Life Photo Meme: Ancient

I have lots of photos of ancient organisms, but I had to go with this picture of fossilized hadrosaur skin. First off, considering how fossils are formed, I am always impressed by seeing fossils such as these, and I am sure other feel the same way. Secondly, they offer a glimpse of what these animals may have looked like alive. Now, scientist are able to use some of these amazing fossils, notably fossilized feathers and protofeathers, and an old technique to get an even better view of what these animals looked like.

Zhang and others have reported that they are able to tell what color the dinosaurs feathers were by taking a look into the preserved parts of the cell using a scanning electron microscope. Protein pigments present in modern-day feathers and fur have unique shapes based on color, and are fairly resistant to breaking down. When these scientists looked at ancient dino (and bird) feathers, they found the same pigment shapes. Now they can tell by looking for the pigment shapes what color the feather was. What's more, by looking at the distribution of those shapes they can see if it had stripes, spots, or mottling.

I am looking forward to the new and improved museum models showing the actual colors of these amazing dinos and birds!

Things to watch...

I saw this over at Pharyngula, and thought it was the neatest thing. Many times science videos like these are either oversimplified and boring, or way over my head and boring. I was very entertained by this, and learned something new!

CreatureCast Episode 1 from Casey Dunn on Vimeo.

New Creature casts are definitely somthing to watch for. Their blog is pretty spiffy too.

Cloning mammoths?!

There's a really interesting article in November's issue of Nature. The author Henry Nicholls answers the question what would it take to clone a mammoth. This is more of an intellectual exercise than an actual doable process at the moment, but only because they don't have the entire genome of the mammoth sequenced yet.

I was very impressed with the detail and clarity of the article, it brought up questions that I never considered. When making a mammoth, figuring out the genome is a relatively easy task. It's fairly easy to read the genes, but which genes go on which chromosomes? How do you then turn that huge library of letters into a set number of chromosomes, when you have no idea what that number is? And what about mitochondria? Those organelles are not built by instructions contained in the nucleus, but are transferred from mother to offspring (in rare cases, the fathers contribute some too). Nicholls does a wonderful job of laying out the problems and suggesting solutions based on research techniques that are currently being used for other (but similar) purposes.

So if you want to know what would be involved in building a mammoth, or you are just interested in learning about some cutting-edge research in cellular biology, check out this article.

Mussels on the Move

Mussels can be a dominate organism in many rocky intertidal communities. Unlike other permanent residents, like barnacles and algae that are permanently attached to the rocks, mussels can move short distances by creating byssal threads. The byssal threads are primarily used as a means of attachment, but by creating and attaching new byssal threads and cutting lose from old ones, mussels can pull themselves along rocky shores.

People who walk around in the intertidal may notice, like the authors of a cool article featured in Science, that mussels often cluster in interesting patterns on the rocks. The authors found that the size of the clusters and the pattern of the clusters is consistent among mussel beds (with similar mussel densities), set out to determine why.

They found that if you spread mussels out evenly in the laboratory, they will spontaneously form clusters similar to those seen in the field, even in the absence of the rocky substratum and wave action found in the field. They also found that if you place mussels in various-sized clusters at the start, there is a difference in movement based on initial cluster size. Mussels in small clusters (with 2-8 individuals) and mussels in large clusters (with 128 individuals) tended to move around and rearrange themselves a lot more than medium size clusters. So, mussels really want to be in a cluster of a certain size... but why?

Large clusters have may have a food limitation. With all of their neighbors filter feeding, having to many individuals around you may limit the amount of food you can capture. When the authors squirted food in the middle of large clusters, the individual mussels were pretty content to stay in the large cluster. But if clustering reduces food, why cluster? When placed back out in the field, individuals who were not in a cluster were more likely to be knocked off by wave action.

So, individual mussel will gather together in a cluster, but when the neighborhood gets too crowded they move. By arranging themselves in the rather interesting maze-like pattern of clusters and spaces often seen in the intertidal, individuals get protection from wave action, and have a higher growth rate than densely-packed mussel beds.

Van de Koppel, J., J. Gascoigne, G. Theraulaz, M. Rietkerk, M. Mooij, and P. Herman. 2008. Experimental evidence for spatial self-organization and its emergent effects in mussel bed ecosystems. Science. 322:739-742.

Playing dead

Just read a neat paper on the heritability of death feigning and how it may be selected for in the wild by Miyatake et al. (2004). Death feigning is when a creature pretends to be dead, either by falling off a twig and curling up its legs, or by freezing, presumably to escape predation. The gray death-feigning beetle pictured above can feign death for up to thirty minutes (according to the beetle dealer). What Miyatake and the others wanted to know was, is this death-feigning ability heritable, and does it actually help them escape predation?

So they took 200 red flour beetles and recorded how long they played dead for after touching them with a stick. The 10 males and 10 females who feigned death the longest were used to start a long line, and the 10 males and 10 females who feigned death the shortest were used to start a short line. They then repeated this procedure for ten generations, allowing only the 20 longest feigners and 20 shortest feigners to reproduce each generation.

After ten generations, they found that the long line feigned death for a longer period of time than the short line did. The long line feigned death for over a minute and a half, while the short line only feigned death for about 5 seconds. They also found a difference in the numbers of individuals who actually feigned death. What they saw was 86% of the long-line individuals feigned death, while only 7% of the short-line individuals feigned death.

So now they know that death feigning is heritable and can be selected for or against in nature, but does it actually work to help save them from predators? Will it actually be selected in nature? To find this out, they introduced a predator and recorded survivorship and behaviors of short-line and long-line individuals. What they found was that the jumper spider used as a predator would lose interest in the beetle if it feigned death. So most of the long-line individuals survived (64%), and most of the short-line beetles were eaten (73%).

So if the beetles have predators in an area that act like the jumper spider, you could expect that the beetles in those areas would have long death-feigning times, but in other areas without such predators, you may expect shorter feigning times. Now all you have to do is go out and test that!

Takahisa Miyatake, Kohji Katayamat, Yukari Takeda, Akiko Nakashima, Atsushi Sugita and Makoto Mizumoto. 2004. Is death-feigning adaptive? Heritable variation in fitness difference of death-feigning behaviour. Proceedings of the Royal Society B. 271: 2293-2296

Two layers or three?

Most creatures in the animal kingdom have three cell layers; endoderm, ectoderm, and mesoderm. Mesoderm is particularly important in increasing complexity, as many of our internal organs are derived from this layer. So when did this layer arise?

To look at this question many researchers have turned to cnidarians (jellyfish & anemones), which only have two layers, to examine the developmental and genetic clues. To make things confusing, some cnidarians posses a third layer, called a entocodon, where some muscle cells reside. Also, all ctenophores (comb jellies) also posses muscle cells. Muscle cells are generally thought to have arisen from mesoderm. So was the ancestor to cnidarians, ctenophores, and bilaterians (everybody else) triploblastic (having three layers), and the cnidarians and ctenophores just lost that layer? Or was the ancestor diploblastic (having two layers) and muscle cells arose separately in all groups?

Looking at some of the genes that are commonly associated with mesoderm, Martendale et al. (2004) found that a majority of these genes are present in his model anemone, and generally tend to be expressed in the endoderm. This means that the tools for creating mesoderm was present in cnidarians, and that most likely, mesoderm arose from endoderm at some later date. However, finding the genes in the endoderm does not completely rule out the possiblity that cnidarians had mesoderm, but that it was lost at a later date.

Burton (2008) reviewed the two possibilities, diploblastic or secondarily diploblastic through mesoderm loss, and makes several excellent points based on numerous papers. First, the third tissue in some cnidarians (entocodon), is not the same genetically or developmentally as mesoderm. The entocodon arises from the ectoderm at a much later developmental time (after gastrulation) than mesoderm. Plus, genes associated with mesoderm are not always expressed in the entocodon, they are more likely to be expressed in the endoderm. So the entocodon is most likely a new cell layer and not a modified mesoderm layer.

Muscle cells found in ctenophores and cnidarians are not the same as those found in bilaterians or even to each other, however the genes are similar. Therefore, it is likely that the genes for muscles were found in the ancestors to ctenophores, cnidarians, and bilaterians and each group slightly modified those genes to get their present shape. In triploblasts, these genes along with others became associated with the mesoderm cell layer, when those cells migrated from the endoderm. Interestingly, in cnidarians the genes associated with mesoderm in bilaterians appear to be used in body patterning. So essentially, cnidarians have two sets of body patterning genes, one of was free to develop into mesoderm and subsequently, internal organs. Even cooler, (I think) ctenophore lack one set of body patterning genes, the Hox genes. Did they lose it? Or did they never have it and we are more closely allied with cnidarians? Do sponges and placazoans have Hox genes? I guess it's time for more reading!

Burton, P.M. 2008. Insights from diploblasts; the evolution of mesoderm and muscle. Journal of Experimental Zoology Part B-Molecular and Developmental Evolution. 310B:5-14

Martindale, M.Q., K. Pang, and J.K. Finnerty. 2004. Investigating the origins of triploblasty: 'mesodermal' gene expression in a diploblastic animal, the sea anemone Nematostella vectensis (phylum, Cnidaria; class, Anthozoa). Development. 131:2463-2474

Book review!

I just got finished reading Sean Carroll's Endless Forms Most Beautiful, and I thought I'd give my thoughts on it. This book is a little more complex than Your inner fish, so I would not recommend it to a complete science beginner. For this book, I think it is better to have a bit of a background in science, particularly in genetics. The book does try to use simplifying language to explain some of the genetic concepts, but I personally found it more confusing, and found my self having to stop and think about what the correct terminology was to understand it.



That being said, it is a fascinating book, that goes a bit more in depth about evo-devo. For me, I most enjoyed the talk about the genes behind wing formation, as one of the discussions I have with my students is about determining if insect wings are purely outgrowths of the exoskeleton. But even more fascinating was how all of these genes are regulated at the 'beginning'. Now the genes are turned on or off, by the presence or absences of certain proteins. These proteins are made be genes that are turned on by the presence or absence of other proteins, and so on and so forth. So what creates the gradient conditions of proteins to turn on the initial proteins?


Carroll puts for the idea that this may be due to uneven deposition of nutrients in the egg. I find this idea interesting and wonder if it has actually been looked at. Is this unevenness repeated in every egg laid down by the mother? Or caused by the first division or subsequent ones? Is there a difference in the 'unevenness' causation or how the initial genes are turned on between organisms which experience determinate vs. indeterminate cleavage?

So for me, the book was most interesting in the additional questions it raised. It also showcased just what one can do in the evo-devo field, and how that relates to variety of other disciples, including paleontology. So if you're a bit more curious about development and genetics, I would recommend this book.

Book review!

I just got finished reading "Your inner fish" by Neil Shubin, and I thought I'd give it a little review, for those of you interested in reading it.

Who it's good for: People with little to no biology background who are interested in how scientists come up with ideas and test them. Great for people who may not understand evolution and want to know a bit about the evidence for it and how that evidence was tested. Simplistic descriptions of fantastically elegant experiments, and the implications of the findings. This is an easy read, so much so that advanced junior high students would have no trouble following, but engaging enough to keep any one's interest.

For those of you with a little science background (or more than a little) this book can keep your interest too. It covers fossils, embryology and development, comparative morphology (fossil and current), as well as genetics. It integrates all of these disciplines nicely to tell the story of evolution. I found myself fascinated by the development chapter, so much so that I aim to take a course in it (or do some research, or both).

This would be a great book to use in introductory biology courses, and especially for non-major's biology courses to get at how the scientific process works, and the evidences for evolution. (Something which most non-major's courses cannot get across well)

Who it's NOT for: People who will be offended by the 'dumbing down' of science. If your picky about your word choices, or very exact in how you phrase things, don't pick up this book. Even I had to cringe over the fact that he referred to Amphioxus as a worm for an entire chapter. Every time I read it, I wanted to write in worm-like! But there is a trade-off between clarity and exactness, and for the most part I felt the sacrifices in the language is made up for by the idea that this will reach a broader audience.

The only other thing I feel compelled to note, was that this book, comprehensive as it was, did not go beyond tetrapods often. As he himself mentioned, the book could have been called 'your inner fly or your inner yeast', but rarely did he point out how invertebrate research fit in with examine the origins of our structures. But he did have an excellent list of further readings broken down by topic. I guess I'll have to look into "Endless forms most beautiful" next.

Research: Questions for colonial reproduction (corals)

Some of the talks I go to which are most interesting to me, are those which make me wonder what if. These researchers were looking at the reproductive output of corals, to see if there was a difference in egg size among the different sizes of corals (small, medium, and large) or morphology (plate and branching). They also examined how reproductive output changed over time.

They found that there was no difference in egg size due to colony morphology or size, but smaller colonies were less likely to spawn a second or third time. They did find that chlorophyll concentration of the eggs increased with increasing size of the colony. This may have been due to the fact that larger colonies were deeper down, so packaged their eggs with more zooxanthellae than the smaller, shallow water colonies.

They also found that eggs sizes within the bundles varied, which interests me because I work on maternal provisioning in a colonial animal too. I find that larvae released by my bryozoans can have up to a 2-fold difference. I am most curious to know how much those eggs varied, since most researchers ignore within brood variability. They also found that the egg sizes varied among spawning events. Generally there was a decrease in the size of the eggs on subsequent spawning events, but a slight increase in the number.

This raises some interesting questions. It would be interesting to find out if the same amount of energy is expended for each of the broods (that is does the increase in number balance the fact that smaller eggs are made). Are these smaller eggs as fit as larger eggs? Are parent colonies more willing to take a chance by producing smaller eggs, since they are assured some reproductive success with the earlier large egg brood?

Finally, if would be fun to know if this down shift in egg size (energy into eggs) is accompanied by an up shift in sperm production. Since the eggs and sperm are packaged in the same bundle, it may be relatively interesting to quantify the egg/sperm ratio. It would also be interesting to see if that ratio is different among the different sizes of colonies. It's generally easier (energetically) to be a male, so would smaller colonies increase their reproductive success by packaging extra sperm?

Original abstract:

EXPLORING CORAL REPRODUCTION IN THE FIELD: DO SIZE AND MORPHOLOGY INFLUENCE THE REPRODUCTIVE OUTPUT OF THE HERMATYPIC CORAL MONTIPORA CAPITATA (SPAWNER)?

Padilla-Gamino, J.L.*, and R. Gates Hawaii Institute of Marine Biology

Modular organisms such as corals grow by adding polyps (or individual modules). This growth is not indefinite however, and eventually colony size will be limited by extrinsic (i.e. nutrient availability, microenvironment within the colony) or intrinsic (i.e. senescence, changes in physiology) factors. Although individual coral polyps grow to full size, polyps do not start producing gametes until the whole coral colony has reached a particular size. While there have been several studies analyzing the size at which corals become sexually reproductive, very few studies have focused on the reproductive ecology of the larger colony size classes, mostly due to the difficulty in transporting huge colonies to aquaria or collecting of the gametes in the field. To better understand the relationships between size, morphology and reproductive capacity, this study examined the reproductive output (gametes) in situ of the hermaphrodite coral Montipora capitata. As this coral grows, the morphological complexity of the colony also increases. This coral is highly morphological plastic in response to environmental factors. For example in areas with lower light levels, these species acquires a more flat-shape morphology than in areas with more light (branching morphology). Gametes from different environments were collected in situ during most of the reproductive season (June, July & August). Regardless of differences in morphology and environment, colonies spawned simultaneously and had similar offspring characteristics (egg size, # eggs/bundle).

The 'eyes' have it

Three reasons why cephalopod eyes are better than human eyes (I am sure there are more):

The joining of the optic nerve bundle to the retina itself in vertebrates causes a blind spot (no photoreceptor are located here). On the other hand, cephalopod optic nerves are attached at different points along the back of the eye (not the inner layer), eliminating the need for a 'bald spot' on the retina.


The photoreceptor in cephalopod eyes actually face towards the light! Vertebrate photoreceptor face away from the light and light must pass through other layer before hitting the photoreceptor.

Another interesting design plus is that squids very rarely get cataracts in the center of their eyes. What they found was that squids, and some other cephalopods (like octopods) have two types of genes responsible for making the proteins for the lenses in their eyes. These genes have an extra insertion, either short or long insertions, (which are basically like extra instructions) that are not found in our eyes. When these extra insertions are translated into the proteins, they give extra stability to the protein so they won’t unfold. Since cataracts are caused by the proteins unfolding (making an opaque part in the lens), squids are less likely to get cataracts.

Now, the long gene produces a more stable form of protein than the short gene. The ‘long gene’ proteins are found in the center of the squid eye, while the ‘short gene’ proteins are found in the edges. This means that the center of the eye is least likely to get a cataract. You may wonder why the squid does not just use all ‘long gene’ proteins. I don’t know, but there may be some energy costs associated with making the larger more stable protein, so that it is more cost effective to use the ‘short gene’ proteins on the edges where they don’t count (hypothesis).


Either way, they are better lenses than what we have.

Another cool thing is, that each group of ‘advanced’ cephalopods has their own special version of the two genes, but they work very similarly. This stuff was very well put together; I can’t wait to read the paper on this. It will probably end up in Science, if it has not been published already!

Here’s the original abstract…

SWEENEY, A*; JOHNSEN, S.

Evolution of High-Acuity Vision in Coleoid Cephalopods

Spherical lenses with a graded refractive index design are required for camera-like vision in aquatic animals. In cephalopods, these lenses are made of a group of closely related proteins collectively called S-crystallins. Our earlier work has shown that an adaptive radiation these S-crystallin genes and positive selection on the electrostatic properties of S-crystallin proteins led to a graded refractive index lens capable of forming high-resolution images in the squid Loligo opalescens. In the L. opalescens lens, S-crystallins with high charge stabilize the optical properties of regions of low refractive index in peripheral layers, and S-crystallins with lower charge are tightly packed in the high refractive index cortex. The mechanistic link between S-crystallin sequence, biochemistry and refractive index allows us to understand in molecular detail the optical evolution of a camera-like eye in cephalopods. To understand the transition from ancestral cephalopod vision to extant camera-like vision in coleoid cephalopods, we used techniques from molecular evolution, biochemistry, molecular dynamics, optical modeling and image analysis. We sequenced 600 S-crystallin genes from most major coleoid taxa, constructed a gene tree from these sequences and analyzed it for patterns of charge evolution. We also measured the optical quality of these lenses by calculating their modulation transfer functions (MTFs). Our gene tree suggests that high-resolution lenses evolved from a low-resolution ancestor multiple times within the coleoid cephalopods. Consistent with our gene tree data, our MTF data show that there is taxonomic variation in lens quality within coleoid cephalopods. We will discuss the correlations between independent adaptive radiations of S-crystallin molecules, high acuity vision in cephalopods and possible evolutionary scenarios in which these changes in visual acuity may have been occurring during the Jurassic radiation of squid.

Development: how big is big enough?

This picture is of a fertilized sand dollar egg. You can see the dark pigment dots and the clear circle around the egg, which is the fertilization membrane, and the light smears which are sperm still trying to get at the egg. However, the fertilization membrane prevents any other sperm from entering the egg.

I read an interesting paper about development and sea urchins. A little background: there are three different developmental modes in many different invertebrate species. One is nonfeeding, where the young develop into adults using only the energy (yolk) provided by the mother. Another is feeding where the young spend more time in the larval stage feeding and that’s where they get the energy to transform into the adult. The final mode is very rare and it is called facultative feeding. In this case the young don’t have to feed to transform, but they can to get extra energy. Unlike the nonfeeding larvae who can’t feed even if they wanted to, because they don’t have a complete digestive track.

As you can imagine egg sizes for these different mode vary. Since the nonfeeding modes rely only on what the mother supplies to get to a suitable spot and change into an adult, they tend to be very large. The feeding ones are smaller, because they only have to have enough energy to create a gut, then they can feed themselves till they become an adult. The facultative ones are in between (in general). It is thought that this mode is a very unstable one, and that the species that have it are on their way from feeding to nonfeeding modes or vice versa.

What these researchers tried to do was to take a facultative feeder and force it to become a feeder by reducing the amount of energy available to the young. They did that by taking 2-cell and 4-cell stage and breaking them apart, so that one treatment had ½ the energy and the other treatment had ¼ the energy.

2-cell stage 4-cell stage

They then raised some of each type with food and without food to see if the young with less energy were eating and growing faster than those with less energy who had no food. Of course, they found that young that had not been manipulated were larger that those that had been halved or ‘fourthed’. What was interesting was that none of the size-manipulated young were forced to feed to complete metamorphosis. All young transformed at the same time!
This means that the mothers gave up to 4 times the amount of energy needed to undergo metamorphosis to their young!

For more info see the original paper: Allen, J.D., C. Zakas, R.D. Podolsky. 2006. Effects of egg size reduction and larval feeding on juvenile quality for a species with faciltative-feeding development. Journal of Experimental Marine Biology and Ecology. 331:186.197

Smells like Home (repost)

So I just got back from a great meeting, and now that my brain is functional again, I wanted to share an interesting talk that I attended. Basically, for those who have never experienced it, when you got to a meeting you get to here a ton of research, most of which is not published yet or in progress. So several days of hearing really smart people doing really cool stuff! (although it can be a mixed bag…) My brain exploded. But now that the knowledge has begun to settle…
The following is a description of some work being done by several people in Australia.

Okay, some background. Most fish have a stage after thy hatch when they float around in the water, before they get big enough to settle out. This would lead to mixing of fish, as they could potentially end up anywhere. However, when they looked at the genetics of some of these fish found on near by reefs, they found that they were very different and not mixing. This means that the baby fish are finding away to keep themselves in the area, or coming back when they are big enough to swim. But how do they know which reef is the one they hatched from?
These researchers looked at larval fish just before they became big enough to settle and tried to see if the babies could ‘tell’ their home by the smell of the water. What they found was that babies found on one reef preferred the water of that reef to any others. They also found that when they kept the babies in the different water for a time to get them to adjust to the new water, they still preferred their ‘home’ water.

Since most of these fish were brooded as eggs on the reef, the researchers were also curious to see when this smell impression was made. Were they impressed while they were in the egg or at hatching? So they took some anemone fish eggs (clown fish), which were known to home not only to reefs, but also back to particular anemones, and ran some tests. Some eggs were kept in anemone water till just before they hatched, and others were only put in anemone water when they were hatching. What they found was that the fish imprinted on the anemone, smelling water immediately after hatching, but not while they were in the eggs.

What it means is that it is possible that some of the fishes on reefs smell the water after hatching, than use the odor to keep themselves from getting too far from their home. So when it comes time for them to settle, they settle on the same area they were born in!
Below is the original abstract with the names and the affiliations of the researchers working on this. I look forward to reading the paper when it gets published.


MILLER-SIMS, V*; ATEMA , J; GERLACH, G; KINGSFORD, MJ
Boston University Marine Program, Marine Biological Laboratories, James Cook University

Olfactory imprinting in coral reef fish

Most marine organisms have a pelagic larval dispersal phase, leading to the question of how far larvae disperse. Larval behavior and odor preferences may play an important role in larval dispersal and settlement. Apogonid larvae prefer the odor of the reef on which they were caught over other reefs and ocean water. It is possible that this response is due to acclimatization to the odor of water the fish have been recently swimming instead of a long-term preference. We tested apogonid larvae settling on One Tree Island by catching them as they came onto the reef and testing their preference for water for One Tree vs. water from Heron Island in a flume preference test. We then held the fish in either One Tree or Heron water and tested them over a period of nine days. The preference for One Tree water declined in both groups over time; there was no significant difference between the animals held in One Tree or Heron water and both groups maintained a preference for One Tree throughout the testing period. Odor preferences remain stable over time despite exposure to other odors and it is possible they are the result of olfactory imprinting to the home reef odor. Olfactory imprinting has been shown in anemonefishes, but the sensitive period is unknown. Breeding pairs of Amphiprion melanopus were held either with or without an anemone. Eggs and larvae were exposed the anemone from egg laying through hatching (1), from egg laying to just prior to hatching (2), just previous to and 1 hour after hatching (3) or had no anemone exposure (4). At 15 days those larvae in groups 2 and 4 had no preference for the anemone while those in groups 1 and 3 showed a strong significant preference for anemone odor. In this species of reef fish larvae must be exposed to the imprinting odor after hatching in order to learn it.