The eggs of current egg-laying mammals lack a calcareous layer and it is likely that a calcified shell evolved only in the sauropsid lineage.

An ordinary chicken egg is the first think to come to mind for most people when they heard the word "egg". Photo by Sun Ladder, extracted from

An ordinary chicken egg is the first think to come to mind for most people when they heard the word “egg”. Photo by Sun Ladder*, extracted from

Eggs without a calcified shell rarely fossilize, and in fact there are no fossil eggs from Carboniferous, Permian and early Triassic, i.e., during all the history of non-mammalian synapsids.

But what’s so good in calcified shells? Well, a calcareous layer helps to prevent water loss from the embryo to the environment, whether to a reduction of relative humidity in the environment or a difference in temperature. Reptiles with non-calcified egg shells use to bury their eggs in damp soil where relative humidity approaches 100%, so dealing with the water loss problem. The increase of aridity from the end of the Permian to the Triassic may have favored the evolution of calcified eggs, but still there is no evidence of synapsid eggs. Could they have buried them in damp soil just as some reptiles do today? It’s possible, but…

Birds and mammals have developed a common feature: endothermy, i.e., “warm blood”. As we all know, birds use that to incubate eggs at elevated temperature, so speeding up the embryo development. It’s quite possible, and likely, that synapsids did the same. But as it was said, the difference in temperature between the egg and the environment also leads to water loss. In birds, the calcified shell solves this problem, but synapsids didn’t seem to have had this advantage.

Observing non-calcified eggs in snakes and lizards, it is possible to notice that they increase in mass by 10 to 100% after being laid. This happens due to water uptake from the environment and, as the shells is not rigid, the egg can also increase in volume, something that cannot happen in rigid-shelled eggs.

According to water uptake, eggs can be classified in endohydric and ectohydric. Endohydric eggs contain all water the embryo needs for the development when it is laid, while ectohydric eggs must take up water from the environment. In non-calcified eggs, it depends mainly of the eggs size. Large eggs may have enough water to sustain the embryo even with some water loss, since their surface:volume ratio is low, but the same cannot be applied to small eggs. And as it is known, the first mammals, and so their direct ancestors, were quite small creatures.

So what we have is an animal with non-calcified egg prone to dehydration and a high body temperature that can help to speed up the embryo development. How to join these two things?

The egg-laying mammal echidna and some marsupials have an abdominal pouch to retain eggs or newborns. It is known that the short-beaked echidnas incubate their eggs in the pouch. Female platypuses don’t have a pouch, but they incubate their eggs by curving their flat tail so that it touches the abdomen, forming a pouch-like enclosure. Inside this pouch, cutaneous secretions from the female’s abdomen would maintain the eggs moist, so preventing dehydration.

An egg of an echidna inside her pouch. (I found this picture on the internet without information about the author and stuff).

An egg of an echidna inside her pouch. (I found this picture on the internet without information about the author and stuff).

A problem in retaining eggs in a pouch is that it constrains the mobility of the parent. To solve this problem, eggs could stay some time inside the pouch to get hydrated and then be removed until it were necessary to rehydrate. This could let the female free from carrying the eggs along all the time and also increase the clutch size beyond the number of eggs that can fit in the pouch. This situation would have favored those females with more cutaneous secretions.

Once the young hatch from the eggs, they could also use the secretion as a source of food, which would lead to a progressive increase in the secretion’s nutritious value until it reached the status of milk.

It makes sense, doesn’t it? It does not contradict any kind of evidence about mammalian evolution and is based on true evidence through fossils and comparison with many kinds of extant groups.

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Oftedal, O. T. 2002. The origin of lactation as a water source for parchment-shelled eggs. Journal of mammary gland biology and neoplasia, 7 (3), 253-66 PMID: 12751890

Oftedal, O. T. 2002. The mammary gland and its origin during synapsid evolution. Journal of mammary gland biology and neoplasia, 7 (3), 225-52 PMID: 12751889

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Does Retallack suffer from Williamson’s syndrome? The land-dwelling Ediacara controversy

by Piter Kehoma Boll

ResearchBlogging.orgAs you may have heard, or read, a paper published this month in Nature claims that the famous Ediacaran biota, a set of fossils from the Ediacaran Period (ca. 635-542 Mya) of the Neoproterozoic Era, is not composed by marine creatures, but rather land lichens. Who made this claim? Gregory Retallack, a geologist at the University of Oregon.

Retallack works on this hypothesis since the 1990s and the main evidences presented by him are related to geological features, like the red color of the rock, which according to him would have a terrestrial origin. Another claim is that if those creatures were soft-bodied animals, they wouldn’t have been so well preserved without compaction, as some fossils have tridimensional features.

Well, I am not a geologist and have no knowledge enough to argue about the geological point of view, neither am I an expert in the Ediacaran biota, but as a biologist I think I can share some thoughts.

First, as it seems, Retallack’s ideas are not accepted by most paleontologists. At the beginning, the innovative view of Ediacaran biota as land-dwelling was interesting, but the arguments to support it are not enough and there are still simpler and more possible explanations for the unusual features of the Ediacaran rocks. This didn’t stop Retallack to pursue in his idea, however, and other paleontologists are getting tired to go on reviewing his papers.

Does such a behavior look familiar? It kind of reminds me of Williamson, whom I talked about some time ago, as you can read here.

Just as Williamson insists in his hybridogenesis idea despite all facts pointing to other directions, so Retallack insists in his land-dwelling lichens hypothesis.

Dickinsonia would have been a land-dwelling lichen, according to Retallack. Photo by Wikipedia user Verisimilus. Extracted from

Dickinsonia would have been a land-dwelling lichen, according to Retallack. Photo by Wikipedia user Verisimilus. Extracted from

Retallack claims that fossils like Dickinsonia and Charnia, despite their bilaterally symmetrical body plan, were lichens. Does anybody know so well symmetrical lichens? And to support this hypothesis, he simply throws any kind of “fungian” explanation for all the fossils, considering the more radially symmetrical ones as bacterial colonies and the more animal-like as simply fungal fruiting bodies. And to explain things like the trace fossils, he talks about land slugs (land slugs during the Proterozoic? Really?) or slime moulds.

But then one might think: does he have any reference to support his ideas? And the answer is: of course, his OWN previous works. There are no other paleontologists claiming the same but himself. It looks just like a case of what I call Williamson’s syndrome.

I’m sure we will find some people supporting his idea, most probably laymen, and they will most certainly use the classical argument “all great scientific discoveries started by being rejected by most of the scientific community”. And I will say that again: Yes, many theories were initially rejected and later proven right, but you cannot forget that many more theories were rejected and later proven wrong. And once you prove that something is wrong or at least highly, highly unlikely, you must think of another possible and more likely explanations and not move on insisting on a fairytale.

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Cobb, M. 2012. The enigmatic Ediacaran biota just got more enigmatic. Or did it? Why Evolution Is True. Available online at < >

Retallack, G. 2012. Ediacaran life on land. Nature. DOI: 10.1038/nature11777

Retallack, G. 2007. Growth, decay and burial compaction of Dickinsonia, an iconic Ediacaran fossil. Alcheringa: An Australasian Journal of Palaeontology, 31 (3), 215-240 DOI: 10.1080/03115510701484705

Switek, B. 2012. Controversial claim puts life on land 65 million years early. Nature. DOI: 10.1038/nature.2012.12017


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Why thymine instead of uracil?

by Piter Kehoma Boll About a year ago, while I was in my class of Techniques of Molecular Diagnosis, an interesting doubt sprouted: why does DNA use thymine instead of uracil as RNA does?

I hope everybody reading this knows about nucleic acids and the difference between DNA and RNA. As a very quick review:

RNA (ribonucleic acid) is a polymer made of ribonucleotides, compound molecules made of three parts, or smaller molecules: a nitrogenous base (adenine, uracil, cytosine or guanine), a ribose sugar and a phosphate group.

DNA (deoxyribonucleic acid) is similar, but instead of uracil it has thymine, and instead of a ribose sugar is has a deoxyribose, so that it is made of deoxyribonucleotides. Another difference is that DNA is a double chain twisted helicoidally, where two nitrogenous bases (each from one of the chains) are connected. Adenine is always connected to thymine and cytosine always to guanine, so that one chain is always dependent on the other.

Currently it’s highly accepted that RNA was the first nucleic acid to exist and that DNA evolved from it, so the changes in the sugar and one of the nitrogenous bases must have some advantage.

To understand that, let’s take a look at the structure of the uracil:


The only difference between it and thymine is the presence of a methyl group at the last one:


In fact, thymine is also called 5-methyluracil. But let’s go to the explanation:

While nucleotides are synthesized, the nucleotide-monophosphates (NMPs), i.e., the set nitrogenous base + sugar + phosphate is dehydroxylated, creating 2’-deoxy-nucleotide-monophosphate (dNMPs), i.e., GMP, AMP, CMP and UMP (for guanine, adenine, cytosine and uracil) are changed to dGMP, dAMP, dCMP and dUMP.

This modification by dehydroxylation has been shown to make the phosphodiester bonds (the bonds of phosphates on the sugar) less susceptible to hydrolysis and damage by UV radiation. It assures that a DNA molecule will not be as easy to be broken as an RNA molecule, which is very useful since DNA carries all the information to build up the organism.

After the dehydroxilation of the nucleotide-monophosphates, the next step, catalyzed by folic acid, add a methyl group to the uracil to form a thymine, so turning dUMP into dTMP.

There are many explanations for that:

1. Despite uracil’s tendency to pair with adenine, it can also pair with any other base, including itself. By adding a methyl group (which is hydrophobic) and turning it into thymine, its position is reorganized in the double-helix, not allowing those wrong pairings to happen.

2. Cytosine can deaminate to produce uracil. You can see in the picture below that the only difference between them is the change from an O in uracil to an NH2 in cytosine. The problem is that, if uracil were a component of DNA, the repair systems would not be able to distinguish original uracil from uracil originated by deamination of cytosine. So using thymine instead makes it way easier and more stable, as any uracil inside DNA must come from a cytosine and so it can be replaced by a new cytosine.


This didn’t evolve for that purpose, of course. Evolution cannot predict what happens. Probably during the earliest times of life, eventually an error changed uracil for thymine and it was found to be more stable to carry information, since such a molecule wouldn’t be destroyed so easily and thus would succeed in passing its “layout” to the next generation.

It makes me wonder… Could some alien life form have found an alternative way to deal with RNA’s (or something equivalent) instability?

– – –

Main Reference:

Jonsson, J. (1996). The Evolutionary Transition from Uracil to Thymine Balances the Genetic Code Journal of Chemometrics, 10, 163-170 DOI: 10.1002/(SICI)1099-128X(199603)10:2


Filed under Evolution, Molecular Biology

Why I Don’t Trust Jack Horner 2: Why the King deserves his crown

by Carlos Augusto Chamarelli

Hey there again. After the previous article about Jack Horner’s plan to transform chickens into dinosaurs, what’s better than go back to showing contempt for his other theories? So let’s talk about his opinions regarding that one elusive theropod nobody ever heard about: the Tyrannosaurus rex.

Most specifically, about the most heinous and debated of his claims: that T.rex was so ill-suited to be a hunter that he had to live entirely of kills from other predators and was no more than a giant vulture. Understandably not many people were happy with this, and many studies since were made to verify if Horner’s claim were true. With mixed results, but not that stopped some to agree with him.

In reality he wasn’t the first to try and discredit T.rex of his predator status; back in 1917, paleontologist Lawrence Lambe concluded Tyrannosaurus couldn’t be a predator because Albertosaurus (yeah, I don’t know either) teeth did not show any sign of wear, which soon enough was pointed out as BS because theropods constantly changed their teeth throughout their lives. So T.rex continued to enjoy his status as the supreme predator he’s cracked to be and the scavenger theory was mostly left aside.

I’m not sure when Horner first proposed T.rex was a scavenger, but his opinions were already present during the early 90’s; during the production of Jurassic Park, in which he was one of the paleontological consulters, he stated that T.rex should be depicted as such. Fortunately, everybody knew better and made him a hunter like Bakker suggested, and we could see the creature in all his glory in the first two movies of the series.

You people, I don’t care if it’s outdated and full of inaccuracies; this is the only place where dinosaurs genuinely feel like they’re real things. Screencap of Jurassic Park. Extracted from

Until the early 2000’s that is, when Horner’s theory came in full power to the public. His TV-special “Valley of the T.rex” was entirely devoted to show the creature as a stinky scavenger, and during the production of Jurassic Park 3, Bakker knew better than participate of this train wreck, leaving the movie at the mercy of Horner as its sole consulter…

And from there, everything went downhill. Screen cap of Jurassic Park 3. Extracted from

As Wikipedia so nicely resumes for us, the main aspects that Horner uses to rationalize the idea of T.rex as a scavenger are as follow:

– Tyrannosaur arms are short when compared to other known predators. Horner argues that the arms were too short to make the necessary gripping force to hold on to prey.

– Tyrannosaurs had large olfactory bulbs and olfactory nerves (relative to their brain size). These suggest a highly developed sense of smell which could sniff out carcasses over great distances, as modern vultures do.

– Tyrannosaur teeth could crush bone, and therefore could extract as much food (bone marrow) as possible from carcass remnants, usually the least nutritious parts.

– Since at least some of Tyrannosaurus’s potential prey could move quickly, evidence that it walked instead of ran could indicate that it was a scavenger.

That said; let’s take a closer look at each of these points, shall we?

– Arms

Ah yes, T.rex arms. Those sorry excuses for limbs are the trademark of the king and his kin. Completely out of proportion and with only two fingers, it’s easily one of its most puzzling characteristics as many theories and no agreement exist about their real utility; ranging from a prosaic, moderately believable but ultimately flawed use like lifting his body when the animal was lying down, to the most reason defying such as picking his teeth or holding struggling prey.

At least it makes him easy to impersonate. Extracted from

But I do believe the answer is in fact quite simple, but lots of people will be outraged exactly because of that.


T.rex most likely didn’t use them for anything because, well, it didn’t need. They were in a process of atrophy*. It’s really sad that the only mention of such occurrence is usually attributed to the outdated theory of Lamarckism, with the law of use and disuse, because, in a way, that’s kind of what happens.
To understand it better: you know that evolution work by mutations, right? They occur at random in the process of reproduction, but as the model always goes, if said mutation proves to be an advantage for that individual, he has higher chances to pass on his genes for the next generations. But sometimes, things go in a different direction.

Let’s make this one model with two different species, a caveman and a T.rex.

Why yes, MS Paint & MS Word work just fine for me. Picture by yours truly.

The caveman is like your average caveman: he has two legs, two arms, a head and a big, spiked club. The T.rex, on the other hand, is actually an ancestor form which have long arms, fictionalized for the sake of the explanation**, he’s like “cool, I can grab things with these, but my mouth already does everything I guess”.

Now say that they both at some point had offspring with mutations that affect their forelimbs, making their arms dwindle and become useless. For the cavemen, this could be fatal since he relies on his hands to grab things, make tools, maybe even socializing, so the natural conclusion is that this bad gene results in a dead caveman who never stood a chance to have children. For the T.rex, his tiny arms doesn’t affect him as much, because his jaws do all the work of killing prey and fighting rivals, which means he can survive normally and pass on his “bad” genes and create an entire dynasty of short-armed dinosaurs.

Putting a magnolia flower on her head is the way to tell she’s a female. Also, poor caveman. Picture by yours truly.

In other words, if a mutation doesn’t have a big impact in the creature’s lifestyle, it probably will carry on to next generations until the whole species has it. Among some examples where this happened we can cite snakes and other legless reptiles (which became, you guessed it, legless), primitive tetrapods (which lost fish characteristics such as fins) and even us humans (which lost our tails).

Degenerated arms are not even an exclusivity of tyrannosaurids; other dinosaurs had similar occurrences, from the small, one-fingered alvarezsaurids such as Linhenykus (whose arms were more like pointed stubs) to giant Abelisaurids, the “T.rexes of the south hemisphere”, so to speak. The latter, in fact, had much more pathetic-looking limbs than T.rex.

I mean, really, what the heck, nature? Carnotaurus skeleton mount from the Chlupáč museum in Prague. Extracted from

There were also the famous terror birds, which appeared in the Cenozoic; these too were large-sized predators with beaks as deadly as their wings where shamefully small. The logical conclusion with all of this is that arms for bipedal predator dinosaurs are overrated, and the fact T.rex had tiny arms as he did is completely irrelevant as evidence for scavenging habits.

Unless you think they were ALL scavengers, but… Why would you think that? Picture by Zdenek Burian.

– Senses

Remember that one scene in Jurassic Park where the T.rex escapes and Grant has to save Hammond’s grandchildren and they stand perfectly still because then the T.rex couldn’t see them? Of course you do, you read about it everywhere how it’s bonkers because he could have smelled them: T.rex had an exceptional sense of smell, just one more of his claims to fame.

Pictured: Bonkers. Screencap of Jurassic Park. Extracted from

T.rex’s sense of smell is thought to be surpassed only by the modern day turkey vulture (Cathartes aura), which is all too convenient to Horner’s theory, right? Except having a good sense of smell is just as useful for hunting animals, as proved by modern canids and felines. “But, PK, those are mammals, we’re talking about dinosaurs! They’re closer to birds!” you might say, but that’s alright, because contrary to what many might believe thanks to the super-sniffing vultures, some non-scavenger birds do have a good sense of smell.

The majority of them use it to detect predators, but there are some species that use it to hunt prey, like the kiwi birds, whose nostrils are so long they actually go all the way to the tip of the beak, excellent for sniffing worms underground.

It is fair compare it with T.rex, right? Right? Extracted from

But even more bonkerous is the fact that, never mind his extraordinary olfaction, he COULD see them!

It’s not always apparent, because most of the time you see pictures of T.rex’s skull in profile, but if you have the chance to look at one from the front, you’ll see that the hind part of the skull is actually visibly wider than the snout, causing the eyes to face forward rather than the sides as it’s more commonly seen in dinosaurs; it’s also at a higher level than the snout, giving it a clearer view and the distinctive shape.

It’s also kinda hard to find such picture, specially one that haven’t been seen around a thousand times. Sue’s skeleton mount at the Chicago Field Museum of Natural History. Extracted from… Do I even need to say that?

Eyes facing forward are a characteristic of animals with good eyesight, such as primates and birds of prey, with the owls being the ultimate example of this; the binocular vision provided is essential for calculating distances better and maintain focused on targets. So that’s a tricky question: if T.rex was a purely a scavenger, then why did it had eyesight akin to predatory birds who are such efficient hunters?

– Teeth and jaws

Tyrannosaurids are an interesting lot when it comes to teeth. Usually, carnivore dinosaurs have slicing teeth shaped like steak knives, efficiently tearing the flesh out of the victim’s bone. T.rex, on the other had, had teeth at one point described as “deadly bananas”: they where thick and with very deep roots, which made them incredibly strong.

Those are medium sized, by the way. Extracted from

In addition, their jaws were also different: the classic model has the jaws roughly the same width; while in T.rex the upper jaw was wider, giving him the characteristic overbite appearance, which allowed him to stress bones in such a way that they could easily crack them.

On top of that, T.rex is thought to have had the most powerful bite in the dinosaur world. How powerful it was? The most recent study, released this year, indicates around 30,000 and 60,000 Newtons. To puts things in perspective, the previous study pointed up to 13,000 Newtons,  enough to crush a car. That being said, I’m not surprised if someone told me that if a T.rex and a tank were in a fight, the dinosaur would’ve won.

Once again the internet proves it has everything. Extracted from

But once again, this isn’t an indicative that T.rex was purely a scavenger, since powerful bites aren’t unique to such behavior. Think of the jaguar (Panthera onca), which isn’t one of the largest big cats out there, but even for its size it has an unusually strong bite that can crack even a man’s skull, and is the apex predator of its habitat.

Hypothetically speaking, if jaguars were to evolve into much larger species, then forms with even stronger bite power could appear. For a creature as big as T.rex, this could be one such scenario; their ancestors could be like the jaguar in size and potency, but things went out of hand and produced a big animal with an insanely strong bite, and being able to feed on bone marrow was just an appreciated bonus.

So anyways, remember that scene in Jurassic Park 3? Yes, THAT scene…

So many bad words were uttered directed at this. Screencap of Jurassic Park 3. Extracted from


The first bite to the neck would’ve been enough to kill the Spinosaurus. See, that’s one reason that makes T.rex lives up to its title: it doesn’t matter if Spinosaurus or Giganotosaurus or any other theropod was larger than him, his absurdly powerful bite would be more than able to overpower them.

But no, Horner had to have things his way and cheated by okaying them into making a Spinosaurus on steroids not care about fish and fight a sub-adult T.rex and survive a bone-crushing bite to the neck. Sorry about that little rant, but it’s all just too unnerving to see such gratuitous mockery of paleontology in one place.

SO MANY. Screepcap of Jurassic Park 3. Extracted from

– Legs and body build

Paleontologists have divergent opinions about the overall build of Tyrannosaurus; two body models commonly followed are the bulky type and the athletic type. The bulky body implies a slow-moving creature with a more limited ability to run, some might say one that would be unable to chase its prey, while the athletic body implies an active running creature.

Paleontologists who support the athletic type suggest that, despite it’s size, the overall proportion of the legs of the T.rex are more characteristic of a running animal, in other words, T.rex was very much able to catch up with its prey in a chase. So naturally this is what makes the most sense if you want to show T.rex as a hunter.

“Look, a Velociraptor!”. Sue’s skeleton again. Extracted from

My opinion? He was a bulky type.

“Say what?”

In reality, nobody is quite sure of how fast Tyrannosaurus was, but from analysis and calculations an estimative can be made, but even those don’t really support the image of T.rex running at overly high speeds as usually shown.

In a optimistic scenario, the top speed for T.rex is somewhere around 30 km/h (18 mph) at best, which isn’t terribly fast. I’ve read about some estimatives being over twice this value, but that seems more like an exaggeration to argue with Horner’s theory in the wrong direction.

Because the larger the creature becomes, the more heavily built it has to be in order to support its own weight, there’s a limit on how light the creature can be until it become too big and heavy to support itself, so a large bipedal creature like T.rex probably needed to have a solid build in order to stand in their feet. Not to mention that, in order to be able to run at the suggested exaggerated speeds, much of its body mass would have to be in their legs muscles.

Whoever, being slow doesn’t rule out the possibility of Tyrannosaurus being a hunter; he maybe just had a different approach. Instead of focusing in speed, Tyrannosaurus could be a robust creature built primarily for strength. Why would did he need to be so? Well, what manner of prey did he had available in his domain?

Spikes, spikes everywhere. Pictures by John Sibbick. Extracted from

Why, just the most dangerous herbivores ever to appear in the Mesozoic era.

Nobody can attribute speed as a quality of ankylosaurids; they had a solid build, covered in heavy armor and short legs for better standing their ground.

Ceratopsians, despite what most reconstructions tend to show, were probably very poor runners: their forelimbs weren’t even appropriate to run, (I intend to talk about this in a future post) so they probably relied more in numbers and their own weaponry for survival than making a dash for it. So if being fast wasn’t needed to catch its prey, the best option would build up endurance, and the apparent running legs of T.rex would be more like a way to trade speed for strength without being completely handicapped.

Meaning the T.rex wasn’t a creature made to pursue its prey. No sir. He was juggernaut made to stay there and fight them, and win. Somehow pure raw strength could prove to be a better strategy than speed to overcome a well armed opponent.

Suddenly this setup makes a lot of sense. Picture by Charles Knight.

While the T.rex could be injured or even killed by his prey, he could also finish it just as easily: biting the head or the backs would have shattered their bones and leave the prey paralyzed in the best of hypothesis, while just ripping a chunk could leave a fatal wound. In this scenario, T.rex’s eyes would then be an invaluable asset to focus on their prey during the fight, rather than be used during a chase. And if he ever needed to run, it would be more like walking real fast.

In a way, one can think that ceratopsians and ankylosaurus where in a mutual armed race with tyrannosaurids, each developing even more powerful weapons against each other: they seemed to be found primary where those types of herbivores thrived (i.e. North America and Asia), and their evolution is somewhat consistent with the appearance and ascension of those herbivores. Now consider this: despite the duckbilled dinosaur’s fame as widespread, they were actually outnumbered by ceratopsians, which means something must have been preying on them to keep their numbers, right?

Oc course, that’s my personal opinion, I might be wrong: there’s no evidence of ankylosaurids with signs of predation yet, but I’m not convinced absolutely nothing would attack them if given the chance, specially something with a bite like T.rex.

And to think for the longest time museums didn’t like those kind of findings because they were “no good for exhibition”. Triceratops sacrum with T.rex bite marks. Extracted from

While there’s evidence that T.rex preyed on both hadrosaurids and ceratopsians (i.e. some show teeth perforations while others healed bite marks in bones that could only be possible if the dinosaur was alive), it’s safe to assume that the horned dinosaurs were his chief prey, at least to the fully mature individuals.

While there’s no official estimative on how fast hadrosaurids could run, it’s certain that they were faster than an adult T.rex, but if it’s true that they could also hunt in packs to a degree, then it could be an explanation for this finding. Alternatively, younger individuals could have preyed on hadrosaurids if they were light built. But even more impressive seem to be the fact that something actually could survive an T-rex attack.

-Anything else?

Actually yes, there’s one more point beyond the ones listed: Energy efficiency.

Modern scavengers like vultures and jackals are allowed the luxury having this lifestyle because they’re small and can cover a large area without wasting too much energy (i.e. vultures are soaring birds, meaning they are able to maintain flight without flapping their wings).

A large creature like T.rex would be doomed to extinction if it was an obliged scavenger because he would probably run out of energy trying to locate the next meal, and even then he has to hope there’s enough left to eat and no other T.rex claimed it already, not to mention this unviable lifestyle would make their population be massively reduced in order to be able to support just a handful of these dinosaurs

So there you have it. Tyrannosaurus might not have been the largest carnivore to ever exist, but he certainly was the most powerful. Despite all those evidences, there’s a consensus among those who support the hunting behavior of T.rex that he was an opportunistic hunter. That is, while he could very well kill his own prey, he wasn’t above stealing or eating carcasses. It’s a free meal after all.

In the end, this is what the whole problem is about: Horner didn’t take in account that the evidence he used to support his theory also had explanations that indicated the opposite. Just to make things clear with the “Why I Don’t Trust Jack Horner” series: while I don’t think he’s a bad paleontologist, I do believe he’s a little misguided about his recent theories. And quite frankly, I’m pretty sure that if Horner went back in time and was face-to-face with the creature he’s sure was a scavenger, he would NOT just stand there calmly.

Thanks for reading!

* Because once the first degeneration took place, nothing would stop it from being further degenerated by a subsequent mutation.

** Early tyrannosaurids did have longer arms, but in the model the dinosaur is already in its later form to illustrate that even a sudden mutation, as opposed to a gradual one, still wouldn’t affect it.
– – –
References & Further Reading:
Erickson, Gregory M. 2005. ‘Um Sopro de Vida no Tyrannosaurus rex’. Scientific American Brasil – Edição Especial: Dinossauros e Outros Monstros.

Wikipedia. Tyrannosaurus. Available on-line in: <>. Acess on May 15th, 2012

BBC – T. rex bite was world’s strongest. Avaiable online at: <;

Science Daily- Birds Can Detect Predators Using Smell. Avaiable online in: <;


Filed under Evolution, Paleontology