An interesting read on science vs humanity study: https://bit.ly/2ITW0eX
A New Haven Register report on our project: https://bit.ly/2mqEnuw
Amplicon or Shotgun-based NGS?
The thing in life
This happened in mid-July, 2016. I’ve clearly been the queen of procrastination…
I was sitting in a bar with two friends. We talked about work, hobbies, and stresses we deal with everyday…I can’t remember how exactly our conversations meandered, but the topic somehow landed on “the thing in life”. My girl friend is quite driven and hard-working. She tries her best to get things she wants in her life. Me? I have to admit a lot of good things in life were handed to me. I am relatively passive and hate projecting myself as being aggressive. It’s clear that my girl friend never agreed with my philosophy but there wasn’t an opportunity in the past for her to blatantly tell me so. Today, with the help of a little alcohol, she opened up. “How can you not have a thing in life?!” she questioned me as she rapidly raised her palms upwards. The guy friend was calmer. He nodded lightly, “one of the most exciting moments in my life was when I debugged my codes…. Nothing else mattered at that moment”. Believing that I was being ganged up against, in a defensive mode, I hardly thought about what their comments really meant or whether that’s relevant to me, I argued back: “what if I just want to live every moment to my liking…if you live to get those “high” moments in life, doesn’t that mean you are unavoidably getting into low moments as well?…”
Truthfully, there may never be a conclusion for debates of this kind. It got me thinking though. Why do we need a thing in life? Sure, it sounds pessimistic when I describe myself as a plankton to my friends (well, I am a marine biologist). But what is exactly the need to have A thing? I love the feeling of achieving a goal in work (the only complaint I have is that my euphoria normally doesn’t last longer than 10 min), but working is not my thing; I long for a deep connection with someone, hopefully a long-term partner, but finding a good husband isn’t my thing; I enjoy dancing tango, and dance in my free style in general, but dancing will never become my thing… Am I hopelessly detached to this world because I do not have a thing? I am passionate for life, for this one and only life I am given, for no other reason rather than just to live it. I don’t have a thing for life. I have a way to live a life: I live it relaxed so I can follow my heart; I live it genuinely so I can be a bad-ass and honest; I live it curiously so I never stop exploring; I live it naturally so I don’t fake anything to impress…by the time I die, I may have no-thing in life (fame, money, or a husband). But what do we get to keep after we die anyway? Or do we really get to keep anything when we are alive? How is living itself not the most important thing in life?
We are born with different dispositions: it’s some people’s instinct to follow a goal and stay on track; some others find it hard to stay focused on one thing but are self-sufficient through different means. I welcome both. I want to have a heart that is so light, so carefree and so calm that come what may, it’ll always have the sensitivity to feel the slightest touch and the tenacity to overcome the mundane struggles. I am not there yet, but the ultimate passion, in my mind, is inner peace. Isn’t it most powerful and beautiful to love life knowing that it is imperfect and even ugly occasionally? I want to conclude this impossible to conclude essay by a bit Taoism: live in the moment; not to be pleased by external gains, not to be saddened by personal losses.
Postscript: I wrote this in July and haven’t done anything to it until today. I don’t know why… I may not be completely happy with what I wrote; I may have lost the momentum to share the post; I may have forgotten all about it…Today, I am brought back to this site because of another reason. Now I decide to post it and add one comment I heard from a dear friend rather recently: I don’t think you are passive. You have a lot of energy. It may not be engaged in particular ways, but that is okay.
An NPR Video Clip on Bacteria
Yes, an NPR video clip on bacteria. Well, HUMAN bacteria, to be specific. If something is directly relevant to men, then it is obviously important. Anyhow, it is a good thing that these tiny guys are getting more and more attention.
Tell right from wrong, can you always?
What I want to talk about today has to do with a very politically and emotionally sensitive subject that has been in CNN’s headlines these days – the fatal shooting of a black man by a white police officer in Ferguson, Missouri. There have been immense confrontation, conflicts and clashes surrounding this subject. I wonder if you have chosen to take a side? Ah, right or wrong, isn’t that what we always want to find out?
Spending a lot of time caring about microorganisms in the water, I lose insights on other stuff. I am not able to dash along on the societal, psychological, political, or humanistic influences of the Ferguson incident. I believe, though, its consequences will likely be passed down in American history as those of another historical event have been- Rosa Parks’ arrest about 60 years ago.
It happened in December 1955, Montgomery, Alabama. A black woman Rosa Parks got on a bus after a day’s work. Later she was arrested because she refused to obey the bus driver’s order to give up her seat to white passengers. Parks’ act of defiance and the subsequent Montgomery Bus Boycott symbolized the modern Civil Right Movement, and was a big win in American history against racial segregation.
Then I read something random today. If you want to spend time googling, the facts are all there. I am not here to repeat the facts. Rather, I want to reflect on a different perspective of how we look at history and how we judge historical characters. Again, that right or wrong stuff…
What many people probably do not know is that nine months before Rosa Parks was arrested, a 15-year-old black girl, Claudette Colvin was already arrested on a Montgomery bus for refusing to give up her seat to a white man. What Colvin struck me as a powerful individual who deserves at least the same level of recognition Parks received was that she was the first person who really challenged the law. A 15 year old, facing a fearful situation to be arrested in public, Colvin shouted “It’s my constitutional right to sit here as much as that lady. I paid my fare, it’s my constitutional right!” I can only imagine the extraordinary courage and the sense of justice it takes to have said and done what Colvin did. And, if I haven’t emphasized it enough, she was only 15!
Then why wasn’t Colvin remembered, and worse even, known by many? Black organizations believed that it would not be a smart move to have a 15-year-old as the face of the anti-segregation movement. It was also suggested that Colvin became pregnant shortly after she was arrested, unmarried. Facing all the difficulties in her own community, Colvin was not able to hold a job and eventually moved in New York in 1958. Parks, on the other hand, was perceived as a good icon for the civil right movement: she was an adult; she had the right hair and look to appear as middle class. Even Colvin herself made the following comment: “Her (Parks’) skin texture was the kind that people associate with the middle class. She fit that profile.”
I couldn’t help but imagine what might have happened. A 15-year-old Colvin, under the overwhelming influence of the public opinions in her own black community, was eventually convinced that Parks was the most appropriate candidate. Although frankly, I can’t imagine there wasn’t any even slight disappointment. What happened later in history supported that having Parks as the front face was strategically an effective decision. As a matter of fact, the strategy may have been brewed on a deeper level than I thought! According to historian David Garrow, Parks’ action of defiance in 1955 was not a spontaneous one. Black civil right leaders had been thinking about what to do about the Montgomery buses for years.
Left: Parks; Right: Colvin
It was a strategic win for the black community! Now, however, allow me to bring up my geeky side: isn’t there an obvious oxymoron here? The Civil Right Movement sought for equality. An unfair treatment is an unfair treatment, to both Parks and Colvin. Yet, the decision on choosing the front-cover person was made on a not-so-equal basis. Colvin was not treated quite equally as Parks was, and did not get the attention she deserved. All men are born equal, despite of their skin colors, how they dress, or how they do their hair. But in this case, in order to achieve the bigger equality, both Parks and Covin were judged by these standards, the exact standards we do not want to be judged by in the pursuit of equality!
What is right? What is wrong? KFC do chicken right, but that is probably a big wrong to the birds. Well, if they could actually express their opinions. Killing a person is wrong. Killing a Nazi soldier sounds heroic. Yet in the eyes of the Nazi soldier’s mother, he was just a loving son who brought warmth to people around. Majority of this world is elusive to the standards of being right or wrong, because man kind are the suckers of this planet and we are far from and will never be perfect.
Probably because confusions about the “right” decisions exist, I really admire people who are hard-headed about what they believe and where they stand. With the right amount of strategies, strength, and persistence, these people often are the driving force to make societal changes for a better world. Meanwhile, for people like me who are in the grey area: Human society is today, not because it followed a “right” path. How history is comprehended and written into the text book, eventually, will depend on who is looking.
I want to end this with two quotes from Friedrich Nietzsche. I’ll admit I know very little about Friedrich Nietzsche. I just read these and I was touched by the smartness, the understanding, and the ultimate forgiveness of human kind’s weakness.
“You have your way. I have my way. As for the right way, the correct way, and the only way, it does not exist.”
“All things are subject to interpretation. Whichever interpretation prevails at a given time is a function of power and not truth.”
The Story of A, B and C
A small business, A, is trying to 1) grow a lot of algae; 2) harvest and analyze algal products (such as lipids) and byproducts (such as pigments) with commercial values; 3)mass produce commercially valuable algae. This company does not own any algal culture; it does not have any analytical instruments to understand the chemicals produced by these algae. Nor does the company have any facility or equipment to mass produce.
A government lab, B, has designated personnel to maintain the stock and supply of many algal cultures. This lab also has people who know about the chemical properties of some of these algae’s bio-products.
A university lab, C, has expertise in isolating and characterizing chemicals produced by algae.
What happens next is A reaches out to both B and C. Soon, A gets promising algal strains from B (for free), tries to mass produce these strains with the expertise provided from B, and sends algal samples to C for chemical characterization (for free). End results? A is now funded by the state agency and aims to very soon sell its big ideas to get rich. What do B and C gain from this practice? B now has A as its constituents. Faced with difficult times such as a threat to shut down the lab, B can rely on A to draft a petition letter to DC for some positive considerations. C gets an opportunity to collaborate with a business outside the university, which can be used in the draft of the next grant proposal.
Perfect. But can’t B and C get connected without A being involved in the first place? For B, making money is never on its agenda. Helping American economy by supporting small business (A)? That certainly is. For C, it didn’t have a reason to initiate a conversation with B. Therefore, by proposing a worthwhile mission, A rightfully serves as the bridge between B and C, and earns itself fame and money. I think it’s valid to ask: what exactly does A bring to the table? Something so essential to the win-win outcome, yet something so intangible.
Biology is a result of evolution. How human society functions today is also a result of its own evolution. Just like mysteries exist in the Biology world (how come H2O is such a perfect substance for so many fundamental processes supporting life?), the rules and how things turn out in human society do not always make sense, either. But since whatever is true is reasonable (Hegel?), we might as well live by it and appreciate its complex functionality.
Classical vs Pop Music
I have to start with a disclaimer: I know nothing about music as a science or a technique. To me, singing with the music and moving with the rhythm is just a reflex. Everyone knows how easy a reflex is- no work needed, it just happens. Then what am I doing here?
I wish I had more exposure to classical music. I did not, and I have my reasons. First, music class was never a big thing throughout my education, worsened by the fact that classical music was never a big thing throughout my history of having music classes. The only memory I had about western music introduction was from high school. The music teacher was truly a character. He always seemed alone and aloft. As the music played, he would narrate on the side about what was going on with the storyline, with his head held up and his eyes looking far away. I couldn’t help but have a kind of unreasoned sympathy for him. I paid so much attention to the teacher’s sad and usually silent expression that I neglected the vocal part- the music. The only segment I still remember was the enormous excitement he brought to the lonely stadium when he introduced Radetzky March… Second, when I was a school kid, talent classes were not so common for our generation. I idled through my younger time without learning how to play any musical instrument. But to be completely fair, my one-year-younger sister learned flute and was once really good at it. I guess I was just impatient and impossible then… Lastly, needless to say, western music (especially the classical) was not as popular in the late 20th century in China as it is today. People were busier with living a materialistically satisfying life than with appreciating the obscure (to me for sure) beauty of classical music.
The easy-to-approach nature of pop music, on the other hand, seeped in every corner of my life. Certain type of music is simply smooth for the ears and you can’t help falling in love with it. I was once clothes shopping and you know how pop songs are always played in the background to disorient the customers. I got lost anyway. I was immediately attracted by the music and bought something to show my appreciation for the shop owner. Till today, I still like pop music and it’s becoming clear to me that I am attracted to more than just the music. Some people can do serious work at the same time of listening to music. I find that really difficult and finally realized I always pay too much attention to the lyrics as I listen, no matter how many times I’ve heard the songs. I sank INTO the lyrics and that takes up a lot of my brain power to process other things, such as work. As a consequence, the typical life cycle of my pop music infatuation includes falling in love with the music, listening to the song, listening to the song over and over again if the lyrics touch certain spots in my heart.
Maybe I just lack the musical knowledge to understand classical music; maybe I am not mature enough to interpret the indefinite possibility hidden in the “speechless” classical music; or maybe I am someone who simply has to be told what the meaning is conferred by the music…Pop music with the right lyrics always does the magic for me. Good lyrics express the most genuine feelings on earth in an unassuming way. It’s so painfully true that it can break my heart and it’s so unrealistically beautiful that it frees me from the mundane world, even for just a while. A few days ago, I read some harsh comments on Jame Blunt’s You Are Beautiful, which was described as being extremely lowbrow. I’d rather believe it’s JB’s later work (which I admit have never followed) that was disappointing to the listener, because You Are Beautiful in my mind, perfectly depicts a random encounter, although with intense feelings aroused, destined to go nowhere. Yet, who does not have one of those moments at least once in our lives? I’ve been listening to a few old Chinese “pop songs” these days and their lyrics happen to be congruent with my mood recently. I totally enjoyed being told by the composers what they want me to know from listening to the songs. Like enzymes meeting substrates, the subsequent chemistry is a very fulfilling, clear and complete joy of life.
With all that’s said, I wish one day I could understand classical music better so not only my comparison will be less biased but also my life will be more colorful with some new elements.
From Biodiversity to Economy
We got a speaker today (a rare event in this lab). He is from my alma mater, Stony Brook University. He is an expert in Environmental Economics and Policy, and his presentation focuses a lot on how to come up with some dollar valuation of an environment. Along that line, what should we measure to evaluate the “healthiness” of an environment, so that knowledge of an ecosystem is translatable between different people, different places, and different research projects? In other words, we need appropriate metrics for ecosystem conditions.
Biodiversity is one of the many parameters we can use to evaluate an ecosystem’s healthiness and it is a very interesting concept. Not that I am not making my contribution to the data pool, but very often, ecologists get so hung up on this idea that it makes me wonder: are we interested in biodiversity mainly because it is difficult to measure? We still don’t fully understand what all the different biodiversity indices mean in a long run, since we can’t even answer the most basic question: does greater biodiversity indicate a healthier ecosystem? On the other hand, it is probably because of the exact reason that we don’t really know how the preservation of one species can have a major impact on our human being 100 or 1000 years from today, we’d rather not run the risk of losing it. Consequently, we take a lot of trouble to understand the diversity, be it richness (simple count of species) or evenness (how equal the abundance of the species are).
Then interdisciplinary subjects such as Ecological Economics emerge and conversations between ecologists and economists start. Some of these efforts focus on explaining what diversity really means by the presenter and how we can incorporate whatever diversity parameters in question into the ecosystem model. I have a crazy idea: if the ecologists won’t understand the real ecological meanings of these biodiversity indices in any time soon (quite like I think, and for my defense, I am an ecologist myself.), why don’t we ask the economist what parameter has the best behavior in a model, however the property “best” is defined by the economist? If the ecological meaning of biodiversity is elusive to us, then we need to pick a definition that at least has some practical sense, economically. Note that I am not suggesting to endanger any of the biodiversity. Rather, I am asking why don’t we approach a complicated issue by focusing on certain parameter(s) (instead of a suite of parameters) that make practical sense to people who don’t give a sh*t about Shannon Index, Simpson Index, or many others I don’t even want to bother mentioning? There are very few occasions when non-scientists would care about the abstract essence of science. When there is a chance to make connections happen, why don’t we?
Is it a cooling or a warming globe?
Don’t get me wrong. I enjoy understanding things and I like how Stephen Hawking described us human beings as an advanced breed of monkeys that are just a little special because we understand the universe. At least try to do so, I’d add.
But in so many cases, having science as a career makes some success-driven minds lucrative. At the disguise of understanding things, explanations can be made up to feed certain expectations or hypes. True, when something is complicated, isn’t it the most convenient and eye-catching to blame the most media-popular scapegoat? Then inevitably, you will see such contradicting even hilarious arguments 40 years apart. Has the trend of the geological event really changed within 40 years? I don’t think so.
I am not sure if there is any one to blame for, the scientists or the media or both. It upsets me.
Growing Up
While I tend to blame myself for not being mature enough to do the right things at the right times in my life, I would still run the risk of misinterpreting the messages from Margaret Mead from about 50 years ago: I was wise enough never to grow up, while fooling people into believing I had. Seriously, what is the rush?
Yuan Liu Presents 