Did Grief Give Him Parkinson’s?

Wow! Thats what I said out loud after I read first few lines. This is an unique and precious view into health which happens very rarely - unveiling the complexities of not just Parkinson's but life itself. 

I highly recommend reading this synopsis of Jack and Jeff's life: 

I had driven up to spend time with Jack, who has Parkinson’s disease, and his twin brother Jeff, who does not. Because they are identical twins with identical genomes, it may appear to be a mystery that only Jack is sick. Yet scientists have long known that genes alone cannot explain why some people get Parkinson’s and others don’t. While a handful of genetic mutations are linked to the disease, about 90 percent of cases of Parkinson’s are “sporadic,” meaning the disease does not run in the family. And twins, even identical twins, don’t usually get Parkinson’s in tandem. In one of the largest longitudinal twin studies of the disease, Swedish scientists reported in 2011 that of 542 pairs in which at least one twin had Parkinson’s, the majority were “discordant,” meaning that the second twin was unaffected. The discordance rate was higher for fraternal twins, who are no more alike genetically than any two siblings. But even identical twins had a discordance rate of 89 percent.

So if genes don’t explain most cases, how about the environment? Several environmental factors have been linked to Parkinson’s, which has been shown to occur at higher-than-expected rates in, for instance, people who were prisoners of war in World War II. There is also a higher rate in people who live on farms or who drink well water, probably because of exposure to certain pesticides.

But the environmental connection is precisely what makes Jack and Jeff so interesting. For almost all of their 68 years, they have lived no more than half a mile apart. They have been exposed to the same air, the same well water, the same dusty farm chores, the same pesticides. They built their homes a five-minute walk from each other, on two plots of their father’s 132-acre farm in eastern Pennsylvania. And since 1971 they have worked in the same office, their desks pushed together, at a graphic design firm they co-own. All this makes their particular discordancy tougher to explain.

The existence of a pair of twins with identical DNA and nearly identical environments in which only one is sick—that’s a researcher’s bonanza. Whatever difference can be untangled in the twins’ physiology probably relates directly to the disease and its origins. The genome can be held constant; environmental toxins and other exposures can be held constant; what remains, researchers are left to think, might be an odd shift in a particular neural pathway that has a relevant function all its own.

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It’s where those parallel lives diverge, though, that might provide a lasting new insight. Beginning on the day in 1968 when Jack was drafted and Jeff was not, Jack suffered a series of shifts and setbacks that his brother managed to avoid: two years serving stateside in the military, an early marriage, two children in quick succession, a difficult divorce, and finally, in the biggest blow of all, the sudden death of his teenage son.

After these key divergences in their lives, Jack went on to develop not only Parkinson’s but two other diseases that Jeff was spared, glaucoma and prostate cancer. The twins place great stock in these divergences, believing they might explain their medical trajectories ever since. Scientists are trying to figure out whether they could be right.

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Their lives diverged between the ages of 18 and 25, tilting their paths off course just enough to remain, forever after, the tiniest bit askew. First they chose different colleges: Jeff went to Moravian College in Bethlehem, about an hour from home; Jack went further away, to Syracuse University. They both reported to the draft board in 1968, but only Jack passed the physical. Jeff, who had had a childhood infection that left him nearly deaf in one ear, was classified 4-F.

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The beauty of stem cell cultures is that they behave in the dish similarly to how they would in the body. That’s what happened in this case. The mid-brain dopaminergic neurons grown from Jack’s cells produced abnormally low amounts of dopamine. The Jeff-derived culture produced normal amounts.

But here was the first surprise: Even though Jeff showed no clinical signs of Parkinson’s or any other neurological disease, the Jeff-derived culture was not exactly normal. Both twins, it turned out, had a mutation on a gene called GBA (a mutation already known to be associated with Parkinson’s disease), and as a result, both of their brain cell cultures produced just half the normal amount of an enzyme linked to that gene, beta-glucocerebrosidase. They also both produced three times the normal level of alpha-synuclein, a brain protein usually broken down by a process involving the GBA enzyme. Alpha-synuclein is thought to be related to Parkinson’s, possibly by leading to the formation of the toxic lesions known as Lewy bodies that are a hallmark of the disease.

So rather than answering questions about the twins’ discordance, these findings only raised more. Jeff had the same Parkinson’s mutation his brother had, and his brain cells in culture behaved just as abnormally in relation to the GBA enzyme and alpha-synuclein. Yet he apparently has been spared. It was a puzzle. The scientists hoped the answer existed somewhere in those two Petri dishes.

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To the twins, the “pressure cooker” way Jack dealt with stress, most grievously the loss of Gabe, helps explain Jack’s added health burden today: the Parkinson’s, the glaucoma, the prostate cancer. Jeff said those might be “physical manifestations” of the different ways they handled stress. “Jack internalizes more than I do,” he said.

The connection between stress and disease is a lively research topic, as scientists discover how life experiences alter gene expression and contribute to diseases ranging from diabetes to the common cold. But while statements about the “gene-environment interaction” have become a familiar trope, the twins’ story offers a different way to look at it. Traditionally, “environment” is defined as external events that occur over a lifetime, or the impact of those events at the molecular level, which is in the realm of epigenetics. According to Steve Cole, a professor of medicine at the University of California, Los Angeles School of Medicine, the relevant aspect of “environment” in terms of the twins might be something more interior and personal. Cole is interested in “the environment we create in our heads”—not what literally happens, but how the individual experiences what happens. “That is the most interesting aspect of the story of the twins,” he told me recently. “Their experiential environments.”

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For now, when they try to explain their divergent medical histories, the twins return to the tyranny of small differences: Jack’s more introverted personality, rockier life, quieter grieving style. In this belief they tap into the suspicions of a small cadre of neuroscientists trying to pinpoint the connection between stress and neurodegeneration. Maybe the twins are on to something the scientists are on the verge of identifying. Or maybe the brothers who have been all but inseparable are trying to protect themselves from the cruel realization that fate can unspool in dissonant ways.

 

10 Misconceptions About Evolution

• Evolution is “only a theory”  - Nope. 

• “Survival of the fittest” means that evolution favors those who are “strongest”  - “Evolutionary fitness” refers to reproductive success; more precisely, it’s a measure of the success of genes in getting themselves projected into the future and is achieved in many ways—including the ability to obtain food, to avoid becoming food for someone else, to overcome diseases, to adjust to local weather and climate, attract mates, and so forth. In a pioneering research report, male European red deer who were smaller and who bore less impressively developed antlers were often more “fit” than the hulking males, because these “sneaky fuckers” (don’t blame me: This descriptive phrase is part of the technical literature) copulated with the females while the more massive bulls were busy fighting antlero-a-antlero with other more physically developed specimens.  

• Evolution explains the origin of life (or it’s supposed to) - Nope. That is primarily a job for biophysics, biochemistry, and geology. 

• Evolution acts for the good of the species - It is estimated that something like 99 percent of species that have existed are now extinct, so if evolution is working for the good of species, it has done a terrible job! What really argues against “good of the species,” however, is the actual way natural selection operates. Although it is possible that species sometimes compete, and, as a result, better adapted ones replace their poorly adapted alternatives, evolutionary competition takes place almost entirely within species, not between them. 

• Evolutionary theory says that living things are the result of chance - No, it doesn’t. There’s a half-truth hidden here; actually, less than half. Natural selection’s power comes from differential reproduction, the logical, unavoidable process whereby some genetic variants are more successful—more fit—than others. As such, its raw material comes from genetic diversity, which is produced by mutations and, in the case of sexually reproducing species, the reshuffling of genes via meiosis and sexual recombination. These processes are essentially random. But that’s just the source of the building blocks employed by natural selection. Natural selection definitely isn’t random—it does the heavy lifting and fitting together, by picking and choosing among various options, with some genes being projected into the future more than their alternatives—i.e., our old friend differential reproduction once again. Then the process happens over and over, repeatedly retaining those that are more fit and abandoning those that are less so. 

• Because we rely more and more on brain power and less and less on our muscles, human beings in the future will have big heads and small bodies - It is similarly easy to get hung up on the Lamarckian assumption that insects, crustaceans, fish, and amphibians that inhabit pitch dark caves are often blind because they stopped using their eyes, which therefore disappeared. Not so. These evolutionary changes, which are entirely compatible with Darwinian natural selection, occur because eyes are useless in the dark—hence, they lose the selective advantage that they convey in lighted environments—and, moreover, they take energy to produce while also being vulnerable to injury and infection. So, go ahead and exercise, use your brains, and hang out in dark places if you wish … but your offspring won’t have larger biceps, bigger heads, or smaller eyes as a result. 

• Gaps in the fossil record argue against evolution - Of course there are gaps in the fossil record! It’s remarkable that we have any such records at all, given how unlikely it is that any given dead critter will be fossilized and preserved, to which we must add an additional low probability that these remains will be discovered and recognized as such, perhaps hundreds of millions of years later. As for “missing links,” picture a line between two taxonomic groups, with as yet unidentified species connecting them; now, identify something between (linking) them: Now you have two new missing links! So, any time we find intermediate forms, there will necessarily be “missing links,” because every time a linking specimen is found (such as the discovery of Australopithecines linking nonhuman primates and Homo sapiens), new missing links are produced. In short, the more fossils, the more “missing links.” 

• Human beings aren’t evolving any more - We are. It’s just that evolution is typically a very slow process, limited by selective pressures (differences in the reproductive success of different traits and the genes that underlie them), along with generation times. It is possible that human beings in the future will have evolved the ability to function and reproduce readily with microplastics and “forever chemicals” in their blood, not to mention Strontium-90 in their bones and DDT in their fat, or maybe enhanced ability to manipulate computer screens, if such individuals have more kids. Each person’s genotype is fixed, so as individuals, we don’t evolve biologically. But Homo sapiens does, and will continue to do so, unless all people and their genes reproduce identically. 

• Because of evolution, living things are always getting “better” - Not necessarily. Early in the Earth’s history, a few billion years ago, life was very simple. Since then, it has evolved increasing complexity and enhanced ability to flourish in a variety of environments. In that sense, living things have gotten “better.” But any notion of improvement is subject to human-centered bias.  

• Evolutionary biology isn’t a science because it’s a historical phenomenon and can’t be tested - Many sciences, notably astronomy and geology, engage uniquely with historical phenomena (we can’t experimentally manipulate stars or continents), and yet they generate impressive empirical testing, often based on detailed observational regimes along with falsifiable predictions. And there is no question of their status as bona fide sciences. Evolutionary biology is no different.  

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Hydromechanics Of Defecation - Most Mammals Need Only 12 Seconds To Poop

 or that mammal will be dinner to a predator. 

Its freaking common sense. 

I wrote about this few years ago: 

If someone breaks this rule daily then their health and/or diet is not good. There is something fundamentally wrong with their microbiome which in turn also affects their thought process, outlook of life and god knows what else we don't know. 

Hence, we could cautiously come up with a heuristic that not only eyes but "time to poop" is also a window to someone's character (I am not sure what soul means so let's stick to observable, known and simple words here). 

It should take 12 seconds. But that technical word "hydrodynamics of defection" is something new I learned today. 

Evolution Under A Microscope

The longest-running and most celebrated of modern evolution experiments is the appropriately named Long-Term Evolution Experiment (LTEE). Started by Richard Lenski in 1988 at the University of California, Irvine, and continuing in the hands of Jeffrey Barrick at the University of Texas at Austin, the LTEE has been running nearly continuously for 80,000 generations of E. coli over nearly 40 years. This is equivalent to two million years of human evolution.

The experiment began when 12 genetically identical populations of E. coli were grown in liquid medium. Every day since then, one percent of the previous day’s culture has been transferred into fresh medium. The medium is a dilute sugary solution limited in glucose, which E. coli uses as its primary carbon source. After about seven generations the glucose runs out and the bacteria stop growing until the next day, when they are transferred into fresh medium. Like Dallinger’s warm water, glucose-limited media is a selective pressure on the microbes, spurring the evolution of adaptations that compensate for a lack of their preferred food source.

Every 75 days (about 500 generations), a portion of LTEE’s cloudy soup of bacteria is stored in a minus-80-degree-centigrade freezer. These remain as frozen fossil records that can be used for direct comparison to their descendants.

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The LTEE has shed light on many unanswered questions about the dynamics of evolution, and experimentally validated long-running speculations. Do species improve indefinitely in a constant environment or will they stop at some maximum level? By comparing evolved E. coli with their ancestors, LTEE found that the rate of adaptation to the environment slows over time, but doesn’t plateau. Even after tens of thousands of generations in a stable laboratory environment, natural selection seems to be able to continuously eke out improvements.

Another major finding was that not all replicate populations follow the same evolutionary trajectory. In one replicate, named Ara-2, the population diverged into two coexisting lineages: one that rapidly consumes glucose and afnother that feeds on a byproduct of glucose metabolism called acetate. From a single population came a community of two.

But the most surprising finding was the observation that after about 31,000 generations, a different replicate, Ara-3, gained the ability to grow on citrate. Natural E. coli can’t metabolize citrate—in fact, it’s one of the defining features of the species—so the emergence of a strain which thrives on this carbon source could represent an entirely new species.

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Today, labs around the world are running evolution experiments of all shapes and sizes, each using microbes to understand a specific facet of evolution. Some study predation by mixing predator and prey species, and observing how each adapts to the other. Other groups have studied starvation by growing bacteria for long periods of time without the addition of any nutrients, nor the removal of dead cells. And by selecting yeasts for increased size, others have directed the evolution of macroscopic multicellularity from single-celled ancestors.

Evolution by its nature takes time. With microbes we’ve been able to condense it down to more manageable timescales, but even 80,000 generations is a blip on the evolutionary clock. As these experiments continue to run, the more we’re sure to learn from them.

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This Cannot Be True... Well I Thought I Was A Pessimistic...

A frozen food company surveyed Americans to find out their favourite and least favourite vegetables but discovered something shocking — a staggering one quarter of respondents had never even eaten one.

The survey of 2000 adults, conducted by research firm OnePoll in May on behalf of Dr. Praeger’s, found that even among those who do eat them, only one third (36 per cent) of their meals actually included a vegetable.

Seventy-two per cent of respondents said they wanted to eat more vegetables and 67 per cent said they felt guilty when they failed to eat vegies with their meal. So what’s holding them back?

One in four Americans said both that vegetables were simply “too expensive” and that “they always rot before I get a chance to eat them”, 24 per cent said they didn’t have convenient access to buying them, 22 per cent said they took too much time to prepare and 19 per cent said they didn’t know how to cook them properly.

“Most of us already know they should be eating more vegetables,” Dr. Praeger’s chief executive Larry Praeger said in a statement. “While more and more people are adopting plant-based diets, there’s still a long way to go toward reaching recommended consumption levels.”

The survey was conducted to promote the company’s Veggie Tracker website.

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What We Still Get Wrong About Psychopaths

While the idea of psychopathy as a “brain disorder” has a long history and has been studied using various technologies, it wasn’t until the year 2000 that scientists began to rigorously test it using structural and functional MRI methods. Since then, dozens of MRI studies have been published, yet the most reasonable conclusion to draw from this research is that no reliable evidence has emerged to corroborate the idea that psychopathy—as measured by the Psychopathy Checklist (PCL)—is correlated with brain abnormalities of any kind.

Overall, the experimental results are predominantly nulls with a few statistically significant but inconsistent effects (often in opposing directions), which might be better explained as a byproduct of confounding variables unrelated to psychopathy, such as substance misuse, medication, or head trauma.

This conclusion raises an important question: If there has never been any clear evidence of brain abnormalities in psychopathic persons, why do so many scientists keep portraying psychopathy as a neurodevelopmental disorder?

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Of course, it is inherently difficult to determine whether the systematic omission of null effects from the review literature is an act of scientific spin or simply an honest mistake of overlooking null effects, or a mixture of both. And perhaps it does not matter what the reason is because, whether the problem boils down to an issue with scientific spin or honest mistakes, the reality is the same: For the past two decades forensic practitioners and legal decision-makers would have been misled if they had followed due diligence and relied on the review literature when seeking information about neuroimaging research about psychopathy. The good news is that in the past years, we have seen the publication of high-quality review studies, where authors are now paying more attention to the extent of nulls.

However, even as the review literature is slowly correcting, readers should be aware that spin about the brain-disorder view of psychopathy is not a problem limited to the scientific peer-reviewed literature. It is arguably more rampant in public media, including op-eds and journalistic interviews, as well as in popular books about psychopathy, sometimes written by leading scientists. A search on YouTube and TikTok will readily yield hundreds of videos (amassing millions of views) where experts are explaining how psychopathy is caused by a brain abnormality, and it is not uncommon for TV documentaries about psychopathy to include a segment with MRI research.

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Similarly, the book The Psychopath Inside by James Fallon (from 2013) conveys an admittedly absorbing story about how Fallon himself, a neuroscientist, accidentally discovered that he was a psychopath by studying his own MRIs. Lastly, in The Psychopath Whisperer by Kent Kiehl (from 2014), the narrative centers around neuroimaging research on psychopathic persons, of which the author, a leading expert, writes that the “consistency of their [psychopathic persons’] brain abnormalities never ceased to amaze me.”

The ideas conveyed in these popular books are, of course, scientifically untenable, and they arguably border on sheer make-believe. While they are undoubtedly entertaining, they come across as a form of spin that ends up doing a disservice to forensic practitioners and legal decision-makers as they perpetuate scientifically misleading views. 

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This is how science works - constantly correcting the past wrongs. 

This is from 2014, I was fascinated by James Fallon's work that I posted on this blog too. Plus, I shared this story with so many people.  I was wrong. Science is correcting it now. 

There is a new book Murderland: Crime and Bloodlust in the Time of Serial Killers by Caroline Fraser which is making a serious impact now. 

I have theory brewing inside me for a few years now and I will post it soon. 

How the Western Diet Has Derailed Our Evolution

Indeed, when Sonnenburg fed mice plenty of fiber, microbes that specialized in breaking it down bloomed, and the ecosystem became more diverse overall. When he fed mice a fiber-poor, sugary, Western-like diet, diversity plummeted. (Fiber-starved mice were also meaner and more difficult to handle.) But the losses weren’t permanent. Even after weeks on this junk food-like diet, an animal’s microbial diversity would mostly recover if it began consuming fiber again.

This was good news for Americans—our microbial communities might re-diversify if we just ate more whole grains and veggies. But it didn’t support the Sonnenburgs’ suspicion that the Western diet had triggered microbial extinctions. Yet then they saw what happened when pregnant mice went on the no-fiber diet: temporary depletions became permanent losses.

When we pass through the birth canal, we are slathered in our mother’s microbes, a kind of starter culture for our own community. In this case, though, pups born to mice on American-type diets—no fiber, lots of sugar—failed to acquire the full endowment of their mothers’ microbes. Entire groups of bacteria were lost during transmission. When Sonnenburg put these second-generation mice on a fiber-rich diet, their microbes failed to recover. The mice couldn’t regrow what they’d never inherited. And when these second-generation animals went on a fiberless diet in turn, their offspring inherited even fewer microbes. The microbial die-outs compounded across generations.

Many who study the microbiome suspect that we are experiencing an extinction spasm within that parallels the extinction crisis gripping the planet. Numerous factors are implicated in these disappearances. Antibiotics, available after World War II, can work like napalm, indiscriminately flattening our internal ecosystems. Modern sanitary amenities, which began in the late 19th century, may limit sharing of disease- and health-promoting microbes alike. Today’s houses in today’s cities seal us away from many of the soil, plant, and animal microbes that rained down on us during our evolution, possibly limiting an important source of novelty.

But what the Sonnenburgs’ experiment suggests is that by failing to adequately nourish key microbes, the Western diet may also be starving them out of existence. They call this idea “starving the microbial self.” They suspect that these diet-driven extinctions may have fueled, at least in part, the recent rise of non-communicable diseases. The question they and many others are now asking is this: How did the microbiome of our ancestors look before it was altered by sanitation, antibiotics, and junk food? How did that primeval collection of human microbes work? And was it somehow healthier than the one we harbor today?

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Most study subjects live in the tropics; their microbial communities may reflect tropical environments, not an ancestral human state. Yet even “extinct” microbiomes from higher latitudes—including from a frozen European mummy—are similarly configured to break down plant fiber, adding to the sense that the Western microbiome has diverged from what likely prevailed during human evolution.

The Sonnenburgs think fiber is so important that they’ve given it a new designation: microbiota-accessible carbohydrates, or MACs. They think that the mismatch between the Westernized, MAC-starved microbiome and the human genome may predispose to Western diseases.

Scientists studying these communities suspect that while mortality is high from infectious diseases, chronic, non-communicable diseases are far less prevalent. At the same time, researchers since the late 20th century have repeatedly observed that even in the West, people who grow up on farms with livestock, or exposed to certain fecal-oral infections, like Hepatitis A and sundry parasites—environments that, in their relative microbial enrichment, resemble these subsistence communities—have a lower risk of certain Western afflictions, particularly hay fever, asthma, and certain autoimmune disorders.

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As Justin Sonnenburg put it, “We have this unsupervised drug factory in our gut.” The question facing microbiologists today is how to properly tend to that factory.

Here, studies of populations living more traditional lifestyles may provide clues. In the past, most people likely imbibed many times more fiber than today. If you eat minimally processed plants, which humans have for millions of years, you can’t avoid fiber. Modern hunter-gatherers and horticulturalists certainly eat loads of it. The Hadza of Tanzania, for instance, consume at least 10 times more than Americans, in tubers, baobab fruit, and wild berries. Agriculturalists, like those Burkina Fasans, also eat more fiber than Western populations, in porridges and breads made from unrefined grains.

Given this constant supply of microbiota-accessible carbohydrates, human microbiomes of the past, the Sonnenburgs argue, likely produced a river of these short-chain fatty acids. That probably changed some with the transition to agriculture, which made diets less diverse. But an even more drastic shift occurred quite recently, with the advent and widespread adoption of refined foods. As a result, westernized populations, the Sonnenburgs think, have lost healthful, fiber-fermenting microbes. And we suffer from a kind of fermentation byproduct deficiency.

So why can’t we supplement our diet with short-chain fatty acids? When I visited Sonnenburg, he showed me one reason why: The ecosystem that produces the acids may be as important as the acids themselves. He brought up two cross-sectional images of fecal pellets still in mice intestines. Most microbiome analyses take a tally, from genetic markers, of what microbes are present and in what abundance. That’s equivalent to imagining what a forest looks like from a pile of wood chips, and gives little sense of how the forest was organized. By some ingenious tinkering, though, one of Sonnenburg’s post-docs had developed a way to freeze the ecosystem in place, and then photograph it.

The resulting picture was unlike any rendition of the microbiome I’d seen before. One animal had eaten plenty of fiber, the other hadn’t. In the fiber-fed ecosystem, similar bacteria clustered with one another, not unlike schools of fish on a reef ecosystem. An undulating structure prevailed across space. But in the non-fiber diet, not only was diversity reduced, the microbes were evenly distributed throughout, like a stew boiled for too long.

At this point, Sonnenburg sat back in his chair and went quiet, waiting for me to notice something. To one side of both images, microbes were mostly absent—the mucus layer on the lining of the gut. But that layer was twice as thick in the fiber-fed mice than the non-fiber fed. That difference amounted to about 30 nanometers, far less than the width of a human hair. But one day we may look back and shake our heads that Western diseases—from diabetes to colon cancer—stemmed from 30 nanometers of mucus that, somewhere along the way, went missing in the developed world.

We think of the Western diet—high in unhealthy fats, sugar, and proteins—as overly rich. But what’s missing from the diet may be just as, and perhaps more, important than what’s abundant.

Years ago, while still a post-doc, Sonnenburg discovered that something very odd occurs when those MAC-loving microbes go hungry. They start eating mucus. “This is the stage where you say, ‘Oh my God. They’re eating me.’ ” Sonnenburg said. “You can see it.”

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The Phageome - A Hidden Kingdom Within Your Gut

You’ve probably heard of the microbiome — the hordes of bacteria and other tiny life forms that live in our guts. Well, it turns out those bacteria have viruses that exist in and around them — with important consequences for both them and us.

Meet the phageome.

There are billions, perhaps even trillions of these viruses, known as bacteriophages (“bacteria eaters” in Greek) or just “phages” to their friends, inside the human digestive system. Phageome science has skyrocketed recently, says Breck Duerkop, a bacteriologist at the University of Colorado Anschutz School of Medicine, and researchers are struggling to come to grips with their enormous diversity. Researchers suspect that if physicians could harness or target the right phages, they might be able to improve human health.

“There will turn out to be good phages as well as bad phages,” says Paul Bollyky, an infectious disease physician and researcher at Stanford Medicine. But for now, it’s still not clear how many phages occupy the gut — perhaps one for each bacterial cell, or even fewer. There are also bacteria that contain phage genes but aren’t actively producing viruses; the bacteria are just living their lives with phage DNA tagging along in their genomes.

And there are lots of phages still unidentified; scientists call them the “dark matter” of the phageome. A big part of current phage research is to identify these viruses and their host bacteria. The Gut Phage Database contains more than 140,000 phages, but that’s surely an underestimate. “Their variety is just extraordinary,” says Colin Hill, a microbiologist at University College Cork in Ireland.

Scientists find phages by sifting through genetic sequences culled from human fecal samples. That’s where researchers found the most common gut phage group, called crAssphage. (Get your mind out of the gutter — they were named for the “cross-assembly” technique that plucked their genes out of the genetic mishmash.) In a recent study, Hill and colleagues detailed a light-bulb shape for crAssphages, with a 20-sided body and a stalk to inject DNA into host bacteria.

It’s not clear whether crAssphages make a difference to human health, but given that they infect one of the most common groups of gut bacteria, Bacteroides, Hill wouldn’t be surprised if they did. Other common groups, which also infect Bacteroides, include the Gubaphage (gut bacteroidales phage) and the LoVEphage (lots of viral genetic elements).

Phageomes vary widely from person to person. They also change depending on age, sex, diet and lifestyle, as Hill and colleagues described in the 2023 Annual Review of Microbiology.

Though phages infect bacteria and sometimes kill them, the relationship is more complicated than that. “We used to think that phage and bacteria are fighting,” says Hill, “but now we know that they’re actually dancing; they’re partners.”

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Phages also keep bacterial populations from getting out of hand. The gut is an ecosystem, like the woods, and phages are bacteria predators, like wolves are deer predators. The gut needs phages like the woods needs wolves. When those predator-prey relationships are altered, disease can result. Researchers have observed phageome changes in inflammatory bowel syndrome (IBS), irritable bowel disease and colorectal cancer — the viral ecosystem of someone with IBS is often low in diversity, for example.

People try to re-balance the gut microbiome with diets or, in extreme medical cases, fecal transplants. Tackling phages might provide a more fine-tuned approach, Hill says. As a case in point, scientists are seeking phages that could be used therapeutically to infect the bacteria that cause ulcers.

Be grateful for the trillions of phages managing your gut’s ecosystem. Without them, Hill suggests, a few kinds of bacteria might quickly come to dominate — potentially leaving you unable to digest some foods and subject to gas and bloating.

The wild and wondrous phageome is a dance partner for bacteria and humans alike.

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Grow Up - Enough With the Fireworks Already

Growing up in India, I enjoyed celebrating Diwali because I could play with fire and be macho. 

As time passed, I grew the fuck up. I grew the fuck up. I learned how much fireworks harm animals, ecosystems and the environment. 

So grow the fuck up and stop using fireworks in name of god knows what. Fireworks has nothing to do with you political ideology. 

Margaret Renkl reminds us that same but more politely than I do: 

For 15 straight years, our old dog Clark — a hound-shepherd-retriever mix who was born in the woods and loved the outdoors ever after — spent the Fourth of July in our walk-in shower. He seemed to believe a windowless shower in a windowless bathroom offered his best chance of surviving the shrieking terror that was raining down from the night sky outside.

Did he think the fireworks, with their window-rattling booms, were the work of some cosmic predator big enough to eat him whole? Did he think they were gunshots or claps of thunder spreading out from inexplicable lightning bolts tearing open the sky above our house?

There’s no way to know what he was thinking, but every single year that rangy, 75-pound, country-born yard dog spent the Fourth of July in our shower, trembling, drooling and whimpering in terror.

Clark was lucky. We have friends whose terrified dog spent one Fourth of July fruitlessly trying to outrun the explosions. The next day a good Samaritan found him lying on a hot sidewalk miles away, close to death. Other friends came home from watching the fireworks to discover that their dog had bolted in terror from their fenced backyard and been killed by a car.

And those were all companion animals, the ones whose terror is clear to us. We have no real way of knowing how many wild animals suffer because the patterns of their lives are disrupted with no warning every year on a night in early July. People shooting bottle rockets in the backyard might not see the sleeping songbirds, startled from their safe roosts, exploding into a darkness they did not evolve to navigate — crashing into buildings or depleting crucial energy reserves. People firing Roman candles into the sky above the ocean may have no idea that the explosions can cause seabirds to abandon their nests or frighten nesting shorebirds to death.

Then there’s the wildlife driven into roads — deer and foxes, opossums and skunks, coyotes and raccoons. Any nocturnal creature in a blind panic can find itself staring into oncoming headlights, unsure whether the greater danger lies in the road or in the sky or in the neighborhood yards surrounding them.

And all that’s on top of the dangers posed by fireworks debris, which can be toxic if ingested, or the risk of setting off a wildfire in parched summertime vegetation. Little wonder, then, that fireworks are banned in all national wildlife refuges, national forests and national parks.

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“All flourishing is mutual,” writes Robin Wall Kimmerer, a botanist and enrolled member of the Citizen Potawatomi Nation, in her best-selling book, “Braiding Sweetgrass.” This is one of the most repeated lines in contemporary environmental literature, and for good reason. It reminds us that all creation, human and other than human, is interconnected. At a time when life on this planet is faltering in every possible way, Dr. Kimmerer gently points out that our own flourishing depends on the flourishing of planetary systems that we are barely beginning to understand.

Addressing climate change and biodiversity loss on a planet with eight billion human residents won’t be simple. How to grow affordable food without using petrochemical fertilizers and pesticides that poison pollinators, for example, is a challenge. How to build enough housing for human beings without also disrupting natural ecosystems is a challenge. Such things are doable, though they won’t be easy.

But there are easy things we can do at no real cost to ourselves. We can eat more vegetables and less animal protein. We can cultivate native plants. We can seek out products that aren’t packaged in plastic, spend less time in cars and airplanes, raise the thermostat in the summer and lower it in the winter. As Dr. Kimmerer points out in “The Serviceberry,” her forthcoming book, “We live in a time when every choice matters.”

In that context, surely, we can give up fireworks. Of all the little pleasures that give life meaning and joy, surely fireworks don’t come close to the top of the list, and it costs us nothing to give them up. This is one case in which doing the right thing requires no significant sacrifice, one case in which doing the right thing has an immediate, noticeable, undeniably positive effect on a suffering world.

The conflation of selfishness with patriotism is the thing I have the hardest time accepting about our political era. Maybe we have the right to eat a hamburger or drive the biggest truck on the market or fire off bottle rockets deep into the night on the Fourth of July, but it doesn’t make us good Americans to do such things. How can it possibly be American to look at the damage that fireworks can cause — to the atmosphere, to forests, to wildlife, to our own beloved pets, to ourselves — and shrug?

The truly American thing would be to join together to make every change we can reasonably make to alleviate the suffering of our fellow creatures, human and other than human alike. The truly American thing would be to plant a victory garden large enough to encompass the entire natural world.

 

Obelisks - Virus-Like Entities in Our Gut

Another example of epistemic humility; we have not even scratched the surface of knowledge (leave alone humans who act like they have passed the end of knowledge). 

Viroids are small, infectious, and circular RNA molecules that are distinct from typical viruses. Unlike viruses, viroids do not possess a protective protein coat. They were initially discovered in plants, causing various diseases, and were later identified in fungi. Viroids are known for their ability to replicate autonomously within host cells, co-opting cellular machinery for their own reproduction.

Initially believed to exclusively infect plants, recent research suggests viroids may extend their reach to other hosts, including animals, fungi, or bacteria. In the current study, researchers delved into the genes of microbes inhabiting the human body, exploring the potential existence of viroids in this domain. They termed newly found viroids “Obelisks” due to their predicted 3D structure resembling a thin rod when they fold onto themselves.

[---]

Recently discovered Obelisks appeared to include instructions for replication enzymes, rendering them more intricate than previously described viroids. However, akin to most viroids, they still lacked directives for a protective outer shell. The impact of these viroids on human health remains uncertain, although they could potentially influence the human microbiome by infecting bacteria. Additionally, ongoing discussions surround the evolutionary relationship between viruses and viroids — fueling the debate & questioning whether viruses evolved from viroids or vice versa.

In essence, these recent discoveries not only add layers to our understanding of human anatomy but also underscore the ongoing process of discovery and refinement in the field of medical science. The impact lies in the potential to enhance our ability to diagnose, treat, and prevent various health conditions through a more comprehensive understanding of the human body’s intricate workings. 

Archaea, Horizontal Gene Transfer et al.,

Since the late 1970s, there have come three big surprises about what we humans are and about how life on our planet has evolved.

The first of those three surprises involves a whole category of life, previously unsuspected and now known as the archaea. (They look like bacteria through a microscope, but their DNA reveals they are shockingly different.) Another is a mode of hereditary change that was also unsuspected, now called horizontal gene transfer. (Heredity was supposed to move only vertically, from parents to offspring.) The third is a revelation, or anyway a strong likelihood, about our own deepest ancestry. (It seems now that our lineage traces to the archaea.) So we ourselves probably come from creatures that, as recently as forty years ago, were unknown to exist.

One of the most disorienting results of these developments is a new challenge to the concept of “species.” Biologists have long recognized that the boundaries of one species may blur into another—by the process of hybridism, for instance. And the notion of species is especially insecure in the realm of bacteria and archaea.  But the discovery that horizontal gene transfer (HGT) has occurred naturally, many times, even in the lineages of animals and plants, has brought the categorical reality of a species into greater question than ever. That’s even true for us humans—we are composite individuals, mosaics.

It’s not just that—as you may have read in magazine articles—your human body contains at least as many bacterial cells as it does human cells. (This doesn’t even count all the nonbacterial microbes—the virus particles, fungal cells, archaea, and other teeny passengers inhabiting our guts, mouths, nostrils, and other bodily surfaces.) That’s the microbiome. Each of us is an ecosystem.

I’m talking about something else, a bigger and more shocking discovery that has come from the revolution in a field called molecular phylogenetics. (That phrase sounds fancy and technical, but it means merely the use of molecular information, such as DNA or RNA sequences, in discerning how one creature is related to another.) The discovery was that sizeable chunks of the genomes of all kinds of animals, including us, have been acquired by horizontal transfer from bacteria or other alien species.

How could that be possible? How could genes move sideways, between species, not just vertically along ancestral lineages? The mechanisms are complex, but one label that fits most of them is “infective heredity.”  DNA can be carried across boundaries, from one genome to another, by infective agents such as bacteria and viruses. Such horizontal gene transfer, like sex, has been a source of freshening innovation in otherwise discrete lineages, including ours—and it is still occurring.

This is an aspect of evolution that was unimagined by Charles Darwin. Evolution is trickier, far more intricate, than we had realized. The tree of life is more tangled.

[---]

These discoveries should not merely complicate our magisterial human self-image, but also help lead us toward a wiser and humbler understanding of our place—collectively and as “individuals” within the “species” Homo sapiens—in the story of life on Earth.

It’s a story in which we humans are important protagonists but not the ultimate and predestined heroes. It’s a story in which heredity has moved sideways as well as vertically and all the conventional hierarchies and boundaries have proven more imperfect, transgressible, and leaky than we had supposed. But these revelations don’t diminish our responsibility, as humans, to respect and preserve the diversity of living creatures, with all their own mosaic genomes and tangled lineages, who cohabit the planet with us. On the contrary, I think. All this should make us only more amazed, respectful, and careful. Life on Earth is wondrous precisely because it’s so complicated.

- More Here

Very Good Sentence On Microbiome, Diet & Health

Inulin, a fiber that we know supports the growth of beneficial bacterial strains, and found we could dampen down the neuroinflammation that is often associated with cognitive decline in aging. This fiber is present in our everyday diet — there is a lot of it in vegetables like leeks, artichokes and chicory. So perhaps if you’re thinking of having a midlife crisis, forget about the motorbike and start growing vegetables.

- Neuroscientist John Cryan (Man and the Microbiome: A New Theory of Everything?)

Distributed!

Old ideas refuse to die hard. 

One human being's knowledge is limited; hence bureaucratic systems fail - soviet style. But yet, Aristotle is celebrated even though numerous ideas of his turned out to be false and some outright dangerous. One thing we can learn from his failures is not to try to be super intelligent and work on everything under the sun. It is impossible for one human to do that. I think he did this to prove Plato wrong (he wasn't selected to lead Plato's academy after Plato). 

Of course, there is this other dangerous guy in recent times namely Rene Descartes!

Brain in a vat theory is wrong. Brain is not omnipotent. Evolution is frugal. It doesn't do central planning and creates redundancies. 

For starters, there are 9 times more connections from gut to brain than the other way around. The ratio of microbiome to human cell is mind boggling. Each organ inside our body has a two way connection to the brain (and other parts). And our environment affects our thinking and health. Living with non-human animals has a wonderful impact and same with plants inside the house and trees all around.  

In short, we are a complex system and the brain is just a part of it. 

I respect people who fight bad ideas of centuries.  

I refuse to read anything consciousness, intelligence et al., if they focus only on "brain" and it's "elegance"; which is 99.9% of the books and researchers. 

Brilliant interview with Botanist Stefano Mancuso; author of new book Tree Stories: How trees plant our world and connect our lives (it's released in UK but not in US yet)

You refer to your field as plant neurobiology. Is this a provocation?

At the beginning, it was not at all. I started to think that almost all the claims I was hearing about the brain were valid also in plants. The neuron is not a miracle cell, it’s a normal cell that is able to produce an electrical signal. In plants, almost every cell is able to do that. The main difference between animals and plants, in my opinion, is that animals concentrate specific functions inside organs. In the case of plants, they diffuse everything through the whole body, including intelligence. So it was not a provocation at the beginning, but there was a big resistance among my colleagues to use this kind of terminology, and so after it became a provocation.

[---]

The idea that plants are intelligent is controversial enough, but you’ve gone one step further by claiming that plants are to some degree conscious…

It’s incredibly difficult to talk about consciousness, first because we actually don’t know what consciousness is, even in our case. But there is an approach to talking about it as a real biological feature: consciousness is something that we all have, except when we are sleeping very deeply or when we are under anaesthesia. My approach to studying consciousness in plants was similar. I started by seeing if they were sensitive to anaesthetics and found that you can anaesthetise all plants by using the same anaesthetics that work in humans. This is extremely fascinating. We were thinking that consciousness was something related to the brain, but I think that both consciousness and intelligence are more embodied, relating to the entire body.

[---]

You argue passionately in favour of filling cities with trees. Why is this so important?

We are producing 75% of our CO₂ in cities, and the best way to remove that CO₂ is by using trees. The closer the tree is to the source of carbon emissions, the better they are at absorbing it. According to our studies, we could put around 200bn trees in our urban areas. To do that, we really need to imagine a new kind of city, completely covered by plants, without any border between nature and city.

You have a fascinating chapter about a tree stump being kept alive for decades by its neighbouring trees. What can humans learn from tree communities?

Plants are so incredibly cooperative with one another because cooperation is the most efficient way to grant the survival of species. Not understanding the strength of the community is one of [humanity’s] main errors. There was a very clever evolutionary biologist at the beginning of the last century, Peter Kropotkin, who said that when there are fewer resources, and the environment is changing, then cooperation is vastly more efficient [than competition]. This is an important teaching for us today, because we are entering a period of reduction of resources and the environment is changing because of global warming.

Max would have loved being in his Walden! 

Neo doesn't know the wild wild world except Max's Walden. 

Behavioural Effects of Toxoplasma Gondii In Wild Animals

It's been decades or so since Toxo broke the myth of free will and "elegance" of the human brain. Our body and mind are a complex system living and dying in an entangled web of multitude of creatures we neither understand nor comprehend. Hence, this blog even has a Microbes and Us label. 

Another paper on Toxo - how it affects Wolves to become pack leaders. 

Wolves infected with a common parasite are more likely than uninfected animals to lead a pack, according to an analysis of more than 200 North American wolves1. Infected animals are also more likely to leave their home packs and strike out on their own.

I bet there is so much research on Toxo over the past two decades because of availability bias and riding fast on past research. I might be wrong. 

But the question is how many other protozoa, bacteria and parasites are affecting humans and how? What about even Toxo's research on human behavior changes et al.,?

Did Fluffy or Garph affect me with Toxo? 

Poop Redux!

When Max was a puppy, it took me a few months to train him to understand the difference between poop time vs walk time.  I wanted to make sure he knew this difference since in case of emergency or bad weather , we can skip the walk. 

He would have to poop in a particular area(s) without walking so that he doesn't take his sweet time to poop. Max understood the difference and for the rest of his life he followed this. 

Yes, Max would take his time to sniff but after he squats, he would poop within 10 to 30 seconds. Neo does the same now. And yes, same for me as long as I could remember. 

So it always baffles me when people sit in the toilet and read New Times for minutes if not hours. 

After years of living with Max and when he got prostate cancer, he started struggling to poop. It would happen to me very rarely when I had too much junk food or not feeling well mentally. 

I don't remember when I came up with this hypothesis but it was long before Max had cancer:  

Evolutionarily, if John squatted to poop in African Savanna's pondering about life for minutes, he would soon be an easy dinner for any predator.  We all are evolved to poop only for few seconds. 

If someone breaks this rule daily then their health and/or diet is not good. There is something fundamentally wrong with their microbiome which in turn also affects their thought process, outlook of life and god knows what else we don't know. 

Hence, we could cautiously come up with a heuristic that not only eyes but "time to poop" is also a window to someone's character (I am not sure what soul means so let's stick to observable, known and simple words here). 

In recent years, there has been a lot of research going on to support my simple hypothesis. Earlier post stating that around 12 seconds should be our optimal poop time!

A new paper is telling us, microbiome helps to extract energy effectively from what we eat and hence we poop within seconds. If someone is struggling to poop then the process of extracting energy from food is not optimized ad takes a long time because of lack of microbial diversity. 

Abstract

Background

It has been hypothesised that the gut microbiota causally affects obesity via its capacity to extract energy from the diet. Yet, evidence elucidating the role of particular human microbial community structures and determinants of microbiota-dependent energy harvest is lacking.

Results

Here, we investigated whether energy extraction from the diet in 85 overweight adults, estimated by dry stool energy density, was associated with intestinal transit time and variations in microbial community diversity and overall structure stratified as enterotypes. We hypothesised that a slower intestinal transit would allow for more energy extraction. However, opposite of what we expected, the stool energy density was positively associated with intestinal transit time. Stratifications into enterotypes showed that individuals with a Bacteroides enterotype (B-type) had significantly lower stool energy density, shorter intestinal transit times, and lower alpha-diversity compared to individuals with a Ruminococcaceae enterotype (R-type). The Prevotella (P-type) individuals appeared in between the B- and R-type. The differences in stool energy density between enterotypes were not explained by differences in habitual diet, intake of dietary fibre or faecal bacterial cell counts. However, the R-type individuals showed higher urinary and faecal levels of microbial-derived proteolytic metabolites compared to the B-type, suggesting increased colonic proteolysis in the R-type individuals. This could imply a less effective colonic energy extraction in the R-type individuals compared to the B-type individuals. Notably, the R-type had significantly lower body weight compared to the B-type.

Conclusions

Our findings suggest that gut microbial energy harvest is diversified among individuals by intestinal transit time and associated gut microbiome ecosystem variations. A better understanding of these associations could support the development of personalised nutrition and improved weight-loss strategies.

 

Lichens Can Help Indicate Change In Sea Level

It takes more than just salt sensitivity to make a lichen a good indicator of whether a site has experienced the first effects of sea level rise. The lichen’s own life history also comes into play.

Species like the powdery medallion lichen (left photo) can be killed if subjected to too much salt water by a storm or flood. But this lichen’s quick reproduction lets it swiftly recolonize after the sea recedes. Larger species with slower growth and reproduction, and also low salt tolerance, like the ruffled blue jellyskin (right photo), can better tell the saltwater history of a site. These salt-intolerant lichens could not have survived and grown if a saltwater event like storm spray or flooding had occurred at any point during their life. Since some lichen species can live for decades or longer, the record they provide can be both hyperlocal in space and extensive in time.

Of the 48 different lichen species Rosentreter and DeBolt found at their two Florida survey sites, 11 are reliable indicators of salt water’s presence. Seven of the species only like to grow in places with very low saltwater impact, while four are salt tolerant, so finding them growing suggests the site has a moderate history of salt and a higher risk of being affected by rising seas.

In general, they found that the species that best indicate if a site will be relatively safe from sea level rise and saltwater inundation are lichens that are larger and leafier and often light green or blue in color. But lichens can be tricky to identify, and some promising indicator species look quite similar to less useful ones. “You’ve got to be at least an intermediate plant person to figure it out,” says Rosentreter.

- More Here

I have been learning more and more about Lichens this year!

How Mud Boosts Your Immune System

Today, many parents may secretly wish their children had the chance to pick up a bit of grime. With the rise of urbanism, and the allure of video games and social media, contact with nature is much rarer than in the past. For many, there is simply no opportunity to get muddy.

What is gained in laundry bills may be lost in the child's wellbeing. According to recent research, the dirt outside is teaming with friendly microorganisms that can train the immune system and build resilience to a range of illnesses, including allergies, asthma and even depression and anxiety.

These findings show that outdoor exercise is not only beneficial because of the chance to roam free – but that certain natural materials, such as soil and mud, also contain surprisingly powerful microorganisms whose positive impact on children's health we are only beginning to fully understand.

[---]

The new research offers a fresh take on the "hygiene hypothesis", first postulated in the late 1980s. According to this idea, the great reduction in childhood infections over the 20th Century had an undesirable side effect on people's immune systems, leading them to become overreactive to the slightest stimulation. The result was thought to be the rise in asthma, hay fever and food allergies.

Many scientists now dislike the term hygiene hypothesis, however, since it seemed to discourage important behaviours like hand-washing. And they balk at the idea that infections, per se, are beneficial for children. "It was quite problematic from a public health perspective," says Christopher Lowry, a professor of integrative physiology and the director of the behavioural neuroendocrinology laboratory at the University of Colorado, Boulder, US.

Instead, it is the non-infectious organisms that are now thought to be key – rather than the ones that actually make our children sick. These "old friends" have been around for much of our evolutionary history. They are mostly harmless, and train the immune system to moderate its activity, rather than overreacting to any potential invader.

Importantly, our bodies meet these old friends whenever we spend time in nature. With increased urbanisation, and reduced outdoor play, many children now lack that exposure – meaning that their immune systems are more sensitive to any threat, and more likely to go into overdrive.

- More Here

Learn, Act, Update Learnings From Action. Repeat - Saul Griffith's Book Electrify & Other Sustainable Practices

Never doubt that a small group of thoughtful, committed citizens can change the world. Indeed, it is the only thing that ever has.

- Margaret Mead

What Margaret Mead missed in the above fact is that even simple changes by a small group of people has the power to change the status quo for good. Nassim Taleb calls it "Minority Rule".

Let us conjecture that the formation of moral values in society doesn’t come from the evolution of the consensus. No, it is the most intolerant person who imposes virtue on others precisely because of that intolerance. The same can apply to civil rights.

Do simple changes to your life everyday instead of signaling, arguing and making language based noise which roughly translates to "I am a good human",  "I am pro market",  "I care for the planet, poor people animals, and nature" and other similar bullshit phrases.

Saul Griffith's Book Electrify: An Optimist's Playbook for Our Clean Energy Future is meant educate us fast.

 “Here, I will try to offer you dinner party-ready talking points for the main questions that people will inevitably have for the main argument of the book. Each topic is worthy of a book in itself. If I dispose of a favorite baby of yours too quickly here, or you think I have it all ass-backward, then we should grab a beer sometime.”

Read the excerpts here and some actionable items: 

Stop the insanity of spreading "I love to travel" bullshit: 

Flying is energy-intensive per minute, but not per mile. Per passenger-mile traveled, it requires approximately the same energy as driving in a car with a passenger. That said, reducing the number of flights taken is one of the most effective ways for individuals to reduce their energy footprints.

Embrace nuclear energy and vote for candidates who will help innovate in nuclear waste management:

America has led the world in nuclear power. The U.S. Navy operates the largest fleet of small reactors in the world, and it boasts an impeccable safety record. Nuclear is a form of electrification, and it fits squarely with the plan to fight global heating. Nuclear power currently delivers around 100 gigawatts of very reliable electricity to America’s grid. Maintaining or even ambitiously increasing this amount would no doubt make the climate solution easier. Today’s best estimates have nuclear energy at approximately double the cost of wind and solar. Without a doubt, those costs could be trimmed enormously given advances in engineering, since most of these plants were designed 50 years ago.

The health effects of nuclear power have been well studied. It is established that nuclear is not as dangerous as we tend to think. But like shark attacks, it’s the prospect of a low-probability event that could release radiation that drives our fears. We can lower that probability further by building dedicated infrastructure like the facility at Yucca Mountain, but the fact remains that for 40 years, policymakers haven’t been sufficiently able to convince people to invest in this kind of infrastructure. Nuclear power will remain a very difficult political topic unless we have a breakthrough in waste management.

Pick a shovel today and plant trees:

Yes, we should — at least a trillion. Grab a shovel!

The best time to plant a tree is 30 years ago. The second-best time to plant a tree is today.

Go plant a tree for your grandkids to climb on. Even better, go plant 30,000.

Remember - Electrify book is meant to enlightened you on how to help yourself not nature. Nature will do just fine with or without humans. 

Gia Mora has small-little-beautiful changes you can make at home to help yourself and your health. 

• Trade Beef for Beans - I eat lots of lentils and beans. Plus no meat in Max's house. 

• Buy Local Instead of Commercial - I haven't been to the grocery store in years and buy everything in small farms.

• Turn Your Food Waste Into More Food - I cook beet leaves like spinach to all parts of cauliflower and broccoli. Start composting for other things. Read the book The No-Waste Vegetable Cookbook: Recipes and Techniques for Whole Plant Cooking by Linda Ly.

• Trade Disposables for a Zero-Waste Kit - Since Max passed away, I have almost replaced all plastic items with bamboo or eco friendly products. Cancer and our health is a complex system, its easy to eliminate bad health triggers from micro-plastic.

• Select Experiences Over Things - This doesn't mean travel (I cannot get over this mindless act from most humans) but go for simple walk, workout, listen to music and zillion other simple pleasures. Read E. F. Schumacher's classic book Small is Beautiful - cross domains and apply to daily life. 

• Get Your Shopping Fix Secondhand - I don't follow this when it comes to clothes. I retain my clothes for decades and donate every year. Quite a few kitchen items I still own are over 2 decades old bought from thrift stores when I had little money. 

• Invest in Quality Instead of Buying Cheap - Prius, Dyson and Apple are expensive but they are worthy long term investments.

• Make Your Own Cleaning Supplies - I don't and opt to buy not tested on animals for 2 decades. 

• Trade Plastic Cleaning Tools for Natural Alternatives - Covered in fourth point above. 

• Choose Reusable Cloths Over Paper Towels - Been doing this for years. Unfortunately when Max got cancer, I had to buy lots of paper towels. Went back to minimal use of paper towels now. 

• Store Food in Glass or Beeswax In Lieu of Plastic - Covered in fourth point above. 

• Reuse (Don’t Toss) Your Old Water - I don't capture rain water. I should start doing it. Watch the classic national award winning Tamil movie Thaneer Thaneer (Water, Water). K.Balachander's insight of increasing awareness of preserving water will make you cry. And stop playing golf and eliminate your lawns. 

• Wash Your Clothes in Cold Water Instead of Hot - Been doing this for 2 decades. Understand - there has been great innovation in the science of laundry detergents to clean effectively using cold water. Most people are unaware of (or under-rate) the innovations in home and body cleaning products. 

• Flush Less - Pee-flush happens once or twice a day. 

• Switch to a Sustainable Toilet Paper - I tried this a few times in the past years but it didn't work. I should try again since there are new products on the market. 

• Unscrew Your Incandescents for LEDs - Done that over a decade ago.

• Control the Temperature Outside of the Thermostat - One of the first adopter of Nest thermostat and it works great. 

• Don’t Just Turn Off—Unplug - I tried this decade ago and it worked. I took an alternate path - plug only lights, computers and coffee maker. I can be more conscientious.

• Switch to Renewable Energy - I am trying. Most solar companies are rejecting me stating I have too many trees - go figure the insanity.

• Trade Your Daily Drive for a Different Commute - I did car pooling to work for over a decade and now it doesn't apply to me. 

• Trade Travel Emissions for Staycations - Read the book Happier at Home: Kiss More, Jump More, Abandon a Project, Read Samuel Johnson, and My Other Experiments in the Practice of Everyday Life by Gretchen Rubin to cure yourself of the cancer called travel. 

I posted a couple of days ago about a meaningless book called What We Owe The Future full of useless philosophy and bullshit thought experiments. 

Stop reading such books and focus on what you can act on in everyday life and act on it continuously. Learn from mistakes and act empowered by new knowledge. Continue this Bayesian cycle untiring until the end of life. 

I am following a lot of things in the above list but the beauty of the Bayesian cycle will help me change soon by showing how much wrong I am doing by sheer blindness and lack of knowledge. Since Max died in 2019, I have made many simple changes in daily life from painful learnings of losing Max. 

This bayesian cycle will not only help your health long term but most importantly it will be your daily ally to your mind see reality as it is.

 

In Praise Of Parasites

By some estimates, nearly half of the species in the animal kingdom are parasites. Most of them remain largely out of sight because they are small, even microscopic. Their ancestors didn’t always start with a parasitic lifestyle: Researchers have so far found 223 incidents where parasitic insects, worms, mollusks or protozoans evolved from non-parasitic predecessors. Some ate dead things. Others killed their prey and consumed it. Then their life strategy evolved because they proved more successful if they kept their prey alive, kept their victims close — so they could feed on them longer. It’s a strategy distinct from those of parasitoids, which outright kill their hosts, Lafferty explains, a glint of mischief in his eye. “Think about the movie Alien.  Remember when the alien sock puppet bursts its head out of John Hurt’s chest? That’s a classic parasitoid.”

[---]

He is also a serious marine ecologist who holds passionately that parasites are worthy of study for how they influence ecological systems and how ecosystems influence them. For years, it was a fairly lonely position to take:  “Ecologists have built hundreds of food webs and they haven’t put parasites in them. And what we’ve lost from that is the ability to even think about parasites and their role in ecology,” Lafferty says. Ecology conferences used to struggle with where to place Lafferty’s talks in their schedules, but nowadays the meetings have dedicated sessions on wildlife infectious diseases. And ecologists, especially younger ones, are starting to recognize that they are missing part of the story if the food webs they model don’t include parasites that can influence predator-prey relationships and competition for resources. As illustrated by the trematode in the killifish, Lafferty says, “parasites are determining who lives and who dies in a way that benefits them.”

Moreover, parasites are a useful way to explore broader ecological questions: How does energy flow through those food webs? What forces maintain ecological stability and keep one species from overrunning all others? What are the implications of robust and healthy biodiversity on human health? Ecologists debate all sorts of competing theories, Lafferty says. What’s clear to him and other like-minded parasitologists: “We cannot answer these questions if we are going to ignore the parasite part of the equation.”

[---]

It hit him that here was an opportunity to break new ground. “Although lots of people had studied parasites for their own sake, or as problems to be solved, it seemed like an open playing field to start asking how parasites fit into natural ecosystems,” he says. He spent the next two years cracking horn snails with a hammer to collect trematodes in estuaries from San Francisco to Baja. His work solidified how the parasites were affecting the snails’ abundance and evolution — finding, for example, that snails in areas with high infection rates have evolved to mature and reproduce early, before they get castrated.

- More here including Toxoplasma gondii. 

We know Toxoplasma causes "feline attraction" but it might also slow reaction times or diminish ones ability to focus, these may be why infected people have a nearly threefold higher chance of being involved in a car accident.

Modular Cognition, Pattern Completion Et Al., - A Hypothesis

This is intelligence in action: the ability to reach a particular goal or solve a problem by undertaking new steps in the face of changing circumstances. It’s evident not just in intelligent people and mammals and birds and cephalopods, but also cells and tissues, individual neurons and networks of neurons, viruses, ribosomes and RNA fragments, down to motor proteins and molecular networks. Across all these scales, living things solve problems and achieve goals by flexibly navigating different spaces – metabolic, physiological, genetic, cognitive, behavioural.

But how did intelligence emerge in biology? The question has preoccupied scientists since Charles Darwin, but it remains unanswered. The processes of intelligence are so intricate, so multilayered and baroque, no wonder some people might be tempted by stories about a top-down Creator. But we know evolution must have been able to come up with intelligence on its own, from the bottom up.

Darwin’s best shot at an explanation was that random mutations changed and rearranged genes, altered the structure and function of bodies, and so produced adaptations that allowed certain organisms to thrive and reproduce in their environment. (In technical terms, they are selected for by the environment.) In the end, somehow, intelligence was the result. But there’s plenty of natural and experimental evidence to suggest that evolution doesn’t just select hardwired solutions that are engineered for a specific setting. For example, lab studies have shown that perfectly normal frog skin cells, when liberated from the instructive influence of the rest of the embryo, can reboot their cooperative activity to produce a novel proto-organism, called a ‘xenobot’. Evolution, it seems, doesn’t come up with answers so much as generate flexible problem-solving agents that can rise to new challenges and figure things out on their own.

The urgency of understanding intelligence in biological terms has become more acute with the ‘omics’ revolution, where new techniques are amassing enormous amounts of fresh data on the genes, proteins and connections within each cell. Yet the deluge of information about cellular hardware isn’t yielding a better explanation of the intelligent flexibility we observe in living systems. Nor is it yielding sufficient practical insights, for example, in the realm of regenerative medicine. We think the real problem is not one of data, but of perspective. Intelligence is not something that happened at the tail end of evolution, but was discovered towards the beginning, long before brains came on the scene.

From the earliest metabolic cycles that kept microbes’ chemical parameters within the right ranges, biology has been capable of achieving aims. Yet generation after generation of biologists have been trained to avoid questions about the ultimate purpose of things. Biologists are told to focus on the ‘how’, not the ‘why’, or risk falling prey to theology.

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 Modularity provides stability and robustness, and is the first part of the answer to how intelligence arose. When changes occur to one part of the body, its evolutionary history as a nested doll of competent, problem-solving cells means subunits can step up and modify their activity to keep the organism alive. This isn’t a separate capacity that evolved from scratch in complex organisms, but instead an inevitable consequence of the ancient ability of cells to look after themselves and the networks of which they form a part. 

But just how are these modules controlled? The second step on the road to the emergence of intelligence lies in knowing how modules can be manipulated. Encoding information in networks requires the ability to catalyse complex outcomes with simple signals. This is known as pattern completion: the capacity of one particular element in the module to activate the entire module. That special element, which serves as a ‘trigger’, starts the activity, kicking the other members of the module into action and completing the pattern. In this way, instead of activating the entire module, evolution needs only to activate that trigger. 

Pattern completion is an essential aspect of modularity which we’re just beginning to understand, thanks to work in developmental biology and neuroscience. For example, an entire eye can be created in the gut of a frog embryo by briefly altering the bioelectric state of some cells. These cells are triggered to complete the eye pattern by recruiting nearby neighbours (which were not themselves bioelectrically altered) to fill in the rest of the eye. Similar outcomes can be achieved by genetic or chemical ‘master regulators’, such as the Hox genes that specify the body plan of most bilaterally symmetrical animals. In fact, one could relabel these regulator genes as pattern completion genes, since they enable the coordinated expression of a suite of other genes from a simple signal. The key is that modules, by continuing to work until certain conditions are met, can fill in a complex pattern when given only a small part of the pattern. In doing so, they translate a simple command – the activation of the trigger – and amplify it into an entire program. 

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We have sketched a set of approaches to biology that rely heavily on concepts from cybernetics, computer science, and engineering. But there’s still a lot of work to do in reconciling these approaches. Despite recent advances in molecular genetics, our understanding of the mapping between the genome on the one hand, and the (changeable) anatomy and physiology of the body on the other, is still at a very early stage. Much like computer science, which moved from rewiring hardware in the 1940s to a focus on algorithms and software that could control the device’s behaviour, biological sciences now need to change tack.

The impact of understanding nested intelligence across multiple scales cuts across numerous fields, from fundamental questions about our evolutionary origins to practical roadmaps for AI, regenerative medicine and biorobotics. Understanding the control systems implemented in living tissue could lead to major advances in biomedicine. If we truly grasp how to control the setpoints of bodies, we might be able to repair birth defects, induce regeneration of organs, and perhaps even defeat ageing (some cnidarians and planarian flatworms are essentially immortal, demonstrating that complex organisms without a lifespan limit are possible, using the same types of cells of which we are made). Perhaps cancer can also be addressed as a disease of modularity: the mechanisms by which body cells cooperate can occasionally break down, leading to a reversion of cells to their unicellular past – a more selfish mode in which they treat the rest of the body as an environment within which they reproduce maximally.

- More Here

The idea of modular cognition is beautiful and I almost fell head-over-heels for it. 

But... once again, people conveniently forget that we are dealing with complex systems. 

Just a cursory second reading of this piece will expose the "know" missing pieces. Microbiomes for starters and there is this thing called "exposome" which covers those "little" things namely the environmental factors. And of-course there are myriads of unknowns. 

Nevertheless, the "why" question they ask - "why biology acts this way" is extremely important. 

I am convinced our generation and many generations to come will fail to answer this question only because people are not used to asking the why question at the micro level. Maybe, someday this question will be answered and should be answered. The hypothesis of "Pattern Completion" is small step forward and kudos to those who are working on such hard problems.