How to Write a Research Paper

In high school, I took something called “Experimental Biology” where all we did was to do experiments and write papers. The culmination of this class was a giant “research” paper based on citations we looked up, old-style via microfiche, on the bacteria we grew in the lab. It took forEVER to find 3 articles on the bacteria I was working with. I will never forget the final, which was a set-up question for a paper written on the fly, in research paper style, during the 3 hours’ final exam time we were given. I was lucky. I had many classes that taught me how to write, two of which were in high school (I took creative writing as well). My old alma mater forced all freshmen to take a “How to Write a Paper” class and you had to pass it or else you spent the rest of eternity taking that class until you did. Thank god I passed the first time ’round.

For the people who aren’t so lucky, I found one (of many) helpful sources: Writing a scientific article: A step-by-step guide for beginners. And for those who want more sources, this paper has some citations to check out.

Dyamxion House

I’m always thinking about my next house. Ideally, I’d have enough money to build one that is efficient and robust, but still spacious enough for me to avoid claustrophobia. One idea I came across is Buckminster Fuller’s Dyamxion House.

Bucky designed a home that was heated and cooled by natural means, that made its own power, was earthquake and storm-proof, and made of permanent, engineered materials that required no periodic painting, reroofing, or other maintenance. You could easily change the floor plan as required – squeezing the bedrooms to make the living room bigger for a party, for instance.

Downdraft ventilation drew dust to the baseboards and through filters, greatly reducing the need to vacuum and dust. O-Volving Shelves required no bending; rotating closets brought the clothes to you. The Dymaxion House was to be leased, or priced like an automobile, to be paid off in five years. 

Buckminster Fuller Institute, Dyamxion House

I don’t need a rotating closet, though, as I’m totally fine with walking into my closet (as long as it’s a reasonable space). What would be cool is to start off with manual controls for various needs that can be adapted later on. A design that’s open to design. However, I’m not sure about the cost of this right now. It may be too prohibitive.

Stuff I looked up in August & September

Lots of things these past 2 months! When I was in high school, someone (probably one of my high school teachers) told me that to earn your PhD you have to contribute to some field’s research with a new idea. At that time I thought, wow, that sounds really hard. I couldn’t imagine any new ideas. Then I got older and learned more. One thing I keep realizing is that the more you look things up and learn, the more you realize what you, or we as humans, don’t know. The hunt for answers only brings up more questions. Can we ever really know everything?

Moyamoya disease

Hyperproliferative lymphocytosis

Hereditary hemorrhagic telangiectasia

Todd’s paralysis – Todd’s paralysis is a neurological condition experienced by individuals with epilepsy, in which a seizure is followed by a brief period of temporary paralysis. The paralysis may be partial or complete but usually occurs on just one side of the body. The paralysis can last from half an hour to 36 hours, with an average of 15 hours, at which point it resolves completely. Todd’s paralysis may also affect speech and vision. Scientists don’t know what causes Todd’s paralysis.

Li-Fraumeni Syndrome – Li-Fraumeni syndrome (LFS) is an inherited familial predisposition to a wide range of certain, often rare, cancers. This is due to a change (mutation) in a tumor suppressor gene known as TP53. The resulting p53 protein produced by the gene is damaged (or otherwise rendered malfunctioning) and is unable to help prevent malignant tumors from developing. Children and young adults are susceptible to developing several multiple cancers, most notably soft-tissue and bone sarcomas, breast cancer, brain tumors, adrenocortical carcinoma and acute leukemia.

Sclerosing mesenteritis – Sclerosing mesenteritis, also called mesenteric panniculitis, occurs when the tissue (mesentery) that holds the small intestines in place becomes inflamed and forms scar tissue. Sclerosing mesenteritis is rare, and it’s not clear what causes it.

PMS2-related Lynch syndrome – In humans, the importance of MMR is underscored by the discovery that a single mutation in any one of four genes within the MMR pathway (MLH1, MSH2, MSH6 and PMS2) results in Lynch syndrome (LS). LS is an autosomal dominant condition that predisposes individuals to a higher incidence of many malignancies including colorectal, endometrial, ovarian, and gastric cancers.

Mevalonate kinase deficiency – Mevalonate kinase deficiency (MKD) is a rare genetic autoinflammatory disorder. Autoinflammatory syndromes are a group of disorders characterized by seemingly random or unprovoked episodes of inflammation generally due to an abnormality of the innate immune system. They are not the same as autoimmune disorders, in which the adaptive immune system malfunctions and mistakenly attacks healthy tissue.

Muckle Wells syndrome – Muckle-Wells syndrome (MWS) is one of the cryopyrin associated periodic syndromes (CAPS) caused by mutations in the CIAS1/NLRP3 gene. These syndromes are characterized by fever, rash and joint pain.

Adult onset Still’s disease – Adult-onset Still’s disease (AOSD) is a rare inflammatory disorder that can affect the entire body (systemic disease). The cause of the disorder is unknown (idiopathic). Affected individuals may develop episodes of high, spiking fevers, a pink or salmon colored rash, joint pain, muscle pain, a sore throat and other symptoms associated with systemic inflammatory disease.

Creatine in seniors

Sarcopenia is associated with reduced bone mass and bone strength and may be a contributing factor for the increased risks of falls and fractures often observed in aging adults. It is well established that resistance training is an effective lifestyle intervention for improving aging muscle mass, strength and bone accretion. Accumulating evidence indicates that creatine supplementation, with and without resistance training, has possible anti-sarcopenic and anti-dynapenic effects. Specifically, creatine supplementation increases aging muscle mass and strength (upper- and lower-body), possibly by influencing high-energy phosphate metabolism, muscle protein kinetics and growth factors. Creatine supplementation has shown potential to enhance bone mineral in some but not all studies, and seems to affect the activation of cells involved in both bone formation and resorption. Creatine has the potential to decrease the risk of falls experienced by aging adults which would subsequently reduce the risk of fracture. Finally, preliminary evidence suggests that creatine may have anti-inflammatory effects during times of elevated metabolic stress, such as during extended/intense aerobic exercise. 

Effectiveness of Creatine Supplementation on Aging Muscle and Bone: Focus on Falls Prevention and Inflammation

I have this giant bottle of Naked Creatine (I got it from Amazon) and I feel that it helps me retain and build muscle just a bit better, as long as I don’t forget to put it in my smoothies. Starting last week, I started to put ~5 grams of creatine into my mom’s protein smoothie, because there seems to be a generally positive effect of creatine use in adults. There’s some research into this topic.

Things I looked up in June

Sorry this is so late! Also, I didn’t have to look up anything rare during July.

Hurler syndrome – Hurler syndrome is the most severe form of mucopolysaccharidosis type 1, a rare lysosomal storage disease, characterized by skeletal abnormalities, cognitive impairment, heart disease, respiratory problems, enlarged liver and spleen, characteristic facies and reduced life expectancy.

Methylmalonic acidemia – Methylmalonic acidemia refers to a group of inherited conditions in which the body can’t breakdown certain parts of proteins and fats.

Dandy-Walker syndrome – Dandy-Walker syndrome is hydrocephalus associated with a posterior fossa cyst and abnormal development of the cerebellum, a portion of the brain located near the base of the skull and important to voluntary muscle movement, balance and posture.

NASA is a busy place

I’m reading NASA’s launch schedules and it is fascinating!

Artemis I will be the first integrated test of NASA’s deep space exploration systems: the Orion spacecraft, Space Launch System (SLS) rocket and the ground systems at Kennedy Space Center in Cape Canaveral, Florida. The first in a series of increasingly complex missions, Artemis I will be an uncrewed flight test that will provide a foundation for human deep space exploration, and demonstrate our commitment and capability to extend human existence to the Moon and beyond.

… the DART spacecraft will slam into the asteroid Dimorphos at roughly 4 miles per second, attempting to slightly change the asteroid’s motion in a way that can be accurately measured using ground-based telescopes. The world’s first full-scale mission to test technology for defending Earth against potential asteroid or comet hazards…

The first flight of NASA’s X-57, a small, experimental airplane powered by electricity…

All of these can be found on the Upcoming Mission Events page.

Research articles on protein supplement or wine effects on health

Note: these are only a handful of studies compared to the multitudes of results I found on each topic. Please read widely to form a balanced perspective.

Effect of whey protein on blood pressure in pre‐ and mildly hypertensive adults: A randomized controlled study.

Moderate red wine consumption and cardiovascular disease risk: beyond the “French paradox”.

Effects of Whey and Pea Protein Supplementation on Post-Eccentric Exercise Muscle Damage: A Randomized Trial.

Effects of Whey Protein Supplementation Pre- or Post-Resistance Training on Muscle Mass, Muscular Strength, and Functional Capacity in Pre-Conditioned Older Women: A Randomized Clinical Trial.

Protein Intake and Exercise-Induced Skeletal Muscle Hypertrophy: An Update.

The history, science, and art of wine and the case for health benefits: perspectives of an oenophilic cardiovascular pathologist. (There is a lot about wine itself in parts 1 – 10, and the parts about wine’s effects on health starts at part 11).

Blueberries and cream cookies

I used Christina Tosi’s recipe.

It calls for dried blueberries. I had fresh blueberries because it’s summer and they’re in season. My mom has a dehydrator. Little did I know, it took the dehydrator 18 hours to dry a pint and a half blueberries HALFWAY. 18 HOURS. So I said, F*** that, and put them in the toaster oven at 225°F for 5 hours and I got my cup of dried blueberries. The rest of the recipe was at least easy to get.

Since I had a bad start to cookies by baking them flat, touching, and burnt a couple of times, I shaved off 25°F from the official temp. I baked mine at 325°F for 15 minutes and they turned out golden tan with a chewy middle. And they did NOT flatten out to the extent that they touched each other! I also hand mixed in the milk crumb and blueberries instead of using the mixer.

Speaking of milk crumb, it is delicious on its own. I’m attempting to make vanilla protein milk crumbs with rolled oats (original recipe plus vanilla protein powder, rolled oats, and a tsp of milk), so I don’t have as much of a guilt trip, but we’ll see.

What was there before the big bang?

The James Webb Space Telescope came out with images lately. One image of, mind-blowingly, the past – 13 billion years ago.

Light from these galaxies took billions of years to reach us. We are looking back in time to within a billion years after the big bang when viewing the youngest galaxies in this field. The light was stretched by the expansion of the universe to infrared wavelengths that Webb was designed to observe. Researchers will soon begin to learn more about the galaxies’ masses, ages, histories, and compositions.

NASA

I got into a conversation about time, then about the start of the universe, and the Big Bang. Some people have a more conspiracy oriented view on the Big Bang and how life began, but neither could imagine what was around before the Big Bang. So I looked it up. It was an interesting trip.

The fading of that last star will only be the beginning of an infinitely long, dark epoch. All matter will eventually be consumed by monstrous black holes, which in their turn will evaporate away into the dimmest glimmers of light. Space will expand ever outwards until even that dim light becomes too spread out to interact. Activity will cease.

Or will it? Strangely enough, some cosmologists believe a previous, cold dark empty universe like the one which lies in our far future could have been the source of our very own Big Bang.

-BBC

Currently, our experiments can simulate conditions that happened when the universe was roughly one trillionth of a second old. That seems like a ridiculously small number for us, but for a photon — a particle of light — it’s a long time, allowing it to travel the diameter of a proton a trillion times. When talking about the early universe, we must let go of our human standards and intuitions of time.

What happened before the Big Bang?

Even if we’re not going to be alive, why does the death of the universe and how it dies disturb people?

Things I looked up in May

Heller Myotomy (via UCSF Department of Surgery): The Heller myotomy is essentially an esophagomyotomy, the cutting the esophageal sphincter muscle, performed laparoscopically.

Achalasia – Achalasia is a rare disorder of the esophagus, the tube that carries food from the throat to the stomach.

Ludwig’s angina – Ludwig’s angina is a form of severe diffuse cellulitis that presents an acute onset and spreads rapidly, bilaterally affecting the submandibular, sublingual and submental spaces resulting in a state of emergency.

odynophagia – Pain on swallowing; painful swallowing

Nutcracker Syndrome

Stevens Johnson syndrome – Stevens-Johnson syndrome (SJS) is a rare, serious disorder of the skin and mucous membranes. It’s usually a reaction to medication that starts with flu-like symptoms, followed by a painful rash that spreads and blisters. 

The workout videos I use

I workout based on my heart rate. That is, I watch my heart rate so that it doesn’t go beyond approximately 145-155 bpm, and when it’s close to that, I rest until it slows down. This way, I prevent asthma attacks yet still get sweaty. Some days, I feel like I can do more, and some days, less… some days, I just feel tired or sore or burnt out, so I go easier. In any case, I have to do mostly low impact movements (no jumping) to prevent asthma attacks. Just so you know, low impact doesn’t mean easy! If there’s jumping in a workout, I just take the jumps out. Here are a selection of workout videos I use on my full body days.

Rejuvenation of naturally aged tissues

The expression of the pluripotency factors OCT4, SOX2, KLF4, and MYC (OSKM) can convert somatic differentiated cells into pluripotent stem cells in a process known as reprogramming. Notably, partial and reversible reprogramming does not change cell identity but can reverse markers of aging in cells, improve the capacity of aged mice to repair tissue injuries, and extend longevity in progeroid mice. However, little is known about the mechanisms involved. Here, we have studied changes in the DNA methylome, transcriptome, and metabolome in naturally aged mice subject to a single period of transient OSKM expression. We found that this is sufficient to reverse DNA methylation changes that occur upon aging in the pancreas, liver, spleen, and blood. Similarly, we observed reversion of transcriptional changes, especially regarding biological processes known to change during aging. Finally, some serum metabolites and biomarkers altered with aging were also restored to young levels upon transient reprogramming. These observations indicate that a single period of OSKM expression can drive epigenetic, transcriptomic, and metabolomic changes toward a younger configuration in multiple tissues and in the serum.

Multi‐omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming

Faster Growth, Fairer Growth

The Niskanen Center is an interesting place to read articles supporting a unique viewpoint that rejects the dichotomy of leftist or rightist. So far, their Faster Growth, Fairer Growth Agenda is an interesting read, showing how our past affect our present and how today is not yesterday. Be aware, it’s long.

Over the past several decades, the American Dream has been caught in a pincer movement. On the one hand, deep-seated social forces have combined to slow down growth and accelerate inequality. At the same time, sustained and dramatic changes in public policy have worked not to counteract those forces, but to exacerbate them.

Brink Lindsey and Samuel Hammond from the Niskanen Center

The Year of Mind, Body, and… Wallet

Without really meaning to, I’ve decided to try to make this a year (or more) of mind, body, and wallet. Meaning that during the same time frame I’ve somehow decided to 1) focus more fully on fitness, 2) read at least 10-20 books of “literature” for 2022, and 3) limit my spending.

The fitness backstory: 2021 was a year of surprise medical problems. From the months of March to May in 2021, during what I felt was a giant positive upswing in my fitness journey (I was looking fit, toned, and strong; I was using my Olympic weight set), I started bleeding. Like, a lot. I was hemorrhaging. I had to go to the Emergency Room twice because the first time, I’d lost a quarter of my blood volume and the second time, I was well on my way to losing half my blood. Both ended up in hospital stays. I got put on different medicines to try to stop the bleeding. They never worked completely. In May, I underwent a hysterectomy and everything that was wrong in that part of my body was taken out. And after I healed (3 whole months for full healing), I had to deal with weakened muscles that ended up in back pain for which I went to physical therapy. After a few more months, I finally felt ready to start my fitness journey over. But during these months, I had gotten out of shape and weak. I wanted to be strong again. I really started rock climbing regularly and did some light weights to start, but it was in December that I felt strong enough to really take my 20- and 30-pound dumbbells seriously. So for 2022 I decided to finish what I’d started 1.5 years ago.

Reading: 2021 was also a year of loss. Like I mentioned before, I inherited a few old books from someone who was gone too soon due to Covid and never visiting the doctor, like, ever. Reading Ulysses (I’m now halfway through it) has ignited within me a desire to read more literary fodder, as in anything that’s not a “quick airport book from a tiny newsstand.” The types of books that you don’t have to think about. I do enjoy the relaxed non-heavy read. But, it’s not like I’ve never read anything substantial. I went through a beatnik phase and a William Faulkner phase. I had a Tom Robbins phase. I took Philosophy classes in college (which forced me to read Plato, Aristotle, Hume, etc.) and I read stuff like Bertrand Russell for fun. My high school had me read a lot of classics because it was 3 years of Honors English and 1 of AP English. But there were still books that were out of my reach or kind of slippery because I was simply too ADD to focus on them. But now I’m 2 decades older, my ADD is controlled, and I have the time and the life knowledge to tackle books I’ve missed. Which books? Well, I’m not sure yet. There are lists of books all over the place. My first thought is to balance the reading so that I’m not reading War and Peace and Anna Karenina at the same time, that there is a difference in time, place, author, and culture. I’d also like to read across genres and points of view. Variety is the spice of life, they say.

So far this year I’ve finished Circe by Madeline Miller and Klara and the Sun by Kazuo Ishiguro. (One of those was deeper than the other.) I’ve got Invisible Cities by Italo Calvino*, All Systems Red by Martha Wells*, Dune, and Rebecca by Daphne du Maurier* on rotation. And of course, Ulysses. From the library I have one Neal Stephenson book, Fall, or Dodge in Hell. On my “next” list is A Portrait of the Artist as a Young Man, The Three Body Problem by Cixin Liu*, and Tropic of Cancer by Henry Miller. On my bookshelf are Infinite Jest by David Foster Wallace, Gravity’s Rainbow by Thomas Pynchon, and the writings of H. P. Lovecraft. There are even more books in my Kindle and on my ebook “to read” list. My intention is to pick books that can make me pause and think, but sometimes, I’m not sure every book I pick will do that. Circe was a lot simpler read than I had thought; it was good but not as dense as I thought it would be. (I’d recommend Galatea by Madeline Miller as a more thoughtful read). In any case, I’m sure I’ll write about the things I read.

The wallet: Suddenly one day I pondered if I could do an entire year of “no spending”. This was after the splurging I did in November and December to set up my workstation at home with 2 4k monitors and a docking station. I also bought a bookshelf. Not to mention everyone’s holiday gifts. Then one day after Christmas, it hit me that I could try to do a “no spend” month where I didn’t buy anything on impulse or that I didn’t really need. I wondered how much money I could save. I thought about what were “approved” spends and “bad” spends — and if you’ve never thought of this before, it is an enlightening exercise. For people doing this, the first thing they must do is to make lists of what’s a “need” versus a “want”, what’s okay to spend on, and what isn’t. (One can look up “no spend year” and find a million links and social media about the topic.) I read this Forbes article to start.

What’s nice about the No Spending thing is that it’s personalized, for the most part. I, for instance, do not need the latest game console or video game, because nothing I do depends on that. Someone else might. Someone else might not need shampoo and conditioner, but I do, or else my hair turns into a giant, out-of-control tumbleweed. I can broadly put down in the “approved” list things like medical bills, medicines, things for health maintenance, insurance, and things for health improvements. Other “approved” spending includes food (nothing carb-loaded or deep fried), gifts (dollar limits depending on what the gift is for), car maintenance, house maintenance, vacation, and replacements for things I already own if they are used up or worn down, like soap. It’s easy to write “No late-night Amazon browsing” and remember it, hence, cutting out the possibility of ordering something half-asleep. Also, it’s easy to remember “no more clothes” and “no impulse buying”. This past week, this “resolution” has reared up at Target, Best Buy, and the grocery store, successfully convincing me to not buy something just for the sake of buying it. It was both difficult and empowering. Once January is over, I’ll try February. I’m hoping that eventually, this will turn into a habit and my wallet will be happier for it.

*Books that are ebook or library loans will have priority.