Thursday, March 23, 2017

Art, Math, Nature and Politics

Saw a video on Facebook about this and decided to look further into it. I love that this artist combines so many aspects into her project!


Wednesday, March 22, 2017

Can stress affect your gut microbiota, and vice versa?

I found this interesting when we briefly talked about the human gut microbiota at the beginning of the quarter, so I did a little digging. Turns out there is quite a substantial amount of communication between the gut microbiome and the HPA (Hypothalamic-pituitary-adrenal axis), which is the center of the neuroendocrine system. This means that the composition of your gut bacteria can affect stress levels in your brain. Meaning a person's diet can affect their stress response.
The following article from the Psychoneuroendocrinology (yes, this is a real word- three words jammed into one) Journal explains this phenomenon in great detail.
Abstract: There is now an expanding volume of evidence to support the view that commensal organisms within the gut play a role in early programming and later responsivity of the stress system. The gut is inhabited by 10¹³-10¹⁴ micro-organisms, which is ten times the number of cells in the human body and contains 150 times as many genes as our genome. It has long been recognised that gut pathogens such as Escherichia coli, if they enter the gut can activate the HPA. However, animals raised in a germ-free environment show exaggerated HPA responses to psychological stress, which normalises with monocolonisation by certain bacterial species including Bifidobacterium infantis. Moreover, increased evidence suggests that animals treated with probiotics have a blunted HPA response. Stress induces increased permeability of the gut allowing bacteria and bacterial antigens to cross the epithelial barrier and activate a mucosal immune response, which in turn alters the composition of the microbiome and leads to enhanced HPA drive. Increasing data from patients with irritable bowel syndrome and major depression indicate that in these syndromes alteration of the HPA may be induced by increased gut permeability. In the case of irritable bowel syndrome the increased permeability can respond to probiotic therapy. Detailed prospective studies in patients with mood disorders examining the gut microbiota, immune parameters and HPA activity are required to throw further light on this emerging area. It is however clear that the gut microbiota must be taken into account when considering the factors regulating the HPA.

Tuesday, March 21, 2017

Is the Holocene Epoch over? Are we now in the Anthropocene Epoch?

So the topic I chose to talk about as you may or not have remembered was about the Anthropocene debate, whether we are in it or not. The Environmentalists make a compelling argument that the Anthropocene is the epoch that is to proceed due to all the changes that humans have caused including mass extinction of certain animals and plants. So I guess the problem is really what we define as change and how we define when a new epoch is to be called upon.

My sources include:

Monday, March 20, 2017

Tiny Toasty Mammals

Though not quite the fossils used in the study, if this dog were
to keep overheating like this for about 10,000 years, we might
start to see a smaller version of it!
     We sure do love looking at small animals, from puppies to miniature pigs to that small mouse we obsessed over in CCS bio that one time. It seems that we could be heading in the direction of smaller mammals again! You might think this is great news, but of course, it's yet another result of good old global warming. This paper by Ambrosia (2107) looks into the fossil record to find if and how mammals have changed size in the past based on the average temperature of the earth. The paper focuses on the time periods known as the Paleocene-Eocene Thermal Maximum(PETM) about 56 million years ago and the Eocene Thermal Maximum 2(EMT2) about 53 million years ago. These two time periods were chosen because they were known as global warming periods. After looking at the tooth size of various fossils found to be from these two time periods, it was found that they decreased significantly in size as the periods went on, more so during the EMT2 time period as opposed to the PETM most likely due to the fact that EMT2 was more of an extreme change in temperature. Why do we care about this stuff? Because it's super cool! Animals get tiny because it gets hot and they need to conserve and that's just wild! It's also an important aspect to look into as we get further into our current global warming period and we need to think about how it could affect the earth and ecosystems over an extended period of time. Read the study to find out a ton more and learn about cool(or hot...) science!

Life Throughout Deep Time

"The Palaeos website is organised along two themes; time, being the geological timescaledeep time, which spans not the mere centuries or millennia of world history, but millions or even billions of years, and mapping out the evolution, specifically the evolution of life on Earth; the diversity of organisms that constitute the tree of life, beginning with simple bacteria and proceeding to ever more complex forms from there, as well as the interrelations between them. There is no reason to doubt that life could also have evolved elsewhere in the cosmos, and we also explore this topic. However, most of Palaeos is devoted to a detailed consideration of the history of life on Earth. "

Vernal Pools are Really Cool! (Ha.)

Vernal pools are an interesting landmark in Santa Barbara, but surprisingly not well known. If you live in the dorms, these unique ecosystems are just a couple hundred steps away. Vernal pools are, essentially, basins that fill up and drain over time, which creates a unique environment for flora, as pictured here:

 The pools are home to many endemic species, such as mole salamanders and fairy shrimp. Due to the nature in which they form, vernal pools usually do not have any fish and are thus able to support species that would not be able to survive in other aquatic environments.

In California, over ninety percent of vernal pools have been destroyed or otherwise damaged by human activity. Thus, restoration efforts have been necessary and have helped to account for some damage. On campus, all of the vernal pools are restored and surveyed by CCBER. 

One paper compares different types of vernal pool restoration and their effectiveness and gives a more in-depth insight on restoration specifically in Santa Barbara.

CCBER Website

Sunday, March 19, 2017

Nonhuman Primate "Talk" Hints at the Evolution of Human Speech

A recent paper in Science ("Learning from monkey 'talk'") described how there are aspects of primate communication that correlate with how humans speak. One of the more interesting points discussed was how nonhuman primate babies babble in the same way that humans do, and if the parents respond to only the appropriately formulated babbles of their babies, the babies will develop adult calls much earlier. This has been seen in humans, too! 

It is also possible that monkeys do not take turns when speaking because this turn-taking is a learned behavior. This particular finding is hard to prove, however, because the two studies that looked into it had opposing conclusions, and rather different methods. Nonetheless, it's an interesting concept to take into consideration. 

Another bit that I found quite cool was how humans and songbirds both have a set of genes involved in rapid articulation and sound sequencing that other species do not. The author, Charles T. Snowden, predicts that this could be the reason for monkeys not exhibiting similarly complex speech. But in reality, we don't know why other primates don't talk as we do. Yay for the unknown!

A link to the article, if you're curious:

P.S. Sorry to post so much so late... I thought we were only supposed to post 2 times. Completely my fault. 

Cool Stuff in Wolfram Alpha

Wolfram Alpha is a great assistant to those of us suffering through tedious MATH 3B homework (so...many...integrals..), but there is a much larger wealth of knowledge and tools that are easily accessible. Some of the cooler things are locked behind Pro, like Wolfram Genomics Assistant, but a broad variety of information is available to an average user. 

Some examples:

Input Output
DNA Sequence Amino acid sequence, melting temperature, occurrence on human genome
Plant Name, image, natural occurrences (and if it occurs in your estimated location!!), distribution, detailed taxonomy
Species X, Species Y, Species Z Compares species, too much information to list

More on the sex-manipulating ferns // Adorably ugly animal distractions

"Precocious dames and nearby laggards split the job of making a hormone"

If you wanted to know more about the very sneaky sex changing female Japanese climbing ferns, this is a simple and short article about the original paper.

However, if you're stressed right now and want to look at animals that are so ugly they're cute (and find out why our brains work like this), below is a fun NatGeo article on that.

The basic idea is that they have big eyes, big heads, and soft bodies, which make us think of babies, and triggers our desire to protect them. Regardless, they're fun to look at.

Plate tectonics: now available in super Earths!

[Plate tectonics on Earth or a faraway planet?]
     Want to get away from Trump and go to another planet? Worried the newly discovered Earth-like planets won't have the plate tectonics you wanted? You may be in luck! According to a study by Valencia and O'Connell (2007), there is a possibility of plate tectonics on some super earths that have been discovered since 2007. This conclusion was reached using previous knowledge of the necessary components for plate tectonics to work as well as what is already known of these super earths.
     Some of the ways these scientists were able to determine that plate tectonics were possible is through a variety of physics concepts (some are way too complex for a person who has not taken physics, but if you have you'll understand completely, if not try your best like I did!) and basic properties of gravity, water, and plate thickness. Because we do not have complex information about the thickness of plates on these planets yet, these are simply assumptions based on the knowledge we have of their type of planet, gravity, etc. The scientists who worked on this paper determined that, because the plates are thin enough to subduct and the gravity of the planet would cause that to happen, there must be plate tectonics. This is crazy and interesting all at the same time because it brings us closer and closer to this idea that planets outside of our solar system may give us hope for continuing life on earth (part 2). The paper is really an interesting read and has a good set of data to back it up. Take a look!
(image from

For da burdz

Interesting paper on speciation from (surprise) the Pliocene-Pleistocene transition... in birds... hence the title.

Friday, March 17, 2017

Plants understand quantum mechanics better than humans do

I mentioned in class that enzymes exploit a feature of quantum mechanics called 'quantum tunnelling' in order to execute proton transfer more efficiently (see papers by Judith Klinman if you are interested, she has done lots of research on the subject and is one of the pioneers of the idea).
However, there is an even cooler example of quantum mechanics seen in plants which explains how they are so incredibly efficient (sometimes nearly 99% efficient) at using energy that they get from sun-light.

First and foremost, we must understand a bit about quantum mechanics.

A mechanical system is, loosely speaking, a system who's state evolves with respect to some parameter (usually time). So a simple mechanical system is, for example, a ball rolling down an inclined plane. If we want to describe the dynamics of this system, we have to ask the following question: what is the information about the system in its present state in order to predict how the system will evolve in the future?

In the case of 'classical' mechanical systems i.e. all intuitive/'real-world' systems such as the one described above, where we have only one object (the ball), the answer is quite simple: we need 3 numbers for the position (one for each of the x,y and z axis) and the same for the velocity in each axis. We also need to know the mass of the object for which we are trying to predict the dynamics of so that we can combine this with the velocity to get the momentum. This information gives us a definite state of the system (i.e. where the ball is right now, and what direction its momentum is pointing in) which, combined with the dynamical equation known as Newtons 2nd Law, gives us a deterministic system for which we can exactly predict the state of the ball for any time, arbitrarily far in the future or the past.

I have described this notion because firstly it will highlight the reasons why quantum mechanical systems are so different to 'classical'/normal ones, and secondly why quantum mechanics is so &$%£?!* cool!

In a quantum systems (generally described as systems that are around the nano-scale, and containing relatively few particles) there is a profound discrepancy between a systems state before and after it is observed (observed, in this context, largely just means 'interacted with by some other system' such as a measuring apparatus). Before a quantum system is measured, we do not have the luxury of knowing exactly what state the system is in. In fact, the best we can do is to have a probability distribution of all its possible states, the information that we get from this being how likely it is for the system to be found in a particular state when it is observed. What's even more strange, is that the probability distribution that we calculate seems to be a real thing, not just a convenient way of describing a system due to lack of information. What this means is that when a quantum system is not being directly observed, it is in what is called a superposition of all possible states, meaning that, for example, a particle is existing in theoretically an infinite number of places all at the same time. Then, when something decides to interact with the particle, it says 'I'd better choose a state' and arbitrarily chooses one, in concordance with the probability distribution.

Now, the biology...

As described in this video, plants receive energy from photons emitted by the sun, which hit the leaves and excite (give energy to) electrons in the chlorophyll molecules. These high energy electrons need to then bounce around from site to site to the reaction centre, where the energy from the electrons is stored for later use. However, the electrons must get there in around 1 nanosecond, otherwise too much interaction with the surrounding molecules will mean it looses its energy and the plant will die. What is more, travelling from receptor to reaction site is no trivial task - there are lots and lots (millions) of possible paths it can take and not even all of these lead to the reaction site. So, how does the electron know where to go? One answer could be that it just randomly bounces from site to site, much like an air molecule diffuses through a room by random interactions with surrounding air molecules, and eventually gets to the reaction centre. But this is certainly wrong; the immense number of possible paths that can be taken by the electron prevent it from plausibly choosing the right path even once, let alone millions of times.

So how then?

Quantum superposition of course! The excited electron exists temporarily in a state of quantum superposition (what was described above) whereby it travels every path at the same time. However, this is not sufficient to explain why the plant is so good at getting electrons to the right place - we said that when observed, a system in superposition will randomly choose a possible state in accordance with a probability distribution. This is where we see that plants have mastered quantum engineering far more that humans. The sites are arranged in such a way that, when the electron is in a superposition of all possible paths, the overwhelmingly probable path is the one that takes it right to the reaction centre! If you havn't realised by now, this is incredible stuff. It also shows that evolution acts not just on the macroscopic and microscopic range, but also in the real of quantum mechanics. There are some far more profound implications of this mechanism, though they cannot be properly understood without a minimum of knowledge about quantum mechanics.

I would recommend this book to those who are curious. It describes the presence of quantum mechanics in biological systems and is written so that even those who have no prior knowledge of either subject can understand. I can personally recommend this book very highly.

Quantum Biology is an emerging field and is absolutely incredible from both the perspective of a physicist looking at how quantum systems can be used to make remarkable mechanisms, and also from the perspective of a biologist looking into just how specialised organisms are. It can also potentially give us measurable statements about life's origins and how DNA/RNA can play an informational role in biological systems, among other things to be discovered.

Tropical Africa + Climate Change Records + Evidence Found in... Ice Cores?!

Ice cores may not be what you were expecting to use to find climate change evidence in tropical Africa, but alas, they have been an amazing new discovery. A great enough discovery, in fact, to be published by Science magazine. (Dang). 
Six ice cores from Kilimanjaro were used to show climate change in the Holocene in eastern equatorial Africa from roundabouts 11.7 thousand years ago. In analyzing the ice cores, it was discovered that there were 3 periods of abrupt climate change during the Holocene, and the last one happened to coincide with the "First Dark Age," or the greatest recorded drought in tropical Africa. What's amazing is that the longest cores that were drilled were only about 50 meters long, yet they held thousands of years of history within them. 
Isotopic enrichment indicates warmer conditions, and reduced concentrations of major aerosol species (Mg2+, Ca2+, SO4 2–, and NO3 –) indicates wetter conditions, and these were prevalent from about 11 to 4 ka. So, there was still ice being formed during the African Humid Period, which occurred during this time and with these conditions. Then, at about 6.5 ka, there was an abrupt 18O depletion in the ice records, which indicates a cooling event. This could have altered the environment significantly (which makes sense). The third abrupt event is seen by a dust layer within the ice, which appears to have been deposited at a very dry period in time. (This supports the reference to the drought, or the "First Dark Age"). 
This has been such an interesting resource to study climate change; however, if the current climate change continues, this ice will most likely melt and we will lose this tool to analyze history. 


It seems that Brain-Computer interface has been exclusively a feat of science fiction only (or the latest season of Black Mirror which is a fantastic forward looking show for those who havn't seen it already - but I cant write a post about this...). However, this paper details the research of a group who are trying to have basic communication with people who are 'locked in'. This term refers to people who are suffering from "complete motor paralysis but intact cognitive and emotional processing"; so are, in more dramatic words, stuck in their brain. The group found that when measuring "hemodynamic responses associated with neuronal activity" that they could successfully communicate with ALS patients who had reached or almost reached this state of 'locked in'. The questions were personal in order to avoid some false positives etc. Soon we will be putting our brains in a chip, the future is here...

Interactive Tree of Life

Found this pretty cool web-app that is an interactive tree of life showing common ancestors/how many species have a particular thing as their common ancestor. Its Nicely comprehensive and slightly like a fractal as more and more branches arranged in a similar pattern become visible the more you zoom in. In fact, it seems almost infinite (I've zoomed in quite a bit and am yet to find the end...).

Here's the link

Have we entered the Anthropocene Era?

Hi all, here's a short summary of what the Anthropocene Era is all about. This idea become popular around 2000 and is currently the topic of heated debate between geologists and environmentalists. The Anthropocene Era is, in short, a proposed new era that the Earth has entered, after the Holocene (which started about 12,000 years ago after the Paleolithic Ice Age), due to the large impact that humans have had on the planet.
There are four proposed start-times of the Anthropocene Era, should it exist:
I) The beginning of modern agriculture, domestication of animals, and large-scale deforestation.
II) The colonization of the Americas and intercontinental exchange of species.
III) The ~1800 CE Industrial Revolution
IV) The "Great Acceleration" of the mid-1900's, when population size increased significantly, the most accepted beginning of the Anthropocene.
The Anthropocene is marked by severe changes in the Earth's atmosphere and stratigraphy (which is very important in the definition of an Era, according to geologists) due to the following factors:
-Technofossils such as aluminum, concrete, and plastic. Plastic takes a very long time to decay, so it is sure to produce lots of fossils.
-Pesticides and fertilizers lead to higher nitrogen and phosphorus concentrations in the soil, causing a lack of oxygen more severe than the rest of the Holocene epoch.
-Fossil fuels disseminating black carbon.
-Mass extinction of plants and animals around the world.
Here's a link to read more!
Image result for anthropocene era comic

Metabolism before life even came about? What??

Here's an interesting article about the possibility of the Kreb's cycle having begun before life itself had evolved. This alternative to the currently accepted "RNA came first" theory questions how RNA could have evolved before the Kreb's cycle if it needs metabolism in order to be created in the first place. Also, it seeks to address the lack of pressure RNA would have had to evolve enzymes, if it did not metabolize. The original paper is cited at the bottom of the article.

Just when you thought designer babies were a thing of the future...

The concept of designer babies has been a hot topic for quite some time, ever since we realized we would one day have the technology to engineer human beings. However, this has mostly been a moral debate of what we would do "when that day comes." Well ladies and gentleman, it seems that "that day" may be upon us, arriving earlier than at least I had expected.

Just about a week ago, on March 9th, the UK granted Britain's Newcastle University scientists a license to use DNA from three people to create babies. You may be wondering: why would they do this?? The idea is to keep women with mitochondrial diseases from passing them onto their fetuses. Scientists take the nucleus of an egg from the prospective mother and insert it into an egg from the donor, in which the nucleus has been removed and BAM! no mitochondrial disease is getting passed on to that fetus!! However, it looks like UK scientists aren't the first to try this. Last year, doctors from the US announced that they successfully created one of these babies in Mexico where the practice is legal.

The creation of these babies raises many ethical questions and has already sparked much debate and controversy. So you must ask yourself: Has science gone too far? Are these really designer babies? Are we playing God? And even if we are, at what point do the moral costs outweigh the benefits to human health and well-being?

Thursday, March 16, 2017

Rhizophora mangle and Cassiopeia

What is Rhizophora mangle, do you ask?
Why it's the red mangroves, of course! If you couldn't already tell that I am mildly obsessed with mangroves, here's your chance to be in on the secret. They're genuinely the coolest. I had the opportunity to travel to the Florida Keys (Big Pine Key, to be specific) a while back, and since then I've been hooked.
So what's the deal with these mangroves? They grow as aerial prop roots, and their roots form almost a weblike structure that catches sediment, creating GREAT nursing grounds for juvenile fish and other organisms.
One of these organisms happens to be the Cassiopeia jellyfish, which can also be recognized as the "upside down jellyfish." It, as suggested, lives floating seemingly upside down. When I was in the Florida Keys, I was able to wade out to one of these mangrove islands and pick up the baby jellies without them stinging me. How rad is that?! Some of my friends picked them up and had their skin irritated, though. Anyway, that was interesting to me, so I found this fascinating paper about a plant that is used to treat inflammation due to the venom of various types of jellyfish, one being the Cassiopeia.
Jellyfish toxins can cause proteolysis, "the breakdown of proteins or peptides into amino acids by the action of enzymes," as well as haemolysis, "the rupture or destruction of red blood cells." In this paper, the plant, referred to as IPA, was tested to see its effectiveness in treating both of these factors. While it was found that the plant neutralized the affect of all factors, the study also found that Cassiopeia jelly toxins only have haemolytic activities, and they lack proteolytic properties. Could that be why my friends and I were able to pick them up without being severely stung? Maybe I'll have to do an experiment to find out.

*I'd like to note that we were told by the scientists at the Marine Institute that we could pick up the jellies. We didn't just grab them willie nillie.*



These are hydrothermal vent shrimp from the Mid-Cayman rise, and they are super cool. They like to aggregate near the top of the vent. I also really enjoy the commentary that goes on in this video. What's cool about these vents (those found in the Caribbean) is that talc, a silicate mineral, is found abundantly. Many other vents tend to be more sulfur-laden, so it's interesting to see the variety of mineral/chemical composition due to the location of the vents.

Sexually Frustrated Fruit Flies Drink Their Pain Away

This study shows just how much insects have in common with us. It seems that fruit flies, with their notoriously simple brains, have the "ability" to consume alcohol as a coping method. Researchers placed male fruit flies female fruit flies together, and observed which males scored and which males got rejected. Afterwards, the males were given two food sources. One food source was soaked in alcohol, and the other was just ordinary food. Researchers expected that all fruit flies would prefer the alcoholic food, since alcohol is known to produce reward chemicals even in the brains of insects. What they found, however, was that fruit flies that had mated would generally avoid the alcoholic food. In contrast, the lonely rejected fruit flies would all flock to the alcoholic food. While the results don't translate directly to human behavior (alcohol consumption in fruit flies is mediated by a chemical called NPF, while no such mechanism exists in humans), it is interesting to see how such a specific (and unhealthy) behavior is found in such wildly different organisms.

Wednesday, March 15, 2017

Hagfish because why not

I recently came across an article about the Hagfish's ability to survive on land due to the fact that their FOUR hearts don't need continuous oxygen to keep pumping. On that note and the fact that I am currently in Deep Sea Biology (a class I highly recommend to anyone regardless of their interests, the deep sea is a crazy place), I felt we could all do well to be graced with 10 cool Hagfish facts that I have come across:

1. They live as deep as 1700m!!!!
2. They have four hearts. The brachial heart serves as the main vessel and three others serve as accessory pumps.
3. These hearts don't require constant oxygen in order to continue to pump which is an advantageous adaptation for the fact that....
4. They feed on decomposing organisms and are often found at the sites of whale falls and other large organisms. Burying themselves inside a dead carcass often causes hypoxic conditions that they can thrive in thanks to...
5. Their extensive capillary system within the skin that provides oxygen to the body while in hypoxic or anoxic conditions.
6. When under stress from predators, Hagfish expel a thick, slimy mucous from hundreds of glands along their body. This slime clogs the gils of predators and suffocates them, in addition to making them very hard to hang on to.
7. They avoid getting suffocated by their own slime by sneezing (yes sneezing) and tying themselves in knots that shield their gils and mouth from the slime.
8. They have incredibly slow, anaerobic metabolism and as a result can go months without food, which is good because population density is very low in the deep sea and they often rely on organism falls for a meal
9. Fossils that date back 300  million years ago suggest that the Hagfish hasn't changed structure much
10. They're boneless but have a brain!! They lack a spine but instead have a notochord, a structure that is later replaced by a vertebral column in all chordates but Hagfish and Lamprey once maturity is reached.

Footage of a whale fall (all of the squirming eel-like creatures are Hagfish eating their way into the whale)

Blue-footed boobies are most known for their mating dance, but did you know food storage influences sibling aggression among their young? Also, young chicks are only fed until after the oldest/biggest chick is full.

Siblicide is a term that is used when an older chick kills the other(s) to obtain more food for themselves. For example, like the Sand Shark embryos that eat each other in the womb.

To learn more visit:

Would you ever pop a pill made out of someone's poop?

Some people today use them for agriculture, but they might be of use to people who suffer from obesity or other certain metabolic syndromes.

To learn more visit:

Want to improve memory by taking ginkgo extract?

Extract of ginkgo leaves is usually considered as a supplement that can improve memory. Actually, scientists in UCLA once published a research, which showed that extract from ginkgo may improve people's memory that extract of ginkgo can significantly improve memory by testing verbal recall of people who were tested in study. Click here to explore more information. However, recently, American Academy of Neurology published a research about ginkgo's effect on improving memory. They started a 3 years' long study, involving 118 people, and finally they found that difference between people who took ginkgo versus the placebo was not statistically significant. Also, University of Hertfordshire published a paper to find whether taking ginkgo extract can improve memory via meta-analysis, and they found "zero impact on the cognitive functions whatever the age of the people". 

Click here to read the full paper.

Tuesday, March 14, 2017

Aquatic Angiosperms - Underwater Flowering Plants

It turns out that some angiosperms felt homesick after a couple hundred million years of being away and decided to go back home to the ocean (I guess they felt like Moana). For a type of plant so specialized for life on land (e.g. sophisticated water transport system, seeds, negating the need for water for reproduction to occur via the development of pollen) it seems strange that they would return to the environment from which they differentiated so greatly from. This of course poses many challenges as many of the adaptations to life on land would prove detrimental to life in the sea, being submerged in water among other things.

I particularly wondered how they overcame the challenge to reproduce underwater - how did the plants undergo pollination in the water? The concept seemed a bit strange, especially considering how water is a lot less dynamic than air, particularly in stagnant or low flow water conditions - the pollen either never being disrupted for dispersal or just sinking to the ocean floor. The answer though is quite simple.

Negating the more complex fluid dynamics description which I do not comprehend very well, the underwater plants pollinate basically by... drum roll please... water pollination (aka hydrophily). Initially, I was expecting something a little more involved. Water pollination is somewhat analogous to the wind pollination that occurs on land between plants. In particular, grasses tend to wind pollinate. Can you guess what type of plants tend to water pollinate? Sea grasses.

Water, however, transports pollen grains somewhat differently than air. This has led the sea grasses to evolve some particular mechanisms to help maximize pollen and stigma contact events. Some pollen grains of sea grasses have lost their outer thick layer known as the exine which the absence of may help the pollen grains stick to and wrap around the stigma more often and efficiently. The plants may also grow in particular patterns which maximize pollen distribution and encounter events, some literature describing regular spacing between the plants that essentially creates a concentration gradient of pollen down the row of plants. The sea grasses have also been observed to occupy different areas relative to one another, shallow and deep sites, which can also help maximize pollination.

Something really cool also happens on the microscopic level. As current flows through the sea grasses, carrying pollen, there is a reduction in the speed of the current carrying the pollen as it approaches the flower arrangement (which is postulated to be because of the extension of the stigma outwards), disrupting the flow. This reduction in speed is thought to help direct pollen grains to  the stigma, acting similar to a filtration device. The reduction in speed may also make it easier for the pollen grain to stick to the the stigma.

Of course, other aspects of these plants have changed as well, many have lost their UV protecting pigments and adapted their light capturing systems to be more efficient for the differential availability of light underwater as opposed to that on land. Sea grasses have also lost stomatal genes and regained some lost abilities/functions such as the ability to live submerged and in a high salinity environment.

If you want to read more about all this, you should visit:

Bitten by a spider? You're probably wrong!

Whenever I talk about spiders with people (as one often does), about 10% of the time someone will bring up an anecdote about waking up with spider bites. I'm sure many of you have heard such stories as well, or maybe see yourselves as victims of spider bites. However, unless you actually saw the spider bite you, what you assume to be a spider bite is probably anything but. As this article perfectly explains, most reported spider bites turn out to be false alarms, and even genuine spider bites are usually no cause for panic.
Some highlights:

  • Out of 182 SoCal patients who claimed to be spider bite victims, only 3.8% were actually bitten by spiders
  • 85.7% of the 182 patients turned out to just have infections
  • Bedbugs, fleas, irritating plants, and allergies are also frequent culprits behind mistaken spider bites
  • Out of about 40,000 known spider species, only about a dozen are known to be dangerous
  • Benign spiders are frequently mistaken for black widows and brown recluses, and even the genuine individuals are not prone to biting
  • Overall, spiders are helpful creatures that should not be regarded as threats. Think of them as little friends who can give 4 times the hugs!

Alliteration of the Day: First Fluorescent Frog Found

Until this was published yesterday, florescence was unheard of in amphibians, which begs the questions: how many more frogs are capable of fluorescing? What is the evolutionary advantage of glowing?

If you're interested, here are some of the particulars about the article (originally published in PNAS and talked of in the "News" portion of Nature):
  • The South American Polka Dot Tree Frog was originally hypothesized to be capable of fluorescing in a soft red tone because of its transluscent skin and a pigment called biliverdin, which is known to tint the tissues and bones of amphibians green.
  • This is not bioluminescence, meaning that the frog emits this bright green glow only when ultraviolet light is shone on it
  • The strength of this emitted light might be enough for the frogs to see by 
  • It is possible that many other tree frogs with transluscent skin also carry this trait

Monday, March 13, 2017

Another mechanism to evole?

We have learned several mechanisms that can promote evolution in a population, but that's it? There is no other mechanism that can change frequency of allele in a population? The answer is positive. According to a study by Uppsala University in 2009, scientists found a special mechanism related to evolution. Interestingly, some genes in our body evolved rapidly. In other word, the speed of evolution in our DNA is different, and scientists found that there is a process called BGC ( biased gene conversion) speeds up changing of our genes, partly. Specifically, there is a trend that AT pairs will be substituted by CG pairs. It happens in everywhere, even in DNA that won't be expressed. Thus, BGC is a special mechanism that contribute to human evolution, and can cause harmful mutations and spread them to whole population.

Click here to read original material.

Fish Otoliths and Ocean Acidifcation, or A More Straightforward Train of Thought

When we were talking about tree rings, I immediately thought of fish otoliths, which are small ear bones that have rings corresponding to growth (See? This train of thought was much more straightforward than the one from my last post). There is an undergrad in my lab who is using these as part of her project about fecundity and parasite load, but I didn't know much about them other than that they can be used to tell a fish's age. I found this paper, which was interesting to me because everyone always thinks of coral reefs when ocean acidification is mentioned, but it affects so much more than that. It's a very brief paper, so I hope you enjoy it! (As a side note, I purposely did not elaborate too much on this topic because I will be presenting on it on Thursday.)

I Can't See It

Did anyone else ever play with those transparent jelly-cube things that completely disappeared when you put them in the water? I think they're called ghost crystals or something. Anyway, this animal is a living ghost crystal and before you ask, it's NOT a jellyfish. Check it out:
This is actually a Moray Eel. In their larval stage (I didn't even know anything other than insects had larval stages) they're almost completely transparent. They're rarely ever seen and after watching this video, I understand why.

You can read the full article here

Logistics of Strasburger's Tree-in-Vat-of-Poison Experiment

Ok, I had SO many questions about this experiment. What could have possibly possessed him to put a MASSIVE tree in a vat of poison??? Why did he need such a big tree? Why didn't he just use a smaller plant? How the hell did he even get it in there? How did he keep it from falling over? What was he trying to test??? Why, just why. In retrospect, his experiment actually makes much more sense (except for the 60-foot tree part, WHY???), however, with knowledge of how plants work (or rather the lack thereof) at his time, it’s much harder to understand the logic behind Strasburger's experiment. 

Obviously, I wanted to read his original paper (particularly the methods section) but it turned out to be surprisingly hard to track down. I checked his Wiki page first, but unfortunately, there was no mention of the vat of poison experiment. I eventually found a textbook ( talking about Strasburger's experiment in more detail (ironically not his own). This was the figure accompanying the description:

(click on it to see it better) (

There are several alarming things about this figure. First of all, treeS, PLURAL, AS IN MULTIPLE TREES! Good god was one tree not enough??? Secondly, these trees were apparently all 21 meters tall (68.9 feet). Those were HUGE trees (were being the operative word here). So many things about this are alarming. Where was he getting these trees? He definitely didn't grow them because that would have taken forever. Did no one care he was taking these massive trees? Did he poach them? How can you discretely steal a 70 foot tree??? How did he even move it? I'm imagining a slightly crazed scientist sneaking out to the local park in the middle of the night armed with a saw and his PPE, cutting down the largest tree he could find, and bodily dragging his kill back to the lab. This is most definitely not how it went down, there's no way in hell anyone could drag a tree that big, but for some reason this is just how I imagine it happening. Thirdly, the trees were saturated up to 20 meters with poison. That's a LOT of poison. I find it slightly alarming that poison appears to have been so readily available in such massive quantities. Perhaps the most alarming aspect of this figure is its label: Strasburger's great work. Just let that sink in. Check this guy's Wiki page, ( it describes him as, I quote: "a Polish-German professor who was one of the most famous botanists of the 19th century." How is killing trees with vats of poison considered the great work of a man who was considered one of the most famous botanists of the 19th century???

Despite raising more questions than it answered, the textbook did give the name of Strasburger's original paper: On construction and function of the conduits in plants - 1891. Overjoyed, I immediately put it into Google Scholar. Nothing. Not dissuaded seeing as it was published in 1891, I repeated the search in normal Google. I found it but was greeted with my first obstacle: the paper wasn't a paper, it was a 1000-page book. Still determined to find my answers I clicked on it anyway and was greeted with my second, much less surpassable obstacle: the entire thing is in German. The actual title is Über den Bau und die Verrichtungen der Leitungsbahnen in den Pflanzen. I still really wanted to find the answers to my questions but because the book is so old, there doesn't seem to be any pdf versions of the text or translations available.

The entire text is available through Google Books ( If anyone can read German PLEASE tell me how he obtained and moved the trees, where he got all the poison, and what his original question actually was.

Datura and the Chumash

We talked briefly about Datura, or Angel's Trumpet, in class and Gil posted about how dangerous it can be if ingested, so it might come as a surprise that Datura used to be a central part of Chumash culture and was used by almost all Chumash people. For those of you who haven't heard of the Chumash, they were a large group of Native Americans that lived in the Santa Barbara area and Channel Islands for almost 13,000 years before European contact. Naturally, they had a long time to become familiar with native plant species, including Datura wrightii which they called momoy. It was used for both spiritual and medicinal purposes. At puberty most boys and girls would be given Datura during a ceremony in which they would fall into a coma for about 24 hours a would hopefully wake up having gained a supernatural guardian to protect them throughout their lives. In Adulthood, Datura could be used whenever someone felt it was necessary: to gather courage, for protection, to contact the dead, or to gain insight into the future. It was also used as an anesthetic, a poultice treatment for hemroids, and even to get rid of tapeworms. The Chumash were very aware of the dangers of taking  Datura, but trained specialists/shamans could pretty consistently prepare doses strong enough to have the desired effect without killing the person taking it. Luckily, if you did die it was believed that those who had drunk Datura would have the strength of spirit for their soul to journey to Similaqsa, the Land of the Dead, rather than falling into the ocean and becoming a frog, turtle, snake, or fish.

Most of this info comes from Chumash Ethnobotany by Janice Timbrook. It's a cool book I would definitely recommend it if you are interested in learning about Santa Barbara's native plants and how the Chumash used them. Also it has lots of pretty watercolor illustrations!

The closest living relative of what???

I was on National Geographic's snapchat story a few days ago and saw these adorable little guys staring back at me:


They're called Rock Hyraxes. The reason you haven't seen them running around campus (or anywhere else in California) is because they are native to Africa, living in rocky scrubland throughout the majority of the country. They live in groups of around 25 and create burrows they spend the nights and excessively temperate parts of the day in. They have trouble maintaining their body temperature in the extremely variable climate of the African shrublands reaching up to 120ºF during the day but dropping to 20ºF at night. They spend most of the day sunbathing and huddle together when it gets cold at night. They are also extremely agile and have rubber-like pads on their feet, enabling them to scale even super steep, smooth rocks.

As cool as all that is, it's not even the best part: guess what their closest living relative is??? I could probably give you ten-thousand guesses and elephant probably wouldn't be one, but that's the answer. These guys are larger than they appear in the pictures, reaching about 1 to 2 feet in length and 10 lbs, but elephants??? That's just insane!!! Obviously, I wasn't going to believe something so outlandish off the word of a snapchat story, even if it was National Geographic's snapchat story, so I looked it up. As it turns out the elephant's closest living relatives are the hyrax and sea cows (eg dugongs and manatees), both of which are quite surprising. I can kind of see the resemblance between elephant's and sea cows, but hyraxes look like very strange, adorable rodents.


You can see their tiny pseudo-tusks in this significantly less cute (still adorable though) picture:


Here are more pictures

(all from

Check them out for yourself at and

Update: global warming Is still screwing up the oceans!

     In case you were still doubting the effects of lovely global warming, here's just another thing it's doing to our beautiful earth. In a recent study published on ( it was found that the oceans are actually losing oxygen content. This is caused by the increase in temperature of oceans which decreases oxygen solubility and, therefore, oxygen content available to organisms.
      It currently seems to be about a 2% overall decrease and even 4% in some areas and is predicted in the study to decrease by 7% by the year 2100. "That's not such a big number!", you might say. You'd be wrong in saying that. Even a 2% decrease in oxygen levels can throw off an entire ecosystem and keep large organisms like sharks, which need more oxygen, from succeeding in their environment and may force them to move to other areas. This clearly poses an issue for the balance of ocean ecosystems and is yet another reason to attempt to decrease our carbon footprint on earth. This issue could raise future evolutionary research as well on how species may evolve to survive using less oxygen, or even split off from a low oxygen environment to populate an area with higher oxygen levels and change the ecosystem there (like the happy rafting lizard).
     Reduce, reuse, recycle, save the ocean oxygen levels.
(Originally found through

Sunday, March 12, 2017

Caterpillar playing chemical trick on corn plant

The fall armyworm larvae leave frass(which I assume is poop) behind while eating the plant. There is a certain compound in their frass that deceives the corn plant. It induces the plant into "thinking" that some pathogenic fungi or bacteria is attacking it; thus, the plant will turn on their defend mechanism for these micros. The important fact is that corn plant could only switch on one defend mechanism at a time. So if it is defending micros, it can't defend against the larvae. I think this is quite an amazing attack that evolved over time. Time and time, nature develop some amazing stuffs to show the world what she is all about!

Birds, like plants, are weird

This is a weird bird. More precisely, it is an bilateral gynandromorph, which essentially says that somehow, cells on one side said "let's be male" and those on the other side said "let's be female." This leads to a ZW/WW chimera that appears female on the ZW side, and male on the ZZ side. Furthermore, the "ova-testes" contain a mix of ZZ and ZW cells. Interestingly, this only occurs on the longitude of the bird, likely because as an embryo forms, cells divide and their daughters tend to be on the same side as they were, leading to half of the cells arising from one of the first two cells. If there is an error in that first division, that can be seen as one half of the mature organism having the error phenotype.
So what kind of life did weird bird live? Well, it lived in Rock Island, IL and ate out of this guy's bird feeder. It was never observed to have a mate or singing and was generally ignored by the other birds. Then the guy whose bird feeder it was never saw it again one day. Which, in my opinion, is a little sad. :(

More reading!
bilateral symmetry:
sex determination of somatic cells in chickens:
the life of weird bird:

Saturday, March 11, 2017

Mycorrhizal Fungi Affect on Plant Growth

During a past lecture, mycorrhizal fungi was very briefly discussed. This is a type of fungus that forms a symbiotic bond with the roots of plants. The fungus will colonize the root system of a plant and provide it with increased nutrient and water absorption, while the plant provides the fungus with carbohydrates produced from photosynthesis.
I became interested in how plants were affected by different mycorrhizal fungi. I found a paper written by John N. Klironomos, where he tested the mycorrhizal fungi's affect on plant growth. He used different mycorrhizal fungi sourced from different locations with their own unique affects on plants and placed them into the roots of one species of plant from one location to observe the different affects of each type of mycorrhizal fungi. His findings were quite interesting. If you are interested to read his paper, a link is provided below.

Link for Paper:

Male and Female - Why?

In class we talked briefly about anisogamy - a condition where gametes are dissimilar, often one being small and motile while the other is very large and lacks motility (sometimes known as oogamy). Understanding why this occurred and the mechanisms behind it would essentially explain why gender exists - and why it has taken on the forms that we recognize today.

There are actually many theories which attempt to provide a mechanism for the evolution of anisogamy. One theory suggests that there are selection pressures which favor high gamete encounter rates (more encounters = more offspring = higher chance of passing genes on to next generation, etc). It turns out that encounter rates are maximized between gametes when one gamete becomes smaller and one larger - an example of disruptive selection, favoring both large and small gametes but not those of intermediate size.

Another argument that John brought to my attention is one that postulates that anisogamy is related to the origin of our organelles by endosymbiosis. Other arguments wrestle with ideas such as a possible pathogenic selection pressure for anisogamy, the uni-parental inheritance of mitochondria as a result of some selective pressure for this situation which may have also been a major driver to anisogamy, and some theories that simply attribute the evolution of anisogamy to the higher fitness of a larger zygote that would be formed from a larger egg.

When you get down to the core of things, it's actually pretty funny how one might truly define gender. One could simply say that the only difference between one gender and the other is found in regards to the motility of their gametes - one of us "likes" to swim around while the other "prefers" a more stationary lifestyle - but I really shouldn't attempt to personify gametes. While many people like to form a firm distinction in regards to what it means to be male and female, the true fundamental differences aren't really that divisive. 

Here are some links if you want to look into this stuff further:

Friday, March 10, 2017

Feeling sleepy? Stressed? Eat some garlic!

A recent study suggests that prebiotics, which serve as food for probiotics (the good bacteria in your stomach), can improve sleep quality and tone down some physiological impacts of stress. Prebiotics are a type of dietary fiber found in chicory, artichokes, raw garlic, and onions. The experiment, lead by Robert Thomson at the University of Colorado Boulder, showed that rats that were fed diets high in prebiotics spent more time in the deep, restful cycles of sleep (NREM) than rats not given prebiotics, especially after exposing the rats to stress. Read this article from Science Daily to learn a little more, or, to learn a lot more, read Thomson's full paper here.

Thursday, March 9, 2017

Bacteria's "Lag Phase" to Teeth in Amphibians

I chose this topic for the blog because it was so tangential to what we actually discussed in class, and that really amused me; I actually found it pretty fun. 

This paper (doi: 10.1111/j.1558-5646.2011.01221.x) describes the "re-evolution" of  teeth in amphibians, and the topic that led me here was the "lag phase" that bacteria can enter to survive until the condition of their habitat is more survivable. I got to this paper through the following process:

1) This "lag phase" is similar to encysted parasites.
2) I researched parasites last week.
3) It's also similar to the "hibernation" of the amphibian in Walking with Monsters (a really enjoyable documentary-type film that I highly recommend, especially since we've been talking about different geological eras and the organisms that lived during them).
4) This amphibian was a Labyrinthodont (it took a bit of digging to find this).
5) There are many papers on Labyrinthodont ear structure and some on their jaws.
6) One of the related papers was about the "re-evolution" of teeth in amphibians.

Thanks for staying with me through that process, and I hope you enjoy this paper!

3D Coral Models!

If you throw your mind back to the CCEBR tour that we did, you may remember talking about databases full of information/pictures/models of various organisms. The Hydrous is an organization that houses 3 dimensional models of corals. This organization is still in its infancy, and is not quite as scientifically oriented as other databases are. Rather, The Hydrous tries to allow people around the world to have interactions with corals, in the hope that this will encourage people to protect it.

Still, the 3D models of the corals are quite cool to look at. The website is a bit vague when it comes to describe the method of making the models, but it does say that it is the result of stitching together underwater photographs and the use of some sort of software. Thus, it is a way to garner characteristics (such as the mass) of the coral without killing it, which is an exciting prospect for marine conservationists. These digital models can also be used to create physical models with a 3D printer.

The Hydrous is also working on the potential educational opportunities that this kind of software provides. As their end goal is to bring more people to interact with the ocean, they are currently working on three virtual reality products that will launch in 2017. The first of these is a virtual reality experience that uses a headset, the second is a virtual reality video of a whole dive, and the third is an exhibit of sorts, with 360 degree video, audio input, and 3D coral models that people could come and interact with.

If you wanna check out some of the 3D models, their collection can be seen at

They also have a website:

Wednesday, March 8, 2017

Agent Orange and its associated diseases

Agent orange is criticized for controversy about causing birth defects, particularly by the chemical 2,3,7,8-Tetrachlorodibenzodioxin. However, as recent report Veterans and Agent Orange: Update 2014 categorized birth defects as "inadequate/insufficient evidence" to determine an association. Nevertheless, these follow two diseases and couples other ones are positively associated with agent orange.
 Hodgkin's disease

Tuesday, March 7, 2017

Walking Frogfish??

Soooo in the spirit of evolution this quarter, here's a really cool organism that has both evolutionarily modified skin and pectoral fins, both which are thought to be mimicry adaptations. Frogfish, part of the family Antennariidae are diverse in color and often physically mimic other organisms. Their modified scales are seen to mimic the texture of sponges, sea urchins, or rocks. Modified pectoral fins that have evolved into stalk or foot-like appendages allow the frogfish to mimic the stalks of plants, in addition to allowing them to walk across the sea floor. This adaptation makes up for their lack of a swim bladder.

 Frogfish Walking (video)!!!!

Bumblebee Soccer

This article shows just how intelligent insects can bee

When bumblebees were made to observe other bumble bees move a ball into a goal in exchange for a food reward, they quickly learned to imitate this behavior. This would already be impressive, but researchers also found that the bees were doing more than just copying behavior. Balls of varying distance from the goal were placed in the testing area, and the first group of bees were made to pull the farthest balls into the goal. The test bees that observed this would still pull the closest balls into the goal. Rather than blindly copying their predecessors' behavior for a reward, the bees were able to identify the specific objective that earned the reward, and identify the most efficient solution for achieving that objective.

Man's Best Friend Can Potentially Sniff Cancer

In class today John spoke about how Giant African Pouched Rats could sniff out landmines as well as tuberculosis (Tuberculosis Rat paper if you're curious). Well it turns out a large number of other animals also show potential for sniffing out disease - including dogs. This study looked at detection of human bladder cancer by having trained dogs sniff human urine and found a mean success rate of about 55%. While that number isn't significant on its own (the dogs still miss quite a lot of cases), it does show that dogs have the ability to smell it and shows a lot of potential for training dogs for this purpose in the future. Could we train a dog to have an 80% success rate? or even 95%? This study looked at dogs as well but in testing for lung cancer on the patients breath. They managed to get even better results with an overall sensitivity (or successful diagnosis) of 71% and a specificity (or successfully saying the person does not have cancer) of 93%. These numbers are pretty high and show just how much potential canines have in determining disease.
Beyond just dogs and rats, a number of other animals and methods have started to be investigated for the purpose of testing for things. Fruit flys have been tested to look for cancer, mice for bird flu in birds, bees for explosives at airports, pigeons for breast cancer and much more. A cool specific example - a company called Inscentinel has developed a handhold device that holds 36 bees inside that uses a vacuum to draw air over the bees from a potential explosive and then the user can see on a screen how many bees "said yes" (and by "said yes" I mean extended their proboscis) allowing for an easier method of explosive detection. Animals are pretty cool!

Monday, March 6, 2017

Fire and Small Mammals (it's less sad than it sounds; it's actually pretty cool)

In class, we talked about fire-driven succession in relation to gymnosperm cones opening, and that's pretty metal (is that scientific enough for this blog?), so I was looking for a paper related to this. However, the zoologist part of me won out, and the paper I found ended up being about how this type of succession affects small mammals.

Here's the link to the paper:,+Northern+Territory&id=doi:10.1071/WR9930803&title=Wildlife+research&volume=20&issue=6&date=1993&spage=803&issn=1035-3712

(If anyone can tell me how to make that link shorter, please comment below or let me know during class. Thanks!)

I found the most interesting parts of this study to be that did not involve the dissection of any specimens (which greatly surprised me) and the use of traps. I had never heard of some of these sampling methods used (i.e. the wheel-point apparatus for plants or Elliott traps for the mammals), and I was also intrigued by the fact that the study calculated how much energy was required to maintain the rodents versus the marsupials (the latter was found to be stable while the former fluctuated). Though I did not entirely understand how this was calculated (the paper cited a formula by Nagy that I have yet to look into), I was curious about how and why this was found. The study originally seemed more “basic” (for lack of a better word) in that it appeared to just consider “what’s there and how many,” so I wonder if this calculation was simply something Masters became curious about once the study started or once he had the data. This made me wonder more about which questions and discoveries were entirely accidental or have just been pursued because they seemed interesting. I found the idea that many of them might be to be somewhat amusing yet comforting.

Sunday, March 5, 2017

Possible Origins of Viruses

During the quarter, we briefly discussed viruses and their possible origins. I decided to delve into this subject. I came across a paper written by Patrick Forterre, a researcher at the Pasteur Institute in Paris, France. In his paper, he described the three main possible theories for the origin of viruses. He goes into great detail about each theory as well as problems with each theory.

If you are interested to read the paper, a link is provided below.