昆蟲和植物撞名

為什麼植物學家和昆蟲學家不事先溝通講好？
教授說因為植物和動物的分類是不同的系統，可是分類學家不是應該讓人們(或至少生物學家)方便、清楚，避免重複嗎？

Anisoptera是

也是

 

Cecropia是

 

也是

The Two Assumptions of Heritability Studies

Evolution cannot occur without at least some traits being heritable. Heritability is a measure of parent-offspring resemblance; so a trait with high heritability has a high genetic component to it, right?
No.

This is one strange and paradoxical thing about heredity studies: heritability is defined as something specific to a certain population in certain circumstances. It is neither a property of an individual nor a property of a trait.

In parent-offspring correlation studies, heritability is simply the slope that measures the resemblance between the average trait value of the two parents and the trait value of the offspring. In twin studies, heritability is the correlation between the trait values of the twins.

From my reading about scientific and philosophical articles on heritability, I figured that two assumptions are implied in those studies without even being mentioned:
(1) Parents and offspring always resemble, instead of differ from, each other. (In other word, the slope of heritability on the parent-offspring graph is always positive.)
(2) Heritability can never equal to zero. This is because of how the math works out. Heritability is a correlation: a covariance over the product of two standard deviations. Covariances and standard deviations are always positive numbers.

Think about it: pick any measurable trait, its heritability will be a non-zero positive number, even if in reality it does not have genetic component. So what does heritability really tell us?

What would our evolution looks like if parents and offspring always tend to differ, not resemble, each other? Would we evolve backwards? Within one generation, the evolutionary response in the offspring will shift in the opposite direction as the selective pressure; however, the response will be cancelled in the grand-offspring generation under the same selective pressure. Just thinking about this weird scenario gave me a giggle fit in my philosophy-biology class.

Interview at Madison Children's Museum

The manager of the Rooftop of Madison Children's Museum interviewed me. She liked the fact that I love insects and I come from Taiwan. Interested in ethnobotany and indigenous agriculture, she hoped to hear about what vegetables and herbs Taiwanese people grow and eat. She also hoped that I could help take care of their cockroaches and meal-worms, and start a cricket culture; so the animals living on Rooftop will have food source, and children can look at those insects. I think it meant that she gladly accepted me as the summer volunteer, so I'll be going to Children's Museum one morning 9 to 1 o'clock per week to help take care of their garden, animals, and play with children!

Growing Food and Sustainability, after reviewing my application for their summer paid internship, said they were impressed by my application and wanted to interview me soon. I hope the interview will go well. I think one of the greatest things university taught me is bettering my BS ability. I wrote so much for the application but I already forgot what I wrote!

Dysdera crocata

I found a medium-sized spider in my house. At first, I was a bit alarmed because I didn't know if this red- and ivory-colored spider with big fangs was poisonous. I checked online and found it's a Dysdera crocata, commonly known as the woodlouse spider. It feeds exclusively on woodlice and its big fangs are used to grab and pierce through the exoskeleton of woodlice! Luckily this spider doesn't cause problems to humans. When I tried to find it again, it was gone, probably went hiding somewhere in my house. It was a pretty spider!

Pictures of spiders of the same species from the internet:

Standardization of production and purification of Manduca hemolymph JHBP (Abstract)

The abstract of my research project for applying the Hilldale award (my project hasn't have a result and conclusion). Many students have attempted on this project and didn't work out a desirable yield of rJHBP. If my future work is anything useful, the results will contribute to the scientific community. It's kind of hard to believe I'm doing it.

The hemolymph juvenile hormone binding protein (hJHBP) is a specific Lepidopteran protein that binds and transports juvenile hormone (JH). JH plays a number of crucial roles in the regulation of insect development and reproduction. This project will employ a transformed E. coli cell line to express recombinant JHBP (rJHBP). Immunological analysis, cell preparation, and protein purification will be explored to produce and purify rJHBP of optimal quantity and quality. Binding studies will confirm the functionality of rJHBP. The results will provide a stable supply of JHBP for future studies on the binding and target cell docking mechanisms and contribute to increasing our knowledge of insect physiology and pest control.

Yew

Finally found the trees that grow those cute red fruits (aril) are called yew, genus Taxus.

They are very poisonous - the leaves can kill the cattle and horses that eat the plants, but the fruits are harmless to birds and allow them to be eaten and dispersed. I wonder if humans can eat the fruits too.

Caterpillar Fighting

Once the graduate student in my lab told me that they have to separate the Manduca caterpillars into cups as they grow bigger, because they would fight each other to death for food if the place is too crowded. I just couldn't imagine such soft-bodied, harmless-looking creatures could be so aggressive. This week, I saw many small caterpillars in one box banging their upper bodies against each other. Some of them struggled intensely. I even saw a hornworm's little tail fell off because of the fighting. They might well be siblings so what a sibling competition. Wow! Never underestimate the aggressiveness of fragile-looking organisms.

Coconut Crab

I saw this on the Internet. WHY IS IT SO BIG!? (It was probably hungry so it was messing up with someone's trash.) I suddenly want to take it home and feed it coconut!

Because Prof. Goodman wasn't there on Saturday ...

Because Prof. Goodman wasn't in the lab on Saturday, I stole 3 liters of double-distilled water home to cook Pu-erh tea and tasted LB medium. When I complained that the Pu-erh tea I cooked tasted awful, Mom suggested me to change the water, because water in Wisconsin is too hard. Double-distilled water did improve the taste significantly! LB medium tasted weird, but not as bad as I thought. It's a bit salty and tasted like protein. I could imagine that bacteria love it.

The E. coli plate I spread by myself; grown after 24 hours.

A shaker-incubator. Prof. Goodman said bacteria need to be shaken all the time to get enough oxygen. Why they no get dizzy?
I set up a schedule to pick up 6 liquid cultures that would have been induced for different times. Unfortunately, this shaker machine broke (because it was too old and some rubber in it broke) when I was collecting the 12-hour culture. I had to start my experiment all over again next time because I couldn't keep the experimental conditions identical for all 6 cultures. I need some luck for my experiment.
I can still use some of the cells for another experiment. I will determine how many fractions we need to collect from the gravity flow column to obtain the most protein tomorrow.

First Successful Dot Blot!

My previous dot blots were failures. If there's something wrong with our method of detecting the JHBP, I can't advance to the extraction process. I tested with hemolymph samples and the results was a weird "negative staining" - the pigment stained the paper, but where the protein is supposed to be remained white. Prof. Goodman said he's never met this problem in his lab. There could be problems with our antibodies, techniques, material, or something else but we didn't know.

Goodman decided that the antibodies in the refrigerator might be expired. We went to the basement on Tuesday to the huge cold room where stores all of his antibodies and other precious stuff. I watched him digging boxes of tubes out of the negative 80 degree Celsius freezer since he hasn't touched them for a long time. Finally he handed me a 50 mL Falcon tube - which reads "MAB #6, 1. 28. 99" - and told me that was the monoclonal mouse anti-JHBP antibody he obtained in 1999.

The process of producing the antibody was expensive and tedious. JHBP was first injected into a mouse and the antibody was produced at peak after a month and half. The mouse's spleen cell was taken out and cultured - a single cell in each well - with spleen cells made cancer. The cells will hybridize successfully in only a few of those cultures, starting to divide indefinitely and producing the primary antibody. This hybrid cancer cell then was injected into the abdominal cavity of another mouse. The poor mouse grew larger and larger with the tumors until it couldn't walk anymore. Its body fluid, a rich source of the antibody, was dripped and collected. Prof. Goodman made a contract with a company that produced this antibody, and he must hand in large quantity of the antigen - the JHBP - in return. However, over a decade he hasn't figured out how to do it.

I was told to separate the antibody into aliquots, because antibody is best not be refrozen. Since Goodman shared his valuable backlog with me, I treated it as deliberately as possible. On the same day, I pipetted the antibody into 108 centrifuge tubes, 100 micro-liter each, and labeled and stored them in the freezer. 

We were suspecting that the problem with the dot blot was the PVDF paper, which didn't seem to absorb the samples, and the dot blot apparatus. Prof. Goodman let me use nitrocellulose paper and just a vacuum instead on Thursday. He killed another Manduca caterpillar for its hemolymph. I prepared the samples, straight hemolymph and 1/10 concentration, and tested them with different concentrations of the primary and secondary antibody.

 

It was a success! Not only we found that nitrocellulose paper absorbs the samples much more efficiently, we also determined the optimal concentrations for each antibody, the ones that stain the samples the darkest while give the lightest background color. It looked like 1:1000 primary antibody and 1:5000 secondary antibody (column #6) is the best combination for detecting JHBP.

A note on the strength of the signal is, I put 2 micro-liter hemolymph on each dot. Goodman said the concentration of JHBP in Manduca hemolymph is 1.4 nano-gram/1 micro-liter. The purple dot we saw there indicated the presence of 2.8 nano-gram of JHBP.

We became much more upbeat, because the problem wasn't the antibodies, which would be a much bigger trouble. Prof. Goodman said this experiment could be my introductory research project. I felt that he looked at me with more appreciation. I'm gradually getting out of the clumsy novice phase. Although it's just start for me, Goodman is also finding that I'm a diligent and capable person - someone he'd like to be in his lab and good for doing science.

P.S.  I asked, "So it means every time I do a Western blot or dot blot, we have to kill a caterpillar?" "That's what they're there for," said Goodman, "We sacrificed trillions of bacteria in the experiments. You can just hear them screaming in the back room 'NO NO NO not me!'" I said, "They're genetically modified to produce a protein that they hate. They probably want to die." "They want to commit bacteriocide!"

The Third Eye of Lizards and Humans

How Humans Lost Our Chance at a Third Eye 

"The chemicals used for light perception in the lizard’s third eye are structurally similar to the psychedelic molecules humans use to open their 'third eye'."

Rita Chen

November 5, 2012

Seraphic Transport Docking on the Third Eye, 2004, Alex Grey

“Opening the third eye” is a cliché slogan and a concept of psychedelic users to describe the extended sight and mental perception under the influence of psychedelics that are beyond the normal state of mind. The phrase might be borrowed from Hinduism, in which the third eye is called ajna chakra and is believed to be positioned in the brain, between the eyebrows. The third eye, an asymmetrical structure, is usually not seen in bilaterians. Nevertheless, a news story published in September, 2012 talked about some species of lizards have a third eye, a little dot on the top of their heads, called the parietal eye. The chemicals that these lizards use to perceive light in the third eye are similar to some of the psychedelic drug molecules, which suggests a connection between the slogan and this ancient body structure.

A tuatara. The little dot on the top of its head is the parietal eye, the "third eye" of this species.

The “lizard species” with the third eye such as tuatara found in New Zealand are actually not lizards in the phylogenetic sense. The parietal eye is not as complex as the other two eyes, but does react to light. Evidence suggests that the structure is present in a shared ancestry of today’s mammals and reptiles. While some lizard species have the parietal eye, it is lost in most extant tetrapods. The development of a third eye is asymmetrical. In those reptiles, the left side of the brain becomes the parietal eye, while the right side of the brain becomes the pineal sac, which secretes melatonin that responds to light.

The position of the pineal gland relative to other brain structures in humans.

In humans, the homology to the pineal sac is the pineal gland, which stays down with the rest of the brain instead of situated at the top of the head. The pineal gland also secretes melatonin, the hormone that regulates biological rhythms. Melatonin is a derivative of serotonin, the major neurotransmitter responsible for the feeling of well-being, happiness, and normal sleeping patterns. The pineal gland secretes some serotonin.

The tryptamine psychedelics are structurally similar to serotonin and melatonin, and act as serotonin agonists when they enter the brain. Examples of naturally-occurring psychedelic tryptamines are DMT, 5-MeO-DMT, psilocin, psilocybin, and bufotenin. Except producing hallucinations, dissociation, and changes in mood and behavior, psychedelia is often associated with extended perception beyond the normal sight and spiritual experiences. According to the news story, because the pineal gland in humans has evolved to maintain a healthy state of mind, instead of light perception, having a third eye could be “at the expense of being able to sleep, be happy, and keep mentally fit.” Ironically indeed, while people attempt using psychedelics to achieve spirituality and see what is beyond the normal two eyes can see, their time and light perception is severely distorted, their mood can be affected in positive or negative ways, and even have a small chance to trigger underlying psychosis. People on psychedelics often see objects becoming more colorful, lights coming out of nowhere, or glowing objects. Since time perception is changed, the trip could feel much longer than it is. An extreme story is that a person feels that he has gone through a life-time experience in a bizarre, alternate universe during a 15-minute DMT trip.

Melatonin (N-acetyl-5-methoxytryptamine), the hormone secreted by the pineal gland to regulate biological rhythm, is a derivative of serotonin.

Serotonin (5-hydroxytryptamine), the neurotransmitter responsible for the feeling of well-being, happiness, and normal sleeping patterns.

Psilocin (4-hydroxy-dimethyltryptamine), a psychedelic tryptamine that is closely related to serotonin, occurred naturally in many species of mushrooms.

The chemicals used for light perception in the lizard’s third eye are structurally similar to the psychedelic molecules humans use to open their “third eye”. However, the pineal gland and melatonin have evolved to serve different functions in lizards and humans. Perhaps, “opening the third eye” is not merely gibberish spoken by people who are high, or a coincidence between the Indian and the Western interpretation on an altered state of mind, but a deep, ancient connection between the physiological structures of related lineages with an evolutionary explanation.