Puzzle Of Horizontal Gene Transfer

To survive in the frigid ocean waters around the Arctic and Antarctica, marine life evolved many defenses against the lethal cold. One common adaptation is the ability to make antifreezing proteins (AFPs) that prevent ice crystals from growing in blood, tissues, and cells. It’s a solution that has evolved repeatedly and independently, not just in fish but in plants, fungi, and bacteria.

It isn’t surprising, then, that herrings and smelts, two groups of fish that commonly roam the northernmost reaches of the Atlantic and Pacific Oceans, both make AFPs. But it is very surprising, even weird, that both fish do so with the same AFP gene—particularly because their ancestors diverged more than 250 million years ago and the gene is absent from all the other fish species related to them.

A March 2021 paper in Trends in Genetics holds the unorthodox explanation: The gene became part of the smelt genome through a direct horizontal transfer from a herring. It wasn’t through hybridization, because herring and smelt can’t crossbreed, as many failed attempts have shown. The herring gene made its way into the smelt genome outside the normal sexual channels.

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Finally, in 2019, a full sequence for the herring genome was published. It let the team better examine the sequences surrounding the AFP gene, some of which appeared to be “transposable elements” (TEs, or transposons), mobile chunks of DNA that can copy and paste themselves in a genome. The herring genome holds many copies of these TEs, but they are absent from other fish—with one telling exception. Three of them flank the rainbow smelt’s AFP gene, in the same order seen around the herring AFP gene.

Graham thinks that these sequences are “definitive proof” that a small chunk of a herring chromosome made its way into a smelt’s. “If anybody wants to dispute this,” she says, “you know, I don’t see how they possibly could.”

Cédric Feschotte, a genome biologist at Cornell University who was not involved in the study, agrees. “It seems unmistakable when you look at the data,” he says. What really intrigues him, though, is how well this finding lines up with work that he and others are doing on TEs and the rise of new genes.

For instance, in a 2008 study published in the Proceedings of the National Academy of Sciences, he and his colleagues identified a new kind of TE found in a disparate group of vertebrates, including a few species of mammals, a reptile, and an amphibian. These TEs were more than 96 percent identical in these species but were strangely absent from other examined genomes. Because the elements seemed to have appeared suddenly, Feschotte and his colleagues dubbed them “Space Invader elements” (“SPIN elements” for short) and concluded that they must have recently moved horizontally between the sundry lineages. These TEs weren’t merely genetic noise in their new hosts, either: Mice, for example, had obtained a whole new functional gene by co-opting a SPIN-element enzyme.

Since the 2008 SPIN paper, thousands of other horizontal TE transfers between animals have been reported. While these putative horizontal transfers were initially met with surprise, much as Graham’s AFP gene was, the evidence is now undeniable.

For context, it’s worth noting that horizontal transfers can be hard to detect: Over time, ever more mutations accumulate in both the original and the recipient lineages, obscuring similarities in a shared gene. Proving that a gene has been horizontally transferred also depends on demonstrating that it wasn’t once present in other related species and then lost through evolution, which can be difficult when some of those species are extinct.

“The rate of actual horizontal transfer is probably much, much higher than we realize,” Schaack says.

- More Here

How Etta Lemon Helped Save the Birds

Never underestimate the power of a small group of committed people to change the world. In fact, it is the only thing that ever has.

- Margaret Mead

Surprise! Surprise! once again, not a well known name from history - Etta Lemon, her story is captured brilliantly by Tessa Boase in her new book Etta Lemon: The Woman Who Saved the Birds. 

The most important thing to understand is she did this impossible act in 1890's! Yes, more than 130 years ago.  

Even today in 2021, most people don't give a crap about animals leave alone birds. I can only imagine the struggles she went through to make a change. People killed trillions of birds for sheer stupidly of wearing feathers on their hats! Never underestimate the stupidly of sapiens. 

So if you ever think and feel alone amongst carnivorous and self-centered sapiens then get your motivations from people such as Etta Lemon and keep going from one moment to another and eventually time will help you. 

Ma'am thank you. Thank you for everything you did and you deeds have not been forgotten and never will be. 

Interview with the author Tessa Boase here: 

Treehugger: What is your background? What drew you to the story of Etta Lemon?

Tessa Boase: I’m an Oxford English Lit grad, an investigative journalist, and a social historian who loves the thrill of the chase. I’d heard a rumor that Victorian women were behind Britain’s biggest conservation charity, and my curiosity was immediately piqued. Could this be true? And if so, why hadn’t I heard of them? When I told the Royal Society for the Protection of Birds (RSPB) I wanted to write their early story, they became very secretive. I wouldn’t find enough material, the librarian told me—and certainly no photographs. The early archive was lost during the London Blitz. 

Here was an irresistible challenge. Two years of painstaking research revealed four distinct personalities, all women. Emily Williamson of Manchester was the gentle, compassionate founder who invited her friends to tea in 1889 and got them to sign a pledge to Wear No Feathers. Eliza Phillips was their great communicator, whose pamphlets pulled no punches. Winifred, Duchess of Portland, animal rights advocate, and vegetarian, was RSPB president to her death in 1954. 

And then there was Honorary Secretary Etta Lemon, a woman (and a name) to be reckoned with. This was the personality that most intrigued me. To her colleagues, she was "The Dragon," to the public, "Mother of the Birds." Determined, single-minded, and "brusque" of manner, here was an eco heroine with a rhino hide. Hard-hitting campaigns need women like Etta Lemon, then and today. 

Can you describe what women's hat fashion was like while Lemon was battling against feather use? 

Etta described the latest "murderous millinery" in every RSPB annual report. Here’s one from 1891: a hat made in Paris and bought in London for three shillings. "The chief feature is the lovely little head of some insect-eating bird, split in two, each half stuck aloft on thin skewers." The bird’s tail sat in the middle of the split head, the wings on either side, while a tuft of the buff plumes of the squacco heron (a small, short-necked, toffee-colored bird from southern Europe) completed the "monstrosity." 

As hats grew in diameter, fashions got more extreme. Milliners heaped their creations not just with feathers but wings, tails, several birds, whole birds, and half birds (owl heads were all the rage in the 1890s). Exotic species, known as "novelties," were particularly prized—but if you couldn’t afford a scarlet-rumped trogon, you could buy a dyed starling. 

What obstacles did she face as a conservationist at that time? 

So many obstacles! In 1889, women couldn’t even book a meeting hall. The ornithological societies of the day were male-only coteries. Emily Williamson founded her all-female society in anger at being barred from the all-male British Ornithologists’ Union (BOU). Luxuriantly bearded Victorians felt deeply proprietorial about nature, and there was much patronizing sneering. The title "Society for the Protection of Birds" was dismissed as "very ambitious" by one British Museum naturalist, "for a band of ladies who do nothing but abstain from personal iniquity in the matter of bonnets." Yet women are good at networking. By 1899, the (R)SPB had 26,000 members of both sexes and 152 branches throughout the British Empire. In 1904 it gained that all-important "R": the Royal Charter. 

The British public was utterly ignorant of birdlife at the start of the campaign. Re-educating people to watch birds, rather than shoot or wear them, was an uphill struggle. The end goal was legislation, and of course, women had no voice in Britain’s Parliament until 1921. Yet Etta Lemon was an impressive speaker, earning the admiration of male journalists at international bird conferences.

What impact was fashion having on various bird species?

By the 1880s, as explorers and shipping routes carved up the world, a fabulous array of exotic bird skins flooded the plumage market. Brightly colored birds such as parrots, toucans, orioles, and hummingbirds were particularly prized. Weekly auctions in London, the hub of the world’s plumage market, would routinely sell single lots containing perhaps 4,000 tanagers, or 5,000 hummingbirds. 

By 1914, hundreds of species risked extinction. The plumed paradise birds, the great and little egret, blue-throated and amethyst hummingbirds, the bright green Carolina parakeet, the Toco toucan, the lyre bird, the silver pheasant, the velvet bird, the tanager, the resplendent trogon ... the list went on. 

In Britain, the great crested grebe was driven to near extinction, hunted for its head feathers, which stand out like a halo when breeding. Sub-Antarctic beaches were photographed heaped with albatross corpses, shot to satisfy the fashion for a single, long plume on a hat. 

What were some of the tactics used to dissuade women from wearing feathers?

Etta Lemon was militant from an early age, calling out any women wearing "murderous millinery" in her London church. In 1903, when an ounce of egret feathers was worth twice as much as an ounce of gold, the RSPB local secretaries were sent on a mission. Armed with visceral pamphlets and a magnifying glass, all 152 of them were to infiltrate high street stores, surprise shoppers, question shop girls, cross-examine head milliners, and lecture shop managers. The term "environmental activism" didn’t exist. Instead, they called it the Frontal Attack. 

In 1911, when most of the world’s egret colonies had been shot out, men bearing gruesome placards showing the life (and bloody death) of the egret were hired to walk the West End streets during the summer sales, and again that Christmas. Women consumers fond of wearing the aigrette or "osprey" were shocked into consciousness. This marked the campaign’s turning point. 

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What is Lemon's legacy?

Etta taught us to feel compassion for birds. We shudder at the sight of those macabre bird hats today, thanks to her efforts. The RSPB would not have become the conservation giant it is today, had it not been for Etta’s vision, tirelessness, determination, and clarity of focus. I found it astonishing she hadn’t been remembered by the charity she built for half a century, 1889-1939. 

Happily, since my book’s publication, Etta Lemon and co-founder Emily Williamson are being propelled into the spotlight. Etta’s portrait has been restored and rehung in pride of place at The Lodge, RSPB HQ. There is to be an ‘Etta Lemon’ hide at RSPB Dungeness, the Kent coastline where she was born.

Meanwhile, the campaign for a statue of Emily Williamson gathers pace. Four bronze maquettes were unveiled on the Plumage Act centenary, 1 July 2021 in Emily’s former garden, now a public park in Manchester. (Vote for your favorite.)

The tool Emma used to make the change is "Moral Frontal Attack". I am sorry to say, people don't change with knowledge nor ethics but if you can target their morality and shame them - they do change. 

"Monkey see monkey do" - is the only way masses change. 

Psychedelics, Lempel-Ziv Complexity, Granger Causality, Maximus & Me

If psychedelics do act on the brain to change predictive processing, it’s not clear how they do it. But in recent studies, researchers have found ways to approach these questions. One way to gauge changes occurring in brains on psychedelics is to measure something called Lempel-Ziv complexity, a tally of the number of distinct patterns that are present in, say, recordings of brain activity over the course of milliseconds using a method called magnetoencephalography (MEG). “The higher the Lempel-Ziv complexity, the more disordered over time your signal is,” says Seth.

To determine the degree of disorder of human brains on psychedelics, Seth’s team, in collaboration with Carhart-Harris, looked at MEG data collected by researchers at the Cardiff University Brain Research Imaging Centre in Wales. The volunteers were given either LSD or psilocybin, the hallucinogenic ingredient in “magic mushrooms.” On psychedelics, their brain activity was more disordered than it was during normal waking consciousness, according to an analysis of the MEG signals that was published in 2017. Seth says that while the increase in disordered brain signals does not definitively explain people’s psychedelic experiences, it’s suggestive. “There’s a lot of mind-wandering and vagueness going on,” says Seth. “The experience is getting more disordered and the brain dynamics are getting more disordered.” But he says there’s more work to do to establish a clear connection between the two.

More recently, Seth, Carhart-Harris and colleagues took another look at the brain on psychedelics, using a statistical metric called Granger causality. This is an indication of information flow between different regions of the brain, or what neuroscientists call functional connectivity. For example, if activity in brain region A predicts activity in brain region B better than the past activity of B itself does, the Granger causality metric suggests that region A has a strong functional connection to region B and drives its activity. Again, using MEG recordings from volunteers on psychedelics, the team found that psychedelics decreased the brain’s overall functional connectivity.

One possible interpretation of these Granger and Lempel-Ziv findings is that the loss of functional organization and increase in disorder is disrupting predictive processing, says Seth. Verifying that would involve building computational models that show exactly how measures of Granger causality or Lempel-Ziv complexity change when predictive processing breaks down, and then testing to see if that’s what happens in the brains of people on psychedelics.

In the meantime, evidence that psychedelics mess with functional connectivity is mounting. 

- Psychedelics open a new window on the mechanisms of perception

In one way or other, for good or bad, psychedelics "open up" the minds of sapiens. The issue is most closed minded people don't want to try it as they don't want to the quintessential oxymoron and hence, impact of psychedelics cannot be captured more rigorously. 

The people who believe in magic camouflaged under pseudonyms such as capitalism,  markets, religion, socialism  ad infinitum; need some profound wiring change to inhale reality as it it. I hope psychedelics help in seeing reality rather than instill different dimensions of magic. In machine learning and statistical lingo - reduced under-fitting and over-fitting. 

I "think" that I am on the fat tail end of open-mindedness but who knows! 

I for one not only think and believe but often write on this blog, living with Max for 13 plus years made me open-minded, live in present, adapt to change and live my life as my favorite quote - Mind as a River.

Understand: the greatest generals, the most creative strategists, stand out not because they have more knowledge but because they are able, when necessary, to drop their preconceived notions and focus intensely on the present moment. That is how creativity is sparked and opportunities are seized. Knowledge, experience, and theory have limitations: no amount of thinking in advance can prepare you for the chaos of life, for the infinite possibilities of the moment. The great philosopher of war Carl von Clausewitz called this "friction": the difference between our plans and what actually happens. Since friction is inevitable, our minds have to be capable of keeping up with change and adapting to the unexpected. The better we can adapt our thoughts to the current circumstances, the more realistic our responses to them will be....

Think of the mind as a river: the faster it flows, the better it keeps up with the present and responds to change. The faster it flows, also the more it refreshes itself and the greater its energy. Obsessional thoughts, past experiences (whether traumas or successes), and preconceived notions are like boulders or mud in this river, settling and hardening there and damming it up. The river stops moving; stagnation sets in. You must wage constant war on this tendency in the mind.

-  The 33 Strategies of War by Robert Greene

But what if just constantly believing that story I tell myself (and others) makes me closed minded? Seeking an answer for that lingering question makes me want to try psychedelics. 

To be precise, the question is: 

Did living with Max for 13 plus years during the peak of my adulthood opened up so many windows as humanely possible and nothing more left to open up or is it just the tip of the iceberg? 

 

I am My Body

I don't have a body, I am a body.

- Christopher Hitchens, Mortality

Growing up in India in the 80's, kids got naturally exposed to death on a regular intervals. There was no sugar coating, no "shrinks", no tailored talks on death and no bullshits to cover the most fundamental education a human being needs to understand and get in terms with. That education was built into the system in the mundanity of everyday life. 

I know intellectually I was going to die one of these days from a long long time. I know emotionally I need to get into the mindset of accepting my shelf life and I have done it with extreme ease - thanks to Buddha, Stoics and Max. Those two levels of acceptance of one's mortality are healthy and good for civilization as a whole. 

Now for the first time, I am feeling that physically. I never wore glasses but for the first time, I am not able to read things I was able to read with ease for decades. My heart hints me that it's kind of getting tried beating for decades now and on occasions tries a different beat. Those two subtle signs are reminding my days on earth are numbered. 

Yes, I am more than healthy and stronger than I was in my 30's and 20's. I can work out with ease, read, think clearly and be active most of hours of the day.  But having seen Max go from a beautiful, playful, and active person to a bed-ridden person in matter of weeks reminds me that my destination would be the the same. It's the part of the deal we all signed up without our consent the day we were born. 

This blog will be a place where I will document my fragility and how my body dissipates in front of eyes slowly over the months or years or decades. Whatever the timeline turns out to be, I will document it here. It's part of evolution and it's important to document the what is happening to the person who I the know best - myself. 

My eyes and heart are the messengers who took my mortal understanding to a visceral level.

What I am curious (but not concerned) about is not that some of my faculties are deteriorating but would other faculties in my body get better to keep me in balance? For example, when a mammal goes blind, his or her hearing gets better.  I don't want to bias myself with changes I had in my body and mind because I lost Max. But I will try observe as humanely as possible if nature has given this mammal an innate capacity to compensate for the losses. 

There might be other questions that I am not aware at this point. Yet another reason for capturing this journey here on this blog which has been a huge part of Max's and my life. 

 If you don't know how to die, don't worry; Nature will tell you what to do on the spot, fully and adequately. She will do this job perfectly for you; don't bother your head about it.

- Michel de Montaigne

The Cultural Implications Of Silence Around The World

 Silence in Listening Cultures

Asian and Nordic countries have listening cultures where silence denotes careful thought. These cultures think that pauses (silence) in a conversation keep the interchange calm. In some cases, silence can be a way to allow everyone to save face. In these cultures, what is not said can be as important as what has been. In group-oriented cultures, it is polite to remain silent when your opinion does not agree with that of the group. 

Since silence has many meanings in listening cultures, it is important to de-code silence in each situation. In Japan, if you are making a presentation to a group and the most senior Japanese closes his eyes and is silent, it can mean conflicting things. His silence could mean agreement with what the presenter is saying; however, it could also mean that he does not want to publicly disagree. How would you know the difference?

Generally, the optimal approach is to slow down your speech and make sure you are speaking in a way that is not too complicated and doesn’t use too many idioms. You might then try asking a question to confirm understanding. 

Silence in Speaking Cultures

Some Western cultures think silence is a sign of lack of engagement in the conversation or even disagreement. Americans, for example, often see silence as indicating the person is indifferent, angry or disagreeing with them. The silence confuses and confounds them since it is so different from expected behavior. Many are even embarrassed by silence and rush to fill the space so they are no longer uncomfortable.

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Handling Silence in Meetings

When attending a multi-cultural meeting, understanding how different cultures respond to silence can help communication flow. If the majority of the attendees are from a culture where silence is discouraged, they will understand that their colleagues who do not speak up immediately do have something valuable to offer, they merely need some silence before joining the discussion. Conversely, if the majority of the participants are from a country where silence is expected, they will understand that their colleagues who are not letting them get a word in are not being disrespectful.

- More here from Carrie Shearer

Quote Of The Day & Thoreau's Walden

I went to the woods because I wished to live deliberately, to front only the essential facts of life, and see if I could not learn what it had to teach, and not, when I came to die, discover that I had not lived.

- Henry David Thoreau, Walden

Henry David Thoreau's is one of those rare humans who taught me how to observe nature and live in nature amidst the self-centered and pandemonium filled sapiens. He validated living in nature is not only beautiful and peaceful but also helps one see and think clearly and enables continuously try to become a better person. 

Since the day Max died, I stopped posting quote of the day on this blog. Even when I had nothing to post, I used to post a quote everyday. I did that to consciously remind myself that I am so lucky to have Max next to me for another day and no matter what happens, I need to immensely grateful for this another day with Max. 

Over the years, every time I posted Thoreau's Walden quote on this blog - it meant, I was going through bad times and for me, bad times only equated to Max being not well. But during Max's younger days, Walden quote meant we are having a wonderful time. 

I found solace in a subjective Walden I had created in my mind while Max objectified that Walden. Max was there always next to me and I was there for him. He gave me more than Walden. I don't if there is heaven or hell and I don't even want to know nor care. But Max gave me heaven on earth. Whatever the beautiful words some of the greatest poets had ever described, Max showed that to me in reality and I was lucky enough to live and experience those poetic world. 

Eighteen months after Max passed away, today we are going to have a real Walden. A peaceful, and beautiful place in the woods. 

This new Walden will help preserve the memories of Max in the home we lived together for thirteen years and this home where Max spent his entire will be the place I will comeback to take my last breathe on this beautiful blue planet. 

I wish Max was there with me to be in the woods. He would have loved it. But he is not here today to come with me. There is nothing in world that can make that happen. So my body and mind does what evolution has gifted me to cope with moments and days like this one - I cry. I miss you Max.