All beings are my parents All beings are my teachers All beings are my children
Do cells take joy in tidying? Absolutely! But how can they tell where the messes are? Any household knows that without cleaning and disposal, nothing else is possible. Things pile up, messes accumulate, everything comes to a standstill. Cells are the same, needing a constant flow of new materials in, trash out, recycling, and cleanups. One of the major kinds of mess in cells is unfolded proteins,…
Different ways of learning go through different parts of the brain. Humans are champion learners. Other animals are smart, but we are smarter, spending more time in childhood soaking up the mysteries of the world around us, and storing them in a larger and better brain. Learning is our calling card, allowing us to adapt to any environment and defeat any foe. Indeed, we have overwhelmed the earth's…
Two whole genome duplications lie at the root of vertebrate evolution. Another week, another story about the power of gene duplication in evolution. While rare during normal reproduction, gene duplication happens pretty frequently over longer time scales. How else would we get a thousand olfactory receptor genes , all similar to each other? But other accidents can occur as well, like whole…
Tracing the breadcrumbs of deep phylogeny through gene duplications. Last week, we discussed the jamboree of mutation that is the MHC locus in animals. One part of that story was the persistent duplication and pseudogene-i-zation (which is to say, the birth and death) of genes in that locus through primate evolution, another consequence of the never-ending arms race with our pathogens. Gene…
The immunologically critical MHC gene cluster plays by its own rules through the arms race of life. Last week, I discussed the very general landscape of variation in the human genome, specifically the tradeoff between prevalence in the population and effect size. Given that the vast majority of variants are deleterious, those that affect our phenotypic traits are more heavily selected against the…
Notes on the genetics, traits, and evolution. Everything about us is a trait. Not everything about our traits is genetic, though. The conundrum of nature vs nurture, of genes vs environment, and the structure and meaning of genetics goes to the heart of biology. A few traits, like eye color, are simple enough. But they are the exception, by far. Body mass index is influenced by practically every…
Billions of years have created some weird tricks in DNA search. Search is all around us, as we increasingly rely on search engines to find everything we need on the internet, want to watch, or want to buy. Search looks into databases, which hold the sought-after information. All our accounts, all the domain names, all the products... everything is held in databases of one kind or another, and…
Review of " The Second Estate ", by Ray Madoff, about how the rich have excused themselves from paying taxes. "A system that requires someone who earns $100,000 to pay almost 30 percent in payroll and income taxes while giving another person who inherits $10 million a free pass is indefensible." As we head into the nation's birthday, we should take stock of how we are fulfilling its founding…
Better modeling, by including the biosphere, retrodicts more of Earth's dynamic climate history. Climate change, while ignored by the current administration, is not ignoring us. The Earth is warming well past where it has been for millions of years. But before that? While the planet has generally had stable climates, they have varied substantially through time, and have gone through occasional…
Not enough appeasement, or not enough deterrence? I have been watching the Harry Potter series of films, a decade or two after first reading the books. Aside from being extremely entertaining, they show Rowling to have been weirdly prescient about the moral dilemmas only developing as she was writing, and now flourishing in grotesque fashion. How large sectors of supposedly civilized populations…
A new paper shows that CART therapies can be unleashed against solid tumors. We are finally in the payoff period in the decades-long war on cancer. Slowly, painfully, precision approaches are being developed to treat specific molecular lesions in ways that are superior to the old blunderbuss kill-everything approaches. At first, these treatments had only marginal effects, at astounding costs. But…
Labor's share of the economy has rarely been lower- what is going on? We will start with a graph of share of income, to labor, vs capital. Note that labor here includes all the highly paid executives- all those fat salaries. The share has been going down for decades, while the profit and capital share has been going up. The seventies were the high-water mark, when unions reached their apogee, and…
Coccolithophores are beautiful, inside and out. As we pump out ever more carbon, burned from fossil sources, we are relying on the great geochemical and biological cycles to take in this waste and clear the air. At the same time, we are impairing these cycles by chopping down forests and acidifying the oceans. Half of photosynthetic productivity happens in the oceans, thanks to phytoplankton.…
Review of Ray Dalio's " How Countries Go Broke ". It is difficult to focus on important policy issues, as the national media is led around by the president's revolving fixations like a cat by a laser pointer. But focus we must, if we are not going to decline faster than we already are due to incompetent and corrupt leadership. One looming area is the federal budget. As a card-carrying acolyte of…
Telling the difference between inner and outer speech. As we understand more about how the brain works, we can decode what is going on inside. But sometimes, the result is oversharing! A recent paper discussed how one lab is filtering out inner speech from intentional outer-directed speech in their BCI: brain-computer-interface. After a very long road of brain research, we understand a great deal…
Are we at peak oil, perhaps even peak burning? Thanks to Donald Trump, renewables are looking better than ever. It turns out that using the oil weapon opens people's eyes to the alternatives. The Saudis have recognized for a long time that stability in oil pricing and supply was the way to keep the world addicted. But in the current wars, Russia has used the natural gas weapon, and Iran has used…
The CCR5delta32 confers resistance to HIV. Where did it come from? We are edging into an age of precision medicine, where the causes of our maladies will be known in molecular detail, allowing treatments that address them at the root. Given the parlous state of medicine today, in the midst of financial breakdown and a continued mediocre level of basic diagnosis , it is hard to believe this is a…
Can politics work without a civic sphere? How can we have a loneliness epidemic when we are connected like never before? It is a problem that perplexed Robert Putnam in " Bowling Alone ". He put it mostly down to TV, internet, and the growth of passive and isolated forms of entertainment generally. When you read between the lines of history of any time before about one hundred years ago, you…
An ornate ion pump manages rapid outflow of calcium. In the beginning, the egg cell experienced a wave of calcium release, triggered by union with a sperm cell. This blocked other sperm from entering, and prepared the egg to become a zygote and embark on embryogenesis. It is but one example of the pervasive role of calcium signaling among animals. Another is the muscle activation cycle, which…
Reflections on junk DNA, and junk transcripts. Some time ago, a large project in molecular biology determined that most regions of the genome are transcribed. The authors and most observers took this to mean that most regions are functional, quite in contrast to the reigning theory up to that point, that our genomes host a smattering of genes floating in a sea of "junk" DNA . That theory was based…
The SLAMF9 gene became non-functional in the human lineage, and then later was re-activated. Why? Biology is amazingly intricate, but it is often also needlessly complex- evidence for the haphazard, if eventually pointed, mechanisms of the evolutionary process. We will take up the discussion of "junk" DNA again next week, but molecular biology is full of redundant and excessive processes, which…
Review of " Understanding Capitalism ", by Richard Wolff. When I picked up this book, I thought it was going to be a sober analysis of capitalism, by a real economist. But what I was met with was something quite different- a Marxist screed with the most flaccid intellectual grounding, disingenuous and dishonest by turns. Wolff apparently has been paid to teach economics at liberal institutions,…
Our foreign policy appears to be led by people whom Trump gets weak in the knees for. Does that serve US or world interests? US foreign policy serves not only US interests. We share an interest in the peaceful, prosperous, and sustainable future of the whole world, and as the leading nation, have an outsize role in its development. That is why Barack Obama got a Nobel peace prize, and why Donald…
For a minor component, it gets a lot of molecular love. As mentioned several times in this space, the ribosome, which synthesizes proteins according to mRNA instructions, is an extremely ancient and complicated machine. Its core, including the catalytic site, is RNA. This marks it as a hold-over from the RNA world, as the thing that made proteins, (probably tiny proteins at first), before proteins…
" Skepticism" about vaccines, or about evolution... isn't skepticism at all. This was going to be a post about the Ediacaran epoch , which is a fascinating time, spanning the hundred million years before the Cambrian, when animals began to appear in the fossil record. First tentatively, as sessile sheets of tissue, then later as beautiful motile segmented discs (below), and later still as…