Category: science

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.

Spacetime from Entanglement

I thought this was cool.

Physicists have been suggesting for over a decade that gravity — and even space-time itself — may emerge from a strange quantum connection called entanglement.

By engineering highly entangled quantum systems in a tabletop experiment, Schleier-Smith hopes to produce something that looks and acts like the warped space-time predicted by Albert Einstein’s theory of general relativity.

One Lab’s Quest to Build Space-Time Out of Quantum Particles
By Adam Becker

Brain on a Chip

In physiology, you learn that cells work with electricity. Action potentials were studied in every physiology class. A while ago, I read that scientists connected a neuron to a computer chip. Today, I wondered: what is the state of that research now? Well, a quick visit to Pub Med (I swear I use Google just a little bit more than I use Pub Med) showed that things were going along.

Lab-On-A-Chip for the Development of Pro-/Anti-Angiogenic Nanomedicines to Treat Brain Diseases

By the way, there are tons of articles about the blood-brain-barrier on a chip (lab-on-a-chip) to study how we can treat diseases of the brain more effectively (because it’s hard to get drugs to go through the BBB as it is neuroprotective). I remember that the first question on the first homework I ever did for neuroscience class was about the BBB. So, very important stuff. For me personally, and if I’m still alive, this research can help find more efficient ways for less medication to work in my brain.

Then there is brain computer interface, which is also highly fascinating but now I’ve run out of time to write and will have to look at the topic later.

Numbers are out of hand

I had a conversation with someone who was so wowed by the AI progress so far (mainly Musks’ AI on YouTube) that he told me we’re going to have a full on replicant on our hands in the near future. As in, maybe we could have a Jetsons style robot maid in 5 years. Or have C3POs walking around. He was convinced, but I wasn’t. This is because you can put anything on YouTube after it’s been edited in Premiere, but also that human brains are so complicated.

The numbers get out of hand really quick for brains. The number of synapses in one human brain is equal to the number of stars in 5000 Milky Way’s. And then every synapse has something on the order of 100,000 molecular switches in it. And these 100,000 switches, protein molecules in every synapse, communicate a lot with one another, they interact a lot. And then that’s in one synapse, and then the, the human has something between 10 to the 14th, and 10, to the 15th synapses. Now, okay, so there’s a lot of complexity. And then to make matters worse, it is intricately arranged in very tight quarters. So the synapse again, there’s a billion of them per microliter of brain volume in a human. remember that each one of those synapses has somewhere between 10 and 100,000, switches in it. 

Why don’t we understand the brain?

I said that unless AI can understand culture, follow directions non-literally, laugh at a joke it hasn’t heard before, and get through an obstacle course it hasn’t seen or been programmed specifically for, and know when enough is enough, then we have created something human-like.

Until then, I’m waiting for the brain-computer amalgamation that would let me do my job while I’m working out.

Diseases and syndromes I looked up in October

Microscopic polyangiitis – This disease, now known as microscopic polyangiitis (MPA), is a primary systemic vasculitis characterized by inflammation of the small-caliber blood vessels and the presence of circulating antineutrophil cytoplasmic antibodies (ANCA). Typically, microscopic polyangiitis presents with glomerulonephritis and pulmonary capillaritis, although involvement of the skin, nerves, and gastrointestinal tract is not uncommon. 

Thygeson’s Superficial Punctate Keratopathy – Thygeson’s superficial punctate keratitis (TSPK) is reportedly a rare disease with an insidious onset, numerous remissions and exacerbations, and a long duration. The corneal lesions are elevated, whitish–grey in colour, and granular in the intraepithelium. 

Acute Eosinophilic Pneumonia – this wasn’t for work. Actually, I was diagnosed with this once a long time ago. I have no idea if this is related, but I found out recently (within the past 10 years) that I have eosinophilic asthma.

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.

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).

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. 

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

Scientists identify antibodies that can neutralize omicron

An international team of scientists have identified antibodies that neutralize omicron and other SARS-CoV-2 variants. These antibodies target areas of the virus spike protein that remain essentially unchanged as the viruses mutate. By identifying the targets of these “broadly neutralizing” antibodies on the spike protein, it might be possible to design vaccines and antibody treatments…

Scientists identify antibodies that can neutralize omicron

Mitochondrial diseases

Sometimes I work on a case with a rare disease. In one year, I probably come across 5-8 rare diseases, which of course I have to look up because, well, what the hell is this?

One kind of disease that scare me are mitochondrial diseases. These are a group of conditions that are caused by genetic mutations in the mitochondrial DNA that make the mitochondria work abnormally. And if you remember anything about high school biology, mitochondrial are the “powerhouses” of the cell — they produce energy for us to use. So one can imagine that if you have something wrong with your power source, you can’t carry out normal functioning. Also, mitochondrial DNA are only carried in the egg cells, so only mothers can pass this down to their children. Sperm cells don’t carry and therefore don’t contribute mitochondria to the next generation.

It’s crazy how such a small thing can generally f*&k up a life. The US Health & Human Services National Institutes of Health website lists common signs and symptoms such as: poor growth, loss of muscle coordination, muscle weakness, seizures, autism, problems with vision and/or hearing, developmental delay, heart/liver/kidney disease, gastrointestinal disorders, dementia, to name some. You can see what mitochondrial diseases affect in this list of free text research articles at PubMed (I don’t have any institutional access, so I look for free text articles). Then I thought about prenatal testing, and found an article that discusses this, a more recent 2021 article of a study in Japan, and recent (as of 2017) advances in mitochondrial diseases. This article from 2020 is about rare genetic diseases in general, and diagnosing them. If there’s anything I’ve learned from skimming through these articles, it’s that there’s still so much we don’t know. Yet.

OMG, Omicron

Research is what I’m doing when I don’t know what I’m doing.

Wernher von Braun

For the past year and a half, if anyone wanted, they could look to see how science is being done just by looking up research on the SARS-CoV-2 virus. If pandemics were a reality show… Now season 3 is upon us, cursing us with another variant. Like the beginning of finding out about the SARS-CoV-2 virus and finding out about the Delta variant, science is trying to figure this one out. I know that it’s frustrating that no one knows the answer right away, but one thing people miss about science is that it isn’t about knowing everything, but it’s about finding things out. And in order to find things out, we need time. However, in a pandemic, time is an enemy. What some people get wrong is that this is confused with “science is the enemy” or “those other people are the enemy” or “this country is the enemy”. Let’s skip the philosophical part and say that basically, we’re afraid of the unknown, especially if the unknown can maim/kill us.

Although science is more about questions than answers, it can and does generate light that we can shine on the unknown. For example, every Mars rover. Because of my science background (where I spent an extremely long time trying to figure out which science field I wanted to be in, while taking every science class there was), I can go through research articles and figure out what’s what. Here’s a controversial idea: every person should take a class on how to look up scholarly articles on any topic in high school. (While we’re here, let’s open up a school and call it “School of Hard Knocks”, in which every class is directly applicable to real life, such as How to Do Your Taxes, or 50 Cheap, Simple, and Healthy Meals). Anyway, for an average person without a science background (which I also once was, in the early 2000s), what sources are there for just plain facts and neutral ground?

So far, here is the general answer:

I’m happy to see that BBC is in the center, because a long time ago, someone told me that if I wanted to find something neutral, a good point of view to consider would be from people outside of the country. I mean, how good are we at being objective about the aquariums we’re swimming in? And I’m also happy to see Reuters next to BBC. What was interesting was that I had thought The Economist was more right leaning than it was. Finally, it’s nice to know others I haven’t thought of, like Associated Press, to add to my bookmarks.

So what about Omicron? Do we need a booster shot for that? How bad is it, compared to what’s happened already? The answer is, We don’t know… yet.

Now, once again, the world is watching as researchers work nights and weekends to learn what a new variant has in store for humanity. Is Omicron more infectious? More deadly? Is it better at reinfecting recovered people? How well does it evade vaccine-induced immunity? And where did it come from? Finding out will take time, warns Jeremy Farrar, head of the Wellcome Trust: “I’m afraid patience is crucial.”

‘Patience is crucial’: Why we won’t know for weeks how dangerous Omicron is

Talking about sources wasn’t random. I liked this article for its readability, its short length, its international tidbits, and that it shares knowledge (PCR, GISAID database, structural biology mapping) without sensationalizing or politicizing anything. In this day and age, it’s like gold.

LitCOVID

All your COVID scientific information in one place!

“LitCovid is a curated literature hub for tracking up-to-date scientific information about the 2019 novel Coronavirus. It is the most comprehensive resource on the subject, providing a central access to 182167 (and growing) relevant articles in PubMed.”

LitCOVID