CapitalistImperialistPig

The central question in biology today is how life originated. It's not only the biggest unanswered question in biology, but it's also central to our understanding of the place of life in the universe. We now know that planets are extremely common in the universe, and it's at least plausible, that a lot of them have or had Earth like conditions. If we understood how life originated on Earth, we would be much more able to understand the probability of it existing elsewhere. Conversely, if we found life elsewhere, it would almost certainly provide potent clues to how life originated on Earth. The past decades have seen considerable progress in understanding some possibilities for early life, but we are far from concrete answers. Natalie Wolchover, writing in Quanta , has some news on one approach, dissipation driven organization. The idea is that some physical systems evolve to maximize their dissipation of energy and entropy increase. The biophysicist Jeremy England ...

Juan Enriquez and Steve Gullans are venture capitalists and authors with an interest in life sciences. Gullans is a former professor at Harvard Medical school. Their book, or I should say micro-book, Homo Evolutus , seems to be based on a TED talk they gave. The subject is their thesis that the human race is about to "speciate," or give rise to a new species of Homo, thanks to the radical advances being made in biotechnology and genomics. Roughly the first half of the book is devoted to background material on the evolutionary history of the various human species (19 so-far known, by their count) and their biological underpinnings. The rest is a quick catalog of some of the extraordinary goings on at the interface of biology and technology, many of which were unfamiliar to me. A couple of examples: Not only did the two Chinese teams take mouse skin cells, and de-differentiate them back into pluripotent stem cells… They then took these stem cells and allowed them to re-g...

Most of the familiar animals (bears, people, fish, insects, worms, squid, snails, starfish) are members of the bilateria , bilaterally symmetric animals with front and back, top and bottom. Most of them are either deuterostomes (e.g., us, fish, starfish) or protostomes (arthropods, worms, clams, squid). They all develop from an egg which divides and forms a hollow ball of cells which dents in during gastrulation and ultimately penetrates to the other side, forming the gut. In deuterostomes, the original dent becomes the anus. In protostomes, it either becomes the mouth (or according to some) both mouth and anus. One of us seems to have got it backwards. How did that happen?

Yeah, I know about the Vikings. But there are some earlier and (to me) more remarkable voyages. Consider the case of the New World Monkeys. Monkeys first evolved about 50 million years ago, in Africa. Somehow, about 30 million years ago, some of them (or maybe just one of them) managed to cross the Atlantic Ocean to South America. Recall that Gondwana, which included Africa, South America, Antarctica, India, and some other stuff split up about 180 million years ago (mya), with Africa and South America parting company about 130 million mya. The Atlantic was narrower than now 30 mya, but still at least 1000 miles wide. While it's possible that some mid-ocean islands existed, pretty extensive sailing, or rather rafting, was still required. Alan de Queiroz has written a book about it, and has a shorter account of it here in The Huffington Post. Many other creatures seem to have made similar voyages. This story and others like demonstrate why evolution can't really be a p...

The average human has a genome that differs from the human reference genome at about 3-4 million sites (out of 3.2 billion). Asian, European, and (Native) American population groups (out of 26 population groups total; 10 Asian, 5 Eur, 6 NA, 5 African) went through extreme population bottlenecks 15-20,000 years ago where the effective population sizes of each were reduced to less than 1,500 individuals. The simultaneous African bottlenecks was a good deal less severe with effective population sizes > 4,500. Most rebounded with extreme population growth shortly thereafter.

But she will. Only a generation or so ago, a Nobel Prize winning molecular biologist could confidently announce that it would never be possible to edit a genome. However, it turns out that the engineering department of molecular biology - bacteria - have been doing it for ages. The discovery of the so-called Crispr Cas9 system has revolutionized gene editing, and is in the process of unleashing a torrent of genetically modified organisms on the world. Jennifer Kahn has a great story about Doudna and Crispr in The New York Times of Nov 9. The tool Doudna ultimately created with her collaborators paired Crispr’s programmable guide RNA with a shortened tracer RNA. Used in combination, the system allowed researchers to target and excise any gene they wanted — or even edit out a single base pair within a gene. (When researchers want to add a gene, they can use Crispr to stitch it between the two cut ends.) Some researchers have compared Crispr to a word processor, capable of effortles...

Shouldn't you first have your genome edited for clarity and errors? The CRISPR/Cas system seems to be making that possibility real. CRISPR (and writing out the acronymn likely won't help you understand it) is a prokaryotic immune system that works by editing the genomes of potential virus enemies, but its editing capabilities can be used for other purposes - see discussion in the Wikipedia link given above. In fact they already have been used to edit out a deleterious gene in mice. People too carry some nasty genetic diseases, and the possibility of editing them out is being aggressively investigated by top genetics laboratories. Of course, if you are going to be editing genes to eliminate congenital blindness or Tay-Sachs disease, maybe you should take the opportunity to stick in some genes for high intelligence, good looks, athletic ability, etc., etc. The age of gene customization is (nearly) on us, and that means that future humans will have some more powers previousl...

The gift of men , in Tolkien's universe, is death. The better life gets, though, the less welcome the gift becomes. Searching for immortality, through magic or religion, is one of the oldest themes in history. The radical advances in average human lifespan that we have seen in the last 100 years have been achieved mostly through science and sanitation, and so science now looks like the most promising venue for further life extension. I suppose it's natural for the most favored to resent "the gift," and if you have a few hundred million rattling around in your pocket, why not give the alternative a shot. You will probably want to know that Google is on the case : Excerpt: Bill Maris has $425 million to invest this year, and the freedom to invest it however he wants. He's looking for companies that will slow aging, reverse disease, and extend life. The easy technical problems of life extension have been solved, or nearly so. Control disease, avoid catas...

The peacock's spectacular tail confounded Darwin. How could something without obvious selective value compete? The answer he came up with, documented again and again, was sexual selection. If one sex prefers some trait, then those with that trait will be preferentially selected for, and over millenia, multiple genes might get involved to produce the elk's antlers, the peacock's tail and so on. Of course that cannot be the end of the story. Selection of an arbitrary trait would not help fitness. It has to be some trait that is correlated with other less observable traits that do affect fitness. Facial asymmetry in in humans (or animals) is not in itself a direct hindrance to fitness but it tends to indicate that the creature in question does suffer from obvious developmental or nutritional deficits. Unsurprisingly, we overwhelmingly prefer the symmetric. Men all over the world tend to prefer certain traits in women, and it is not coincidental that those traits are tho...

The deepest mystery in biology, and in science generally, is the origin of life and the genetic code. Life as we know it cannot exist without DNA and the information it stores. But DNA and the genetic code cannot have come before life because it takes a vast and intricate system of molecular machines just to reproduce DNA and translate it into the proteins that do the actual business of metabolism and constitute the machinery of life, including all the machinery to turn DNA into protein. It's the chicken and egg problem in it's sharpest molecular form. DNA is not translated directly into protein. First it must be transcribed into messenger RNA, which in turn is translated into protein by a complex apparatus that consists of proteins and other kinds of RNA molecules. This fact is probably one element that suggested that maybe RNA was the molecule that came before gene and protein. Proteins are the most versatile components of our molecular machinery, acting as structural e...

Probably no intellectual tool is more powerful than that of abstraction - the ability to see analogies and the development of general rules that apply to diverse and apparently different situations. Our most powerful tool for abstraction is language - itself a peculiarly potent abstraction from reality, creating a deep analogy between sound patterns and the events and objects of the world. Language, though, is itself kind of an analogy with some mostly pre-existing representations of the world that exist in our minds. This strongly implies that humans didn't invent abstraction or analogy. The most fundamental abstraction we know of seems to be the genetic code. Patterns of nucleotides in DNA are translated through a vast and complicated apparatus into proteins and all the mechanisms that support life.

Newsweek reports that children of older mothers are much taller and thinner. By a significant margin, children born of older mothers were the clear winners: they were much taller and thinner than those whose mothers were younger. The difference wasn’t because the older parents were themselves taller and thinner; in fact, the researchers weren’t sure how to explain the findings, which are in line with observations made a few times in the past. Perhaps, they suggested, the hormonal mix produced during pregnancy by an older woman differs from that made by her younger counterpart. Not sure how they decided that that was an unalloyed good thing. Maybe Kent Sepkowitz, the author, is a basketball fan.

Something like 3500 Mendelian (single gene) genetic diseases have been discovered but the vast majority of our genetic diseases appear to be multi-genic. Something like 90 genes are known to be associated with Schizophrenia. Some of these involve proteins that have functions that can be directly linked to the brain. Four of them code subunits of a calcium channel protein, that is, a protein involved in the flow of ions into and out of cells, known to be active in nerve cells. Elucidating the exact way each of these contribute to disease will take a while, but diseases are not the only area where modern genomic statistical analysis will elucidate genetic influence. Height, running speed, and adult IQ are all other areas known or strongly suspected to be under the control of multiple genes. Genomic analysis has developed powerful tools for discovering the function of identified genes, and investigators have gotten rather good at designing customized mice. The designer human will a...

It's a commonplace but rarely appreciated fact that our planet is being managed mainly for the convenience of a bunch of billion year-olds. These ancient ones have been around almost since the formation of the planet. They change very slowly, just a few little tweaks every million years or so. They are parasites of a sort, carrying on their business in fish, trees, people and even bacteria. Of course if they were the sort to talk, they might say it differently. They might say that the bacteria, trees, and people are just convenient dwelling spaces they have devised for their accomodation. I'm writing, of course, about the society of DNA molecules, each of them a clone of a clone and descended in unbroken lineage from some first DNA molecule 3.5 billion years or so ago. With DNA clones though, there is little distinction between the copy and the original, since each new molecule incorporates half of the original and is a copy of it, so in effect each of those DNAs today *i...

One of the most mysterious questions in science is that of how the whole intricate apparatus of life arose in the first place.  All Earthly life is very much the same at the fundamental level, the vast chemical factory of the cell.  Three critical elements are the mechanism of information storage (DNA), the apparatus for translating the directions written in the DNA into proteins (RNA & proteins), and the proteins that do all the chemical and mechanical work of the cell.  None can carry out their function without the other two. Recent work has given us a clue, though.  RNA can't compete with proteins in general catalysis, but it does turn out to have some catalytic roles.  Most importantly, it turns out to be the RNA of the ribosome (rRNA) that does the all important task of catalyzing the formation of the peptide bond in the ribosome, the step that produces a protein out of amino acids. This strongly hints that RNA got there first.

A lot of learning molecular biology is looking at pictures. The last 60 years has produced very instructive pictures of the molecular machines that underlie biology - that constitute the secret of life - and the best way to get an understanding of how they work is to spend a lot of time looking at those pictures and understanding how they work. Some other branches of science are pretty picture oriented too, though I can't think of anything to match molecular biology. Fluid dyanmics comes to mind. Every would be fluid dynamicist should spend a hundred or more hours looking at pictures and movies of fluid phenomena.

I love this science video (via Andrew Sullivan ) - presented at a frenetic pace that inhibits any boredom:

The toughest problem in evolution has always been origins. Once scientists figured out the way the skills of life were partitioned among DNA, RNA and proteins, the question became how the whole complex system could have originated. Bacterium, yeast, tree, worm, dinosaur and human looked pretty different until we started figuring out how they all worked, but once we had they all started looking pretty similar. Inside each is (almost) the very same system of DNA genes, RNA helpers and proteins, doing the same things to keep us all alive. This fact is stupendously obvious signal of the common origin of all life, but it’s a lot more silent on the question of what those origins were. We have a pretty clear if imperfect picture of how tree and dinosaur evolved out of bacteria, but we have many fewer clues as to how the first bacteria evolved out of non-living chemicals. The real problem is that neither contemporary life nor the fossil record has preserved anything much in the way of in...

Would you want to know when you are going to die, or at least when the physical decrepitude of age will overwhelm you? It seems that there is a message, if not exactly to the main , at least to sophisticated molecular analytic engines, written in your cells . For the most part, we live longer than our individual cells. Cells are constantly breaking down, being shed, and replaced by the products of new cell division. There is a problem with the replication of chromosomes that takes place prior to cell division however, in that the enzymes that mediate it cannot fully replicate the ends of the chromosomes. Consequently, in order to protect us from losing genes with every division, our chromosomes are equipped with special end caps, called telomeres . Cell division does shorten these telomeres however, and this limits the number of times a cell can divide. Consequently, every cell division is a step toward ultimate doom. You might want to ask why the Intelligent Designer would pl...

Human culture seems to have undergone some sort of major phase transition when we started living in cities. Progressive citification has only intensified in the last century or so as technology has permitted a smaller and smaller number of farmers to feed the rest of us. So what's so special about cities? Are they more than just a convenient way to stack a lot of people in a small amount of room? It may not have taken a physicist to intuit the answer, says Jonah Lehrer, writing in the New York Times Magazine , but if you want the insight codified in some equations, a physicist, namely Geoffrey West, is the man. West used to think about physics, but the cancellation of the Super Collider in 1993 caused him to look for new worlds to think about. His first big score was in biology, West has been drawn to different fields before. In 1997, less than five years after he transitioned away from high-energy physics, he published one of the most contentious and influential papers in modern b...