Tag: science

N of 1 Experiment: Hafnia Alvei for Weight Loss

~ cafebedouin

“An experimental probiotic aids weight loss in overweight people following a calorie-control diet.

Previous studies by Pierre Déchelotte at Rouen University Hospital in France and his colleagues suggest that orally administering the gut bacterium Hafnia alvei helps obese mice lose weight. The probiotic produces a molecule called ClpB that mimics the appetite-reducing hormone alpha-MSH.

Now, the researchers have found that the bacterium has similar effects in people who are overweight, presenting their results at the Targeting Microbiota 2022 conference in Paris last week.

The researchers counselled 212 people with an overweight body mass index (BMI) on how to reduce their calorie intake by one-fifth for three months. BMI is a measurement that uses your weight and height to calculate if your weight is healthy. The participants were asked to maintain their existing level of physical activity.

Over the three months, roughly half of the participants also took a pill containing H. alvei twice a day. The remaining participants took a twice-daily placebo. The people in both groups were of a similar age, height and starting weight.

Among those who took the probiotic, 55 per cent lost at least 3 per cent of their body weight, compared with 41 per cent of the people taking the placebo.”

-Carissa Wong, “Appetite-suppressing probiotic helps overweight people lose weight.” New Scientist. October 26, 2022

Procedure is fairly straight-forward. Take one capsule in the morning, one in the evening for 3 months. You can buy the capsules used online. Do it for science.

Histotripsy: Solid Tumor Oblation With Ultrasound

~ cafebedouin

“Early tests suggested that the sound waves successfully decimated up to 75 percent of liver tumor material in the rat bodies, which enabled the little critters’ immune systems to jump into action and beat the leftover cancerous tissues out of existence, preventing reemergence…

…The new treatment is called “histotripsy,” and it noninvasively directs ultrasound waves so that the target tissue is mechanically destroyed — and with millimeter precision. This novel technique is presently being deployed in a human liver cancer trial in both the U.S. and Europe.

This is significant because a great number of clinical situations preclude direct (read: invasive) interventions, because of the size of the tumor, its location, or stage. But this new study looked at reducing only a portion of the cancerous bodies, leaving behind much of the tumor intact. This method also enabled the team of UM researchers to exhibit the effectiveness of the novel approach in less than ideal conditions.

-Brad Bergan, “A new technique successfully fried up to 75 percent of tumors using ultrasound.” Interesting Engineering. April 18, 2022.

Lots of interesting developments with ultrasound. There’s point of care ultrasound, which is bringing ultrasound imaging into the clinic. And now, there’s an interventional technique for solid tumors. Really interesting.

Information != Knowledge != Wisdom

~ cafebedouin

“In many academic fields, the number of papers published each year has increased significantly over time. Policy measures aim to increase the quantity of scientists, research funding, and scientific output, which is measured by the number of papers produced. These quantitative metrics determine the career trajectories of scholars and evaluations of academic departments, institutions, and nations. Whether and how these increases in the numbers of scientists and papers translate into advances in knowledge is unclear, however. Here, we first lay out a theoretical argument for why too many papers published each year in a field can lead to stagnation rather than advance. The deluge of new papers may deprive reviewers and readers the cognitive slack required to fully recognize and understand novel ideas. Competition among many new ideas may prevent the gradual accumulation of focused attention on a promising new idea. Then, we show data supporting the predictions of this theory. When the number of papers published per year in a scientific field grows large, citations flow disproportionately to already well-cited papers; the list of most-cited papers ossifies; new papers are unlikely to ever become highly cited, and when they do, it is not through a gradual, cumulative process of attention gathering; and newly published papers become unlikely to disrupt existing work. These findings suggest that the progress of large scientific fields may be slowed, trapped in existing canon. Policy measures shifting how scientific work is produced, disseminated, consumed, and rewarded may be called for to push fields into new, more fertile areas of study.

Johan S. G. Chu and James A. Evans, “Slowed canonical progress in large fields of science.” Proceedings of the National Academy of Sciences. Oct 2021, 118 (41) e2021636118; DOI: 10.1073/pnas.2021636118

Too much information leads to the inability to determine what is important and what is not important. This slows the rate of change and supports the status quo.

Next time someone tells you that the Internet is a liberating force providing people with more information than they have ever had before, you can point to Sturgeon’s Law. If 90% of everything is crap, increasing your volume, indiscriminately, leads to a clogged filter — less knowledge and wisdom, not more, on a volume basis. It is only a benefit when we can filter the 10% from the 90% efficiently, which is a skill few, if any, of us have and probably implies lower volume or some sort of pre-filter.

The Star Chamber, Cancel Culture and Living for the Bench

~ cafebedouin

“By all accounts intense and single-minded, Dr. Kariko lives for “the bench” — the spot in the lab where she works. She cares little for fame. “The bench is there, the science is good,” she shrugged in a recent interview. “Who cares?” …

…Dr. Kariko’s struggles to stay afloat in academia have a familiar ring to scientists. She needed grants to pursue ideas that seemed wild and fanciful. She did not get them, even as more mundane research was rewarded.

“When your idea is against the conventional wisdom that makes sense to the star chamber, it is very hard to break out,” said Dr. David Langer, a neurosurgeon who has worked with Dr. Kariko.

-Gina Kolata, “Kati Kariko Helped Shield the World From the Coronavirus.” The New York Times. April 8, 2021.

The Star Chamber was an English court that was “originally established to ensure the fair enforcement of laws against socially and politically prominent people so powerful that ordinary courts might hesitate to convict them of their crimes. However, it became synonymous with social and political oppression through the arbitrary use and abuse of the power it wielded,” according to Wikipedia. It strikes me as an apt phrase to indicate received opinion and how power is used to enforce conformity, where there is often an inverse relationship between how much deviation and the power applied to deviants.

When I read about The Star Chamber, the analogy to Twitter was obvious. Of course, there are relevant differences too. For example, while both serve as a kind of extra-legal enforcement mechanism, the Star Chamber was a sanctioned institution populated by legal professionals, whereas Twitter is closer to a mob.

There’s a tension. On one hand, society needs some kind of mechanism to hold the powerful into account. On the other, this mechanism tends to get out of control and used arbitrarily.

A think one way of thinking about how it should be used is the same rule that makes for comedy. You need to punch up, at the rich, the powerful, or the famous. But, if your comedy is targeting the weak or defenseless, then it isn’t really comedy.

Same goes for the checks on the powerful. If it’s moving in to act on the weak, then it’s not really doing its job, and the critiques of “cancel culture” are on point.

But, I think the real nuance comes in with people that are different. People can be different, and not necessarily weak. Perhaps they have a different focus, like Dr. Kariko living for “the bench”. A think a real sign of a strength of a culture is how well variance is tolerated within niche communities of the larger culture. Among scientists doing bench top research, is there an effort to be inclusive of interests that lie outside of the mainstream?

All of which is academic. The people who are rich and powerful will make these decisions. What the general population thinks they “should” be doing is largely irrelevant to them. So, the question for each of us is what should we be doing? I think Dr. Kariko is one good answer. Focus on the things you care about and get by. Don’t get involved in the larger culture wars that sap your time and energy away from what you’d rather be doing.

On a slightly more broader level, I think it is a call for each of us to try to see where we can support people of divergent views, backgrounds, etc. because it is by fostering an environment where different perspectives can be expressed and supported that we create conditions better for human flourishing, which in turn helps for more flourishing communities – a virtuous circle.

Science is The Foundation of The Walls We Build

~ cafebedouin

“Science, at its best, also espouses such cosmopolitan ideals. That data is neutral, and science is apolitical, makes for an alluring narrative. By clinging to it, the scientist appears assured, almost noble, rising above the messy and the mundane by sheer force of intellect.

But reality does not conform to such convenient self-delusion. Pretending to be above and beyond politics is by itself a political position; in adopting it, one has aligned with the state and sided with the powerful…

…A scientist can journey to the end of Earth and the edge of time, but never leave the narrow corridors of prejudice…

…In the eyes of the settler, the border is no man’s land; the natives are part of the wilderness, waiting to be claimed. From charting night skies to splitting the atom, the advancement of science at both ends of the physical scale accompany a story of exploitation and conquest. The applications of science guard the border, capturing bodies and confining the imagination. To realize science’s liberatory potential, the work must start with reimagining the architecture of society, where walls are no more…

…Diversity threatens absolute power. What deviates from the center must be destroyed…

…We all inhabit an unjust system and make our compromises in order to live. When confronted with our complicity, the instinctive response is to deny and look away. This is why the border and the frontier have such strong holds on our collective consciousness. Both come in various forms. The prison, as Angela Davis and Gina Dent explained, is also a border. As long as the criminal, the foreigner, the other, are kept behind walls, we can hold on to the world as we know it and recognize our place in it.”

-Yangyang Cheng, “The edge of our existence: A particle physicist examines the architecture of society.” Bulletin of the Atomic Scientists. December 7, 2020.

Lab Notebooks

~ cafebedouin ~ 2 Comments

“* Always in pen

Your goal is not to preserve the outcome of your thoughts — that’s your code. Your goal is to preserve the process of your thoughts. So no erasing, no blacking out. You can put a single line through anything spelled or written incorrectly.

* Always during

Write down what the problem is, what you’re about to do, and what you expect the result to be. Treat your work as an experiment! This is especially valuable for junior developers who are still in a “try everything until something works” frame of mind. Forcing yourself to hypothesize what’s actually wrong is really valuable; and there’s nothing wrong with expecting a negative result (“I don’t think the problem is X, but it’s easy to prove it, so…”) If during the actual process, you deviate from your written plan, write down the deviation, and why you’re doing so. Don’t wait until after you’re “done” — because “done” might mean six hours from now.

* Always forward.

If you write something on Monday and realize you were wrong on Tuesday, write the correction in Tuesday’s entry. This is a lab journal — from the French “daily”. If you had a misconception, you want a record of that, as well as a record of why you were wrong. You can (and should) add a small note to the original entry pointing to the page where you correct yourself — but don’t obscure what you originally wrote.

* Keep a table of contents

The first pages of your notebook should be a table of contents; with a few words summarizing what is on each page. Make it easy to answer questions about what you did, and why, even if years have passed.

* Keep a habit

At the start of each day, read yesterday’s pages. Write down what you intend to do today. At the end of each day, read through today’s pages, and add an entry to your table of contents.

* Summarize when necessary

If you’ve spent a messy week going round in circles, and you lab notebook has become hard to follow, feel free to take a page to summarize what you’ve learned and where you ended up. Flag it specially in your table of contents.

* Store safely

At the end of a project, label the spine of your notebook, and store it safely with your others. It should be easy to access if questions ever come up.”

—Sam Bleckley, “Lab Notebooks.” SamBleckley.com.

OKIDO Magazine

~ cafebedouin

“OKIDO’s philosophy is a simple one: every child is a creative scientist.

The OKIDO world immerses young children in a spectrum of playful activities and media, all intelligently designed by science and education experts. 

Whether watching the TV show ‘Messy goes to OKIDO’, engaging in family events and school workshops, or reading high quality publications and products, OKIDO children learn through play.

At the heart of it all lies STEAM learning (that’s science, technology, engineering, the arts and mathematics). Everything in the OKIDO world is designed by science and education experts to encourage collaboration, curiosity, exploration, discovery, creativity and critical thinking.

WHERE DID IT ALL START?

Messy grew up on the pages of OKIDO Magazine. An independent publication started by parents from a kitchen table in Brixton in 2007, it was designed to fire up young imaginations and spark a life-long love of art and science. Today its founders, scientist Dr Sophie Dauvois (PhD BSc PG Dip.) and artist Rachel Ortas, are still every bit as passionate about engaging young kids in the scientific world around them using play, art and fun.

FOR WHO? EVERYONE, OF COURSE!

OKIDO’s fun and games are for all genders. The OKIDO world is a stereotype-free zone, because we believe in promoting equality for all children.

–OKIDO

CRISPR Enzyme Programmed to Kill Viruses in Human Cells

~ cafebedouin

“Many of the world’s most common or deadly human pathogens are RNA-based viruses—Ebola, Zika and flu, for example—and most have no FDA-approved treatments. A team led by researchers at the Broad Institute of MIT and Harvard has now turned a CRISPR RNA-cutting enzyme into an antiviral that can be programmed to detect and destroy RNA-based viruses in human cells.”

—Broad Institute of MIT and Harvard, “CRISPR enzyme programmed to kill viruses in human cells.” Phys.org. October 10, 2019