kottke.org posts about biology
From a blog about the science of dogs, a comparison of photos of purebred dogs from 1915 to those of today. You can see how much the dogs have changed in just under 100 years, in some cases for the worse. For instance, the difference in the Bull Terrier (aka the Spuds MacKenzie dog) is marked and a bit disturbing:
Pure breeding has also introduced medical problems for some breeds.
The English bulldog has come to symbolize all that is wrong with the dog fancy and not without good reason; they suffer from almost every possible disease. A 2004 survey by the Kennel Club found that they die at the median age of 6.25 years (n=180). There really is no such thing as a healthy bulldog. The bulldog's monstrous proportions makes them virtually incapable of mating or birthing without medical intervention.
The monarchs are late. Usually by the 1st of November, the forests of central Mexico are swarming with them. Last year, they came in record low numbers, only 60 million. This year? A week late and only 3 million. And this happening to insects across the spectrum.
A big part of it is the way the United States farms. As the price of corn has soared in recent years, driven by federal subsidies for biofuels, farmers have expanded their fields. That has meant plowing every scrap of earth that can grow a corn plant, including millions of acres of land once reserved in a federal program for conservation purposes.
Another major cause is farming with Roundup, a herbicide that kills virtually all plants except crops that are genetically modified to survive it.
As a result, millions of acres of native plants, especially milkweed, an important source of nectar for many species, and vital for monarch butterfly larvae, have been wiped out. One study showed that Iowa has lost almost 60 percent of its milkweed, and another found 90 percent was gone. "The agricultural landscape has been sterilized," said Dr. Brower.
My friends at Tinybop have released their first app, The Human Body, in which "curious kids ages 4+ can see what we're made of and how we work, from the beating heart to gurgling guts". Kelli Anderson did the illustrations for the app and they look amazing. Can't wait to try this out with Ollie and Minna.
This is what the trees look like near Chernobyl when you cut them down. It's a biiiit tricky but see if you can spot when the nuclear plant disaster happened...
Not surprisingly, researchers have found evidence that the radiation has affected the growth of trees near the accident site. From the paper:
Mean growth rate was severely depressed and more variable in 1987-1989 and several other subsequent years, following the nuclear accident in April 1986 compared to the situation before 1986. The higher frequency of years with poor growth after 1986 was not caused by elevated temperature, drought or their interactions with background radiation. Elevated temperatures suppressed individual growth rates in particular years. Finally, the negative effects of radioactive contaminants were particularly pronounced in smaller trees. These findings suggest that radiation has suppressed growth rates of pines in Chernobyl, and that radiation interacts with other environmental factors and phenotypic traits of plants to influence their growth trajectories in complex ways.
A mammoth recently found in Siberia was so well preserved that when researchers were chipping it out of the ice, liquid blood flowed out.
Semyon Grigoriev, chairman of the university's Museum of Mammoths and head of the expedition, said: "The fragments of muscle tissues, which we've found out of the body, have a natural red colour of fresh meat. The reason for such preservation is that the lower part of the body was underlying (sic) in pure ice, and the upper part was found in the middle of tundra. We found a trunk separately from the body, which is the worst-preserved part."
The temperature was ten degrees celsius below zero when the mammoth was found, so the discovery of liquid blood was a shock. "It can be assumed that the blood of mammoths had some cryo-protective properties," Grigoriev said. "The blood is very dark, it was found in ice cavities below the belly and when we broke these cavities with a pick, the blood came running out."
More photos and information here. Bring on the mammoth clones, John Hammond. (via @carlzimmer)
Despite progress in recent years on causes and cures, colony collapse disorder has wreaked havoc on honeybee colonies across the country.
A mysterious malady that has been killing honeybees en masse for several years appears to have expanded drastically in the last year, commercial beekeepers say, wiping out 40 percent or even 50 percent of the hives needed to pollinate many of the nation's fruits and vegetables.
Which is like, yeah, big whoop, it's just bees, right? Except that:
The Agriculture Department says a quarter of the American diet, from apples to cherries to watermelons to onions, depends on pollination by honeybees.
Well, here's something potentially interesting: researchers at Cardiff University think they have found fossils in meteorite fragments from Sri Lanka.
The most startling claims, however, are based on electron microscope images of structures within the stones (see above). Wallis and co say that one image shows a complex, thick-walled, carbon-rich microfossil about 100 micrometres across that bares similarities with a group of largely extinct marine dinoflagellate algae.
They say another image shows well-preserved flagella that are 2 micrometres in diameter and 100 micrometres long. By terrestrial standards, that's extremely long and thin, which Wallis and co interpret as evidence of formation in a low-gravity, low-pressure environment.
Gotta take this with a massive grain of salt, but it will be interesting to see how this one plays out.
Update: One of the authors of this study holds some unusual views about life on Earth.
On May 24, 2003 The Lancet published a letter from Wickramasinghe, jointly signed by Milton Wainwright and Jayant Narlikar, in which they hypothesized that the virus that causes Severe Acute Respiratory Syndrome (SARS) could be extraterrestrial in origin and not originated from chickens.
Wickramasinghe and his mentor Fred Hoyle have also used their data to argue in favor of cosmic ancestry, and against evolution.
Like I said, big grain of salt. (thx, onno)
There's an assumption that because of the relationship between metabolic rates, volume, and surface area, animals get an average of one billion heartbeats out of their bodies before they expire. Turns out there's some truth to it.
As animals get bigger, from tiny shrew to huge blue whale, pulse rates slow down and life spans stretch out longer, conspiring so that the number of heartbeats during an average stay on Earth tends to be roughly the same, around a billion.
Mysteriously, these and a large variety of other phenomena change with body size according to a precise mathematical principle called "quarter-power scaling".
It might seem that because a cat is a hundred times more massive than a mouse, its metabolic rate, the intensity with which it burns energy, would be a hundred times greater. After all, the cat has a hundred times more cells to feed.
But if this were so, the animal would quickly be consumed by a fit of spontaneous feline combustion, or at least a very bad fever. The reason: the surface area a creature uses to dissipate the heat of the metabolic fires does not grow as fast as its body mass.
To see this, consider a mouse as an approximation of a small sphere. As the sphere grows larger, to cat size, the surface area increases along two dimensions but the volume increases along three dimensions. The size of the biological radiator cannot possibly keep up with the size of the metabolic engine.
Humans and chickens are both outliers in this respect...they both live more than twice as long as their heart rates would indicate. Small dogs live about half as long.
Looking to live forever? You might want to take a close look at the immortal jellyfish. This death-defying creature ages, but researchers studying the jellyfish found that, instead of dying, it started "to age in reverse, growing younger and younger until it reached its earliest stage of development, at which point it began its life cycle anew." (If beginning the life cycle anew means another trip through junior high, count me out.) From NYT Magazine: Can a Jellyfish Unlock the Secret of Immortality?
Birds can detect the magnetic field of the Earth, which gives them an incredible sense of direction. Curiously, this sense of direction doesn't work in darkness. This led scientists to discover that some birds can actually see the directions overlaid on their normal vision, like a heads-up display.
According to the new model, when a photon of light from the Sun is absorbed by a special molecule in the bird's eye, it can cause an electron to be kicked from its normal state into an alternative location a few nanometres away. Until the electron eventually relaxes back, it creates an 'electric dipole field' which can augment the bird's vision - for example altering colours or brightness.
Crucially, the alignment of the molecule compared to the Earth's magnetic field controls the time it takes for the electron to relax back, and so controls the strength of the effect on the bird's vision.
There are many such molecules spread throughout the eye, with different orientations. So from the patterns on top of its vision, and the change of these patterns as it moves its head, the bird learns about the direction of Earth's magnetic field.
In this transcript of a talk given to the attendees of the Joint Summits on Translational Science, Carl Zimmer highlights an important aspect of understanding the human body and how to treat its many maladies: the ecosystem of microbes.
The microbes in your body at this moment outnumber your cells by ten to one. And they come in a huge diversity of species -- somewhere in the thousands, although no one has a precise count yet. By some estimates there are twenty million microbial genes in your body: about a thousand times more than the 20,000 protein-coding genes in the human genome. So the Human Genome Project was, at best, a nice start. If we really want to understand all the genes in the human body, we have a long way to go.
Now you could say "Who cares? They're just wee animalcules." Those wee animacules are worth caring about for many reasons. One of the most practical of those reasons is that they have a huge impact on our "own" health. Our collection of microbes-the microbiome-is like an extra organ of the human body. And while an organ like the heart has only one function, the microbiome has many.
When food comes into the gut, for example, microbes break some of them down using enzymes we lack. Sometimes the microbes and our own cells have an intimate volley, in which bacteria break down a molecule part way, our cells break it down some more, the bacteria break it down even more, and then finally we get something to eat.
Another thing that the microbiome does is manage the immune system. Certain species of resident bacteria, like Bacteroides fragilis, produce proteins that tamp down inflammation. When scientists rear mice that don't have any germs at all, they have a very difficult time developing a normal immune system. The microbiome has to tutor the immune system in how to do its job properly. It also acts like an immune system of its own, fighting off invading microbes, and helping to heal wounds.
While the microbiome may be an important organ, it's a peculiar one. It's not one solid hunk of flesh. It's an ecosystem, made up of thousands of interacting species.
Here's an interesting hypothesis: that all current life on Earth originated from a planet-wide super-organism named LUCA.
The latest results suggest LUCA was the result of early life's fight to survive, attempts at which turned the ocean into a global genetic swap shop for hundreds of millions of years. Cells struggling to survive on their own exchanged useful parts with each other without competition -- effectively creating a global mega-organism.
It was around 2.9 billion years ago that LUCA split into the three domains of life: the single-celled bacteria and archaea, and the more complex eukaryotes that gave rise to animals and plants (see timeline). It's hard to know what happened before the split. Hardly any fossil evidence remains from this time, and any genes that date that far back are likely to have mutated beyond recognition.
You know how your hands and feet get all wrinkly when they're immersed in water for a long time? There's speculation the wrinkles might be an adaptation that allows for better gripping in wet conditions.
Now a paper in the journal Brain, Behavior and Evolution offers more evidence that wet wrinkles serve a purpose. Much like the tread on a tire, they improve traction.
In the study, an evolutionary neurobiologist and his co-authors examined 28 fingers wrinkled by water. They found that they all had the same pattern of unconnected channels diverging away from one another as they got more distant from the fingertips.
The wrinkles allow water to drain away as fingertips are pressed to wet surfaces, creating more contact and a better grip.
Evolutionary biologists are increasingly studying organisms (like mice, fish, and bacteria) in urban areas like New York City to find out how they evolve to urban conditions.
Dr. Munshi-South and his colleagues have been analyzing the DNA of the mice. He's been surprised to find that the populations of mice in each park are genetically distinct from the mice in others. "The amount of differences you see among populations of mice in the same borough is similar to what you'd see across the whole southeastern United States," he said.
LeafSnap is a new iPhone app that uses facial recognition techniques to identify trees based on photos of their leaves.
Leafsnap contains beautiful high-resolution images of leaves, flowers, fruit, petiole, seeds, and bark. Leafsnap currently includes the trees of New York City and Washington, D.C., and will soon grow to include the trees of the entire continental United States.
Wow. Garden Design has more info. (thx, claire)
Whoa, watch the video at the top of this article to see how the human face develops in the womb from an age of one-month to ten weeks. It all just comes together right at the end!
If you watch it closely, you will see that the human face is actually formed of three main sections which rotate and come together in an unborn foetus.
The way this happens only really makes sense when you realise that, strange though it may sound, we are actually descended from fish.
The early human embryo looks very similar to the embryo of any other mammal, bird or amphibian -- all of which have evolved from fish.
Your eyes start out on the sides of your head, but then move to the middle.
The top lip along with the jaw and palate started life as gill-like structures on your neck. Your nostrils and the middle part of your lip come down from the top of your head.
There is no trace of a scar; the plates of tissue and muscle fuse seamlessly. But there is, however, a little remnant of all this activity in the middle of your top lip -- your philtrum.
Carl Zimmer in Slate:
Redfield blogged a scathing attack on Saturday. Over the weekend, a few other scientists took to the Internet as well. Was this merely a case of a few isolated cranks? To find out, I reached out to a dozen experts on Monday. Almost unanimously, they think the NASA scientists have failed to make their case. "It would be really cool if such a bug existed," said San Diego State University's Forest Rohwer, a microbiologist who looks for new species of bacteria and viruses in coral reefs. But, he added, "none of the arguments are very convincing on their own." That was about as positive as the critics could get. "This paper should not have been published," said Shelley Copley of the University of Colorado.
There may only be a few dozen albino redwoods in the world; they're difficult to find so no one knows the real number. The albinos lack chlorophyll, making them unable to produce their own food, so they freeload off of a parent tree.
KQED has a short video segment about the albino redwoods as well.
NASA's astrobiology announcement is that they've found a new kind of life that incorporates the normally toxic arsenic into its DNA.
Life like us uses a handful of basic elements in the majority of its biochemistry: carbon, hydrogen, oxygen, and nitrogen for the most part. But phosphorus is also a critical element in two major ways: it's used as the backbone of the long, spiral-shaped DNA and RNA molecules (think of it as the winding support structure for a spiral staircase and you'll get the picture), and it's part of the energy transport mechanism for cells in the form of ATP (adenosine triphosphate). Without it, our cells would literally not be able to reproduce, and we'd be dead anyway if it were gone. There are many other ways phosphorus is used as well, including in cell membranes, bones, and so on. It's a key element for all forms of life.
Amazingly, using radioisotope-tagged molecules containing arsenic, they were able to find that the microbes incorporated the arsenic into their very DNA! It's hard to stress how shocking this is; as I understand it, saying something like that to a microbiologist without evidence would've had them slowly backing away from you and looking for weapons or an escape route.
I guessed wrong about what NASA was set to announce today, but the actual announcement is much more interesting than the mere discovery of extraterrestrial life. Aliens are inevitable -- we're going to find them sooner or later -- but a new kind of DNA, that's not something that happens every day. Exciting! (thx, jon)
Here's a curious press release from NASA:
NASA will hold a news conference at 2 p.m. EST on Thursday, Dec. 2, to discuss an astrobiology finding that will impact the search for evidence of extraterrestrial life. Astrobiology is the study of the origin, evolution, distribution and future of life in the universe.
I did a little research on the news conference participants and found:
1. Pamela Conrad (a geobiologist) was the primary author of a 2009 paper on geology and life on Mars
2. Felisa Wolfe-Simon (an oceanographer) has written extensively on photosynthesis using arsenic recently (she worked on the team mentioned in this article)
3. Steven Benner (a biologist) is on the "Titan Team" at the Jet Propulsion Laboratory; they're looking at Titan (Saturn's largest moon) as an early-Earth-like chemical environment. This is likely related to the Cassini mission.
4. James Elser (an ecologist) is involved with a NASA-funded astrobiology program called Follow the Elements, which emphasizes looking at the chemistry of environments where life evolves (and not just looking at water or carbon or oxygen).
So, if I had to guess at what NASA is going to reveal on Thursday, I'd say that they've discovered arsenic on Titan and maybe even detected chemical evidence of bacteria utilizing it for photosynthesis (by following the elements). Or something like that. (thx, sippey)
Update: According to Alexis Madrigal, the answer to the hyperbolic question in the headline is "no".
I'm sad to quell some of the @kottke-induced excitement about possible extraterrestrial life. I've seen the Science paper. It's not that.
Clinical trials are about to begin where embryonic stem cells will be injected into the eyes of people with Stargardt's macular degeneration.
Robert Lanza, the company's chief scientific officer, said that the first patient could receive the stem cell transplants early in the new year and although the trial is designed primarily to assess safety, the first signs of visual improvement may be apparent within weeks. "Talking to the clinicians, we could see something in six weeks, that's when we think we may see some improvements. It really depends on individual patients but that's a reasonable time frame when something may start to happen," Dr Lanza said.
Evolutionary speaking, premature ejaculation may not be such a bad thing after all.
So given these basic biological facts, and assuming that ejaculation is not so premature that it occurs prior to intromission and sperm cells find themselves awkwardly outside of a woman's reproductive tract flopping about like fish out of water, what, exactly, is so "premature" about premature ejaculation? In fact, all else being equal, in the ancestral past, wouldn't there likely have been some reproductive advantages to ejaculating as quickly as possible during intravaginal intercourse-such as, oh, I don't know, inseminating as many females as possible in as short a time frame as possible? or allowing our ancestors to focus on other adaptive behaviors aside from sex? or perhaps, under surreptitious mating conditions, doing the deed quickly and expeditiously without causing a big scene?
Still, for recreational sex, it blows. (As it were.)
Does quantum entanglement hold DNA together? Some physicists say it's possible.
Rieper and co ask what happens to these oscillations, or phonons as physicists call them, when the base pairs are stacked in a double helix.
Phonons are quantum objects, meaning they can exist in a superposition of states and become entangled, just like other quantum objects.
To start with, Rieper and co imagine the helix without any effect from outside heat. "Clearly the chain of coupled harmonic oscillators is entangled at zero temperature," they say. They then go on to show that the entanglement can also exist at room temperature.
That's possible because phonons have a wavelength which is similar in size to a DNA helix and this allows standing waves to form, a phenomenon known as phonon trapping. When this happens, the phonons cannot easily escape. A similar kind of phonon trapping is known to cause problems in silicon structures of the same size.
The OpenPCR project is trying to raise $6,000 on Kickstarter to design and build a DNA Xerox machine that costs less than $400, thereby enabling DNA hacking in one's garage.
In 1983, Kary Mullis first developed PCR, for which he later received a Nobel Prize. But the tool is still expensive, even though the technology is almost 30 years old. If computing grew at the same pace, we would all still be paying $2,000+ for a 1 MHz Apple II computer. Innovation in biotech needs a kick start!
PCR machines currently cost $4-10,000. (via modcult)
The man/machine union marches ever closer.
Scientists have embedded a nano-sized transistor inside a cell-like membrane and powered it using the cell's own fuel. The research could lead to new types of man-machine interactions where embedded devices could relay information about the inner workings of disease-related proteins inside the cell membrane, and eventually lead to new ways to read, and even influence, brain or nerve cells.
When I first saw the headline, I thought that it said "embedded a nano-sized transistor radio"...now that would be something. (via jb)
There are a ridiculous number of microbes in the Earth's oceans.
During an 11 month study in 2007, scientists sequenced the genes of more than 180,000 specimens from the Western English Channel. Although this level of sampling "far from exhausted the total diversity present," they wrote, one in every 25 readings yielded a new genus of bacteria (7,000 genera in all).
That's genus, not species. Kevin Kelly translates:
This suggests there is a long tail of life in bacteria, with a few species super-abundant, but many many species with very thin populations. At the far end of the tail there may be a billion species with only a few individuals. [...] And like other kinds of long tails, the sum of all these small bits total up to exceed the sum of individuals in the most popular species. As the microbiologists involved in the Census of Marine Life like to say, this survey reveals life's "hidden majority."
Recent evidence suggests that bacteria in clouds may have evolved the ability to make it rain as a way of dispersing themselves around the globe.
The theory-called bioprecipitation-was pioneered by David Sands, a plant pathologist at Montana State University, in the 1980s. But little information existed on how the rainmaking bacteria moved through the atmosphere until Christner and his colleagues began their work in 2005. Sands told National Geographic News that the critters may even employ creative means of transportation: For instance, they could "ride piggyback" on pollen or insects. "We thought [the bacteria] were just plant pathogens [germs], but we found them in mountain lakes, in waterfalls, in Antarctica-they get around," Sands said.
Writing for National Geographic, Carl Zimmer on the fascinating plants that eat animals. Like the Venus flytrap, "an electrical plant":
When an insect brushes against a hair on the leaf of a Venus flytrap, the bending triggers a tiny electric charge. The charge builds up inside the tissue of the leaf but is not enough to stimulate the snap, which keeps the Venus flytrap from reacting to false alarms like raindrops. A moving insect, however, is likely to brush a second hair, adding enough charge to trigger the leaf to close.
Volkov's experiments reveal that the charge travels down fluid-filled tunnels in a leaf, which opens up pores in cell membranes. Water surges from the cells on the inside of the leaf to those on the outside, causing the leaf to rapidly flip in shape from convex to concave, like a soft contact lens. As the leaves flip, they snap together, trapping an insect inside.
See also the accompanying photo gallery.
A recent study indicates that the wing shapes of North American birds are changing in response to deforestation.
He found that over half of the species he examined demonstrated changes over time with boreal birds developing more pointed wings and temperate birds developing rounder wings. These results support the hypothesis that habitat isolation is spurring evolutionary changes in birds.
Boreal forests have suffered severe deforestation over the past century, and so Desrochers had predicted that increased distances between habitat patches would select for more pointed wings in birds. Pointed wings are associated with more energy-efficient sustained flight.
One of the big bummers about quantum computing is the cold temperatures required (hundreds of degrees below zero). However, a number of researchers believe that certain algae and bacteria perform quantum calculations at room temperature.
The evidence comes from a study of how energy travels across the light-harvesting molecules involved in photosynthesis. The work has culminated this week in the extraordinary announcement that these molecules in a marine alga may exploit quantum processes at room temperature to transfer energy without loss. Physicists had previously ruled out quantum processes, arguing that they could not persist for long enough at such temperatures to achieve anything useful.
Recent evidence of horizontal gene transfer -- in which genes are exchanged from other organisms, not from ancestors -- has some scientists thinking that the dominant form of evolution for most of the Earth's history was between non-related organisms and not among ancestors.
In the past few years, a host of genome studies have demonstrated that DNA flows readily between the chromosomes of microbes and the external world. Typically around 10 per cent of the genes in many bacterial genomes seem to have been acquired from other organisms in this way, though the proportion can be several times that. So an individual microbe may have access to the genes found in the entire microbial population around it, including those of other microbe species. "It's natural to wonder if the very concept of an organism in isolation is still valid at this level," says Goldenfeld.
Read on for their hypothesis about how horizontal evolution drove innovation -- development of a universal genetic code and genetic innovation-sharing protocols -- in life forms early on in the Earth's history. Fascinating.
In addition to its utility in organizing the World Wide Web, researchers say that Google's PageRank algorithm is useful in studying food webs, "the complex networks of who eats whom in an ecosystem".
Dr Allesina, of the University of Chicago's department of ecology and Evolution, told BBC News: "First of all we had to reverse the definition of the algorithm. "In PageRank, a web page is important if important pages point to it. In our approach a species is important if it points to important species."
The researchers compared the performance of PageRank and found it comparable to that of much more complex computational biology algorithms.
As reported previously, colony collapse disorder seems to have multiple causes. In the NY Times' Room for Debate blog, several scientists and other bee experts offer their commentary on what we currently know about CCD and what's being done about it.
Meanwhile, individual beekeeping operations have been damaged, some beyond repair because of this malady. Others have been able to recover. The overall picture is, however, not quite as bleak as the press and the blogosphere might lead you to imagine. Colony numbers in the U.S. show the resiliency of American beekeepers.
Scientists have created a really fast bacterial computer that can solve, among other things, a specialized case of the travelling salesman problem.
Programming such a computer is no easy task, however. The researchers coded a simplified version of the problem, using just three cities, by modifying the DNA of Escherichia coli bacteria. The cities were represented by a combination of genes causing the bacteria to glow red or green, and the possible routes between the cities were explored by the random shuffling of DNA. Bacteria producing the correct answer glowed both colours, turning them yellow.
But just as vacuum tube and silicon chip-based computers became capable of more abstract calculations, perhaps the bacteria computer will follow the same developmental trajectory.
The NY Times on the progress being made in explaining how life arose on Earth.
With these four recent advances -- Dr. Szostak's protocells, self-replicating RNA, the natural synthesis of nucleotides, and an explanation for handedness -- those who study the origin of life have much to be pleased about, despite the distance yet to go. "At some point some of these threads will start joining together," Dr. Sutherland said. "I think all of us are far more optimistic now than we were five or 10 years ago."
This week in the New Yorker, Elizabeth Kolbert tells us that up until modern times, there have been five big mass extinctions of life on Earth. Most biologists now agree that we are in the midst of the sixth big mass extinction, one caused by humans.
Currently, a third of all amphibian speicies, nearly a third of all reef-building corals, a quarter of all mammals, and an eighth of all birds are classified as "threatened with extinction." These estimates do not include the species that humans have already wiped out or the species for which there are insignificant data. Nor do the figures take into account the projected effects of global warming or or ocean acidification. Nor, of course, can they anticipate the kinds of sudden, terrible collapses that are becoming almost routine.
See also a related audio clip by Kolbert, the Holocene extinction event, and colony collapse disorder.
Chemist John Sutherland has discovered a process by which ordinary chemicals could spontaneously form RNA molecules, the suspected building blocks of the first life on Earth.
Scientists have long suspected that the first forms of life carried their biological information not in DNA but in RNA, its close chemical cousin. Though DNA is better known because of its storage of genetic information, RNA performs many of the trickiest operations in living cells. RNA seems to have delegated the chore of data storage to the chemically more stable DNA eons ago. If the first forms of life were based on RNA, then the issue is to explain how the first RNA molecules were formed.
On the Zeitgedächtnis, or time-sense, of honeybees.
Flowers of a given species all produce nectar at about the same time each day, as this increases the chances of cross-pollination. The trick works because pollinators, which in most cases means the honeybee, concentrate foraging on a particular species into a narrow time-window. In effect the honeybee has a daily diary that can include as many as nine appointments -- say, 10:00 a.m., lilac; 11:30 a.m., peonies; and so on. The bees' time-keeping is accurate to about 20 minutes.
Bone is a springy and salty wonder that is proving much more functional within the human body than originally thought.
The skeleton is a multipurpose organ, offering a ready source of calcium for an array of biochemical tasks, and housing the marrow where blood cells are born. Yet above all the skeleton allows us to locomote, which means it gets banged up and kicked around. Paradoxically, it copes with the abuse and resists breaking apart in a major way by microcracking constantly. "Bone microcracks, that's what it does," Dr. Ritchie said. "That's how stresses are relieved." [...] But like all forms of health care, bone repair doesn't come cheap, and maintaining skeletal integrity consumes maybe 40 percent of our average caloric budget.
The article leads off with the story of Harry Eastlack, whose body repaired itself with bone-building cells no matter what the injury, essentially giving him a not-so-Wolverine-like second skeleton. Here's a photo I found of Eastlack's skeleton, which is housed at the Mutter Museum of the College of Physicians.
Have Spanish scientists found a cure for colony collapse disorder, which affects millions of honeybees around the world? The sole cause, according to the scientists, is a fungal parasite called nosema ceranae. This finding doesn't jibe with the recent Scientific American article written by two American CCD investigators. They say that nosema is one factor out of many.
In the gut contents we found spores of nosema, single-celled fungal parasites that can cause bee dysentery. The spore counts in these and in subsequent samples, however, were not high enough to explain the losses. Molecular analysis of Hackenberg's bees, performed by the other of us (Cox-Foster), also revealed surprising levels of viral infections of various known types. But no single pathogen found in the insects could explain the scale of the disappearance.
Update: Some beekeepers have solved bee death problems in their hives by using comb with smaller cell sizes.
In case you weren't aware, and I wasn't for a long time, the foundation in common usage by beekeepers results in much larger bees than what you would find in a natural hive. I've measured sections of natural worker brood comb that are 4.6mm in diameter. This 4.6mm comb was drawn by a hive of commercial Carniolans and this 4.7mm comb was drawn on the first try by a package of commercial Carniolans. What most beekeepers use for worker brood is foundation that is 5.4mm in diameter. If you translate that into three dimensions, instead of one, that produces a bee that is about half again as large as is natural. By letting the bees build natural sized cells, I have virtually eliminated my Varroa and Tracheal mite problems.
The cell size in commercially available combs has been increased over the years to increase the honey yield. (thx, brian)
In an article for Scientific American, two scientists who are working on the causes of colony collapse disorder (CCD) say that they and other researchers have made some progress in determining what's killing all of those bees.
The growing consensus among researchers is that multiple factors such as poor nutrition and exposure to pesticides can interact to weaken colonies and make them susceptible to a virus-mediated collapse. In the case of our experiments in greenhouses, the stress of being confined to a relatively small space could have been enough to make colonies succumb to IAPV and die with CCD-like symptoms.
It's like AIDS for bees...the lowered immunity doesn't kill directly but makes the bees more susceptible to other illness. One the techniques researchers used in investigating CDD is metagenomics. Instead of singling out an organism for analysis, they essentially mixed together a bunch of genetic material found in the bees (including any bacteria, virii, parasites, etc.) and sliced it up into small pieces that were individually deciphered. They went through those pieces one by one and assigned them to known organisms until they ran across something unusual.
The CSI-style investigation greatly expanded our general knowledge of honeybees. First, it showed that all samples (CCD and healthy) had eight different bacteria that had been described in two previous studies from other parts of the world. These findings strongly suggest that those bacteria may be symbionts, perhaps serving an essential role in bee biology such as aiding in digestion. We also found two nosema species, two other fungi and several bee viruses. But one bee virus stood out, as it had never been identified in the U.S.: the Israeli acute paralysis virus, or IAPV.
Every year, a professor from Liberty University takes his Advanced Creation Studies biology class to the Smithsonian Museum of Natural History to check out the opposition.
"There's nothing balanced here. It's completely, 100 percent evolution-based," said DeWitt, a professor of biology. "We come every year, because I don't hold anything back from the students."
Creationists, who take their view of natural history straight from the book of Genesis, believe that scientific data can be interpreted to support their idea that God made the first human, Adam, in an essentially modern form 6,000 to 10,000 years ago.
A 2006 poll by the Pew Forum on Religion & Public Life found that 42 percent of Americans believe humans have always existed in their present form. At universities such as Liberty, founded by the late Jerry Falwell, those views inform the entire science curriculum.
This review of Superorganism, a new book by Bert Hölldobler and Edward O. Wilson, is chock full of fascinating facts about ant societies and how they organize themselves.
The progress of ants from this relatively primitive state to the complexity of the most finely tuned superorganisms leaves no doubt that the progress of human evolution has largely followed a path taken by the ants tens of millions of years earlier. Beginning as simple hunter-gatherers, some ants have learned to herd and milk bugs, just as we milk cattle and sheep. There are ants that take slaves, ants that lay their eggs in the nests of foreign ants (much like cuckoos do among birds), leaving the upbringing of their young to others, and there are even ants that have discovered agriculture. These agricultural ants represent the highest level of ant civilization, yet it is not plants that they cultivate, but mushrooms.
My grandpappy used to say to me, "Them dolphins is smart. The chefs of the sea they are!"** Scientists have observed bottlenose dolphins preparing cuttlefish for consumption.
Considering they can't wield a knife or cleaver, dolphins make impressive butchers. Researchers in Australia recently observed a bottlenose performing a precise series of manoeuvres to kill, gut and bone a cuttlefish. The six-step procedure gets rid of the invertebrate's unappetising ink and hard-to-swallow cuttlebone.
** This is not true.
Remarkable photo of a gynandromorphic cardinal with bilateral asymmetry, meaning that the left side of the bird is male and the right side is female...a red/brown split right down the middle.
Not Photoshopped, although the phenomenon is more common with butterflies. (thx, jason)
Update: Here's a two-tone lobster caught in Maine in 2006. (thx, nicole & jim)
Steven Johnson really likes a book called Eating the Sun: How Plants Power the Planet by Oliver Morton; he calls it his favorite book (so far) of 2008. From a Publishers Weekly review:
The cycle of photosynthesis is the cycle of life, says science journalist Morton (Mapping Mars). Green leaves trap sunlight and use it to absorb carbon dioxide from the air and emit life-giving oxygen in its place. Indeed, plants likely created Earth's life-friendly oxygen- and nitrogen-rich biosphere. In the first part, Morton, chief news and features editor of the leading science journal, Nature, traces scientists' quest to understand how photosynthesis works at the molecular level. In part two, Morton addresses evidence of how plants may have kick-started the complex life cycle on Earth. The book's final part considers photosynthesis in relation to global warming, for, he says, the Earth's plant-based balance of carbon dioxide and oxygen is broken: in burning vast amounts of fossil fuels, we are emitting more carbon dioxide than the plants can absorb. But Morton also explores the possibility that our understanding of photosynthesis might be harnessed to regain that balance.
Scientists are saying that we can make ourselves a whoolly mammoth for as little as $10 million. All it takes is a mammoth genome, a lot of painstaking work, and much computing power.
If the genome of an extinct species can be reconstructed, biologists can work out the exact DNA differences with the genome of its nearest living relative. There are talks on how to modify the DNA in an elephant's egg so that after each round of changes it would progressively resemble the DNA in a mammoth egg. The final-stage egg could then be brought to term in an elephant mother, and mammoths might once again roam the Siberian steppes.
The article also notes that if this works for the mammoth, it might also be possible to do the same for a Neanderthal. What an age we live in.
DARPA is soliciting research proposals for people wishing to solve one of twenty-three mathematical challenges, many of which deal with attempting to find a mathematical basis underlying biology.
What are the Fundamental Laws of Biology?: This question will remain front and center for the next 100 years. DARPA places this challenge last as finding these laws will undoubtedly require the mathematics developed in answering several of the questions listed above.
We've heard from the sex workers about the Spitzer affair. Now the psychologists. This article compiles many ideas about why Spitzer did what he did:
Psychologist Christopher Ryan, author of "Sex in Prehistory," says the desire for sex with more than one person has always been there -- for leaders and followers alike. "The desire is not a function of status or power -- it's a question of availability."
What's relatively new to the human race, he said, is the ability to exercise power and the connection between power and sex.
That's because, for most of human existence, there was only so far a man could coerce others when food was essentially free and hard to hoard. And until relatively recently, sex with multiple partners was the norm. "It would have been very unusual 100,000 years ago for a person to have one sexual partner for 30 years," said Ryan in an interview from Barcelona.
And here's the evolutionary psychological point of view:
She points out that, while powerful men throughout western history have married monogamously (they had only one legal wife at a time), they have always mated polygynously (they had lovers, concubines, and female slaves). Many had harems, consisting of hundreds and even thousands of virgins. With their wives, they produced legitimate heirs; with the others, they produced bastards (Betzig's term). Genes and inclusive fitness make no distinction between the two categories of children. While the legitimate heirs, unlike the bastards, inherited their fathers' power and status and often went on to have their own harems, powerful men sometimes invested in their bastards as well.
As a result, powerful men of high status throughout human history attained very high reproductive success, leaving a large number of offspring (legitimate or otherwise), while countless poor men in the countryside died mateless and childless.
Update: And one more from Natalie Angier:
Yet as biologists have discovered through the application of DNA paternity tests to the offspring of these bonded pairs, social monogamy is very rarely accompanied by sexual, or genetic, monogamy. Assay the kids in a given brood, whether of birds, voles, lesser apes, foxes or any other pair-bonding species, and anywhere from 10 to 70 percent will prove to have been sired by somebody other than the resident male.
Nurture is really kicking ass these days....first the IQ thing and now this.
The offspring of expensive stallions owe their success more to how they are reared, trained and ridden than good genes, a study has found. Only 10% of a horse's lifetime winnings can be attributed to their bloodline, research in Biology Letters shows.
That suggests, a la Moneyball, that buying horses with so-so lineages and training them really well could make for a better return on investment.
Chart of the possible shapes and forms of leaves. For instance, you could have a leaf of lanceolate shape with a crenate margin and reticulate veins.
Update: kottke.org reader Flip passes along this article about the wavy edges of flowers, leaves and even garbage bags, summarizing it thusly:
Basically, as the leaf grows it is constrained to a 2-d surface, but the cells of some leaves reproduce fast enough to require more surface area than a pi-r-squared plane surface can provide. Its only recourse is to buckle out-of-plane, giving the wrinkles. Since the exuberant growth continues as the leaf grows outward, the buckling process repeats and you get the multi-scale (ripples on ripples on ripples) shape that you see in kale and daffodils.
As part of a 2006 Shuttle mission, researchers sent salmonella germs into space to see how they were affected. The result: 167 genes changed in the salmonella during the short trip and "mice fed the space germs were three times more likely to get sick and died quicker than others fed identical germs that had remained behind on Earth." Holy crap!
Some recent research on the wrist bones of the so-called hobbit skeleton suggests that Flores man is an ancestor of modern humans and not just diseased homo sapiens. The debate continues. (via npr)
Langstroth's crucial insight -- "I could scarcely refrain from shouting 'Eureka!' in the open streets," he wrote of the moment of revelation -- was the concept of "bee space." He realized that while honeybees will seal up passageways that are either too large or too small, they will leave open passages that are just the right size to allow a bee to pass through comfortably. Langstroth determined that if frames were placed at this "bee-space" interval of three-eighths of an inch, bees would build honeycomb that could be lifted from the hive, rather than, as was the practice up to that point, sliced or hacked out of it. He patented L. L. Langstroth's Movable Comb Hive in 1852. Today's version consists of a number of rectangular boxes-the number is supposed to grow during the season-open at the top and at the bottom. Each box is equipped with inner lips from which frames can be hung, like folders in a filing drawer, and each frame comes with special tabs to preserve bee space.
So says Elizabeth Kolbert in an article about colony-collapse disorder, a bee disease that's wreaking havoc on beehives and food production around the US. Bee space! I'm unsure whether similar research has been done to determine the proper "human space", although the placement of houses in a suburb, tables in a restaurant, blankets at the beach, or social space in elevators might provide some clues as to the proper measurement.
But returning to the bees, a coalition of scientists working on the problem has found a correlation between bee deaths and Israeli acute paralysis virus. An infusion of bees from Australia in 2004 may also have contributed to the disorder's development. Full details are available on EurekAlert.
The social life of plants: plants can tell their relatives from strangers. "Plants grown alongside unrelated neighbours are more competitive than those growing with their siblings -- ploughing more energy into growing roots when their neighbours don't share their genetic stock."
Global warming + evolution = species explosion!!!
Cities are often thought of as organisms or ecosystems, but the authors of a new study find that metaphor lacking. "The one thing that we know about organisms whether it be elephants or sharks or frogs, is that as they get large, they slow down. They use less energy, they don't move as fast. That is a very important point for biological scaling. In the case of cities, it is actually the opposite. As cities get larger they create more wealth and they are more innovative at a faster rate. There is no counterpart to that in biology."
Among the many interesting things in Online Journalism Review's article about using eyetracking to increase the effectiveness of news article design is this odd result:
Although both men and women look at the image of George Brett when directed to find out information about his sport and position, men tend to focus on private anatomy as well as the face. For the women, the face is the only place they viewed. Coyne adds that this difference doesn't just occur with images of people. Men tend to fixate more on areas of private anatomy on animals as well, as evidenced when users were directed to browse the American Kennel Club site.
That is absolutely fascinating. I'd love to hear an evolutionary biologist's take on why that is.
I'm also heartened by the article's first featured finding: that tighter writing, more white space, and jettisoning unnecessary imagery helps readers read faster and retain more of what they've read.
The cover story in this week's NY Times Magazine is called Darwin's God and covers, from an evolutionary biology standpoint, why people believe in God. Most scientists studying the matter believe that humans have a built-in mechanism for religious belief. For instance, anthropologist Scott Atran sometimes conducts an intriguing experiment with his students:
His research interests include cognitive science and evolutionary biology, and sometimes he presents students with a wooden box that he pretends is an African relic. "If you have negative sentiments toward religion," he tells them, "the box will destroy whatever you put inside it." Many of his students say they doubt the existence of God, but in this demonstration they act as if they believe in something. Put your pencil into the magic box, he tells them, and the nonbelievers do so blithely. Put in your driver's license, he says, and most do, but only after significant hesitation. And when he tells them to put in their hands, few will. If they don't believe in God, what exactly are they afraid of?
Or rather, why are they afraid? One possible reason is that humans are conditioned to be on the lookout for "agents" and we tend to find them even when they're not there:
So if there is motion just out of our line of sight, we presume it is caused by an agent, an animal or person with the ability to move independently. This usually operates in one direction only; lots of people mistake a rock for a bear, but almost no one mistakes a bear for a rock.
What does this mean for belief in the supernatural? It means our brains are primed for it, ready to presume the presence of agents even when such presence confounds logic. "The most central concepts in religions are related to agents," Justin Barrett, a psychologist, wrote in his 2004 summary of the byproduct theory, "Why Would Anyone Believe in God?" Religious agents are often supernatural, he wrote, "people with superpowers, statues that can answer requests or disembodied minds that can act on us and the world."
Another reason for the instinctive religious impulse may be that people are able to put themselves in other peoples' minds, to think about how another person might be feeling or thinking:
Folkpsychology, as Atran and his colleagues see it, is essential to getting along in the contemporary world, just as it has been since prehistoric times. It allows us to anticipate the actions of others and to lead others to believe what we want them to believe; it is at the heart of everything from marriage to office politics to poker. People without this trait, like those with severe autism, are impaired, unable to imagine themselves in other people's heads.
The process begins with positing the existence of minds, our own and others', that we cannot see or feel. This leaves us open, almost instinctively, to belief in the separation of the body (the visible) and the mind (the invisible). If you can posit minds in other people that you cannot verify empirically, suggests Paul Bloom, a psychologist and the author of "Descartes' Baby," published in 2004, it is a short step to positing minds that do not have to be anchored to a body. And from there, he said, it is another short step to positing an immaterial soul and a transcendent God.
There's lots more in the article...it's well worth a read.
Honeybee populations across the US are falling due to a mysterious disease. "Almond crops are immediately vulnerable because they rely on honeybee pollination at this time of year. And the insect decline could potentially affect other crops later in the year, such as apples and blueberries."
Richard Dawkins answers some questions from readers of the Independent. "Terrible things have been done in the name of Christ, but all he ever taught was peace and love. What's wrong with that?"
A classic article by Stephen Jay Gould on the changing biological features of Mickey Mouse. Over the years, Mickey has become more well-behaved and his appearance more juvenile (larger eyes, short pudgy legs, relatively large head, short snout, etc.). "When we see a living creature with babyish features, we feel an automatic surge of disarming tenderness."
Tom Coates recently checked out the Royal College of Art Summer Show in London and ran across this project by Tim Simpson:
...three plants compete to reach the light that feeds and nourishes them. The first one to succeed survives. The other two are automatically cut down in their prime.
First plant to grow close to the proximity sensors wins. A simple and elegant idea.
Sarah Trigg's work combines geographic maps with biological forms. "The explorer system [in colonial North America] caused the Native American system to change its normal functioning, much like cancer cells do to normal cells." More here. (via moon river)
Profile of Daniel Dennett, "Darwinian fundamentalist" and author of a new book that argues that "religion, chiefly Christianity, is itself a biologically evolved concept, and one that has outlived its usefulness".
Update: Review of Dennett's book in the New Yorker.
To Dr. David Hague, human pregnancy is a struggle between the fetus and mother. Evolutionarily speaking, the fetus "wants" as many resources as possible for itself while the mother "wants" to do what she can to spread her resources across as many children as possible. In theory, this is a cause of the many serious health problems surrounding pregnancy.
Update: Carl Zimmer has more about this on his blog.
Pruned has collected some lovely petri dish scenes full of fractal patterns.
Billions and billions of bacterial landscape architects pruning -- no less in environments poisoned with antibiotics -- other bacterial landscape architects, dead or alive, to form dazzling arabesque parterres. The self-organizing embroidery of organisms in constant Darwinian mode.
More here. See also ferrofluid.
Justin reports on his family's results of a neat project called the Geneographic Project, co-produced by National Geographic and IBM. If you purchase a testing kit, they'll trace the specific genetic markers of your ancestors back to (possibly) our common African root.
Scientists find "lost world" of undiscovered animals in the Foja Mountains of western New Guinea. "Their finds included more than 20 new frogs, 4 butterflies and a number of plants, including 5 new palms and rhododendrons with the largest flowers on record."
The world's coolest parasite; it makes zombie cockroaches! When it wants to lay its eggs, the Ampulex compressa wasp stuns a cockroach, numbs its brain, steers it back to its nest, lays an egg inside it, and eventually a larvae forms, it lunches on the cockroach's insides, and then hatches fully grown. Just...wow. (thx, tien)
Short (and a wee bit hostile) inteview with Daniel Dennett. "Nerve cells are very complicated mechanical systems. You take enough of those, and you put them together, and you get a soul."
Scientists say there may be two different forms of laughter -- authentic laughter and that associated with humor -- and that the two developed millions of years apart during the course of human evolution.
Not only is Intelligent Design bad science, it's also bad religion. "Self-defeating and incoherent, Intelligent Design is worse than useless, not only as science but also, one imagines, for religious folks who might be attempting to understand God by working backwards from the world as their body of evidence."
"The only debate on intelligent design that is worthy of its subject". Hootingly funny. (And I have no doubt that someone from the other side of the debate could construct something equally as amusing, so...)
Is it strange that every time I go into my bathroom and look at the box of tissues sitting on the shelf, I see Charles Darwin looking back at me?
It does look like Darwin, yes? Or have I been reading far too much about science and evolution lately?
Note: My bathroom Darwin orchid has nothing to do with Angraecum sesquipedale, an orchid that Darwin discovered in 1850. At the time, he speculated that in order for the plant to be pollinated, a moth with a 12" proboscis would have to do it, even though no such moth had been shown to exist. This freakish moth was eventually discovered (not in my bathroom) in 1903, 20 years after Darwin's death.
Flowers don't smell as good as they used to and part of the reason is breeding...they're breeding flowers for looks and longevity, not for scent. I believe Michael Pollan discusses this in his excellent The Botany of Desire (tulip chapter).
First photos of the giant squid ever captured. In capturing the photos, they ripped one of the squid's tentacles off, which has made the squid a bit angry.
Profile of Robert Trivers who "came up with the first Darwinian explanations for human cooperation, jealousy and our sense of justice that made genetic sense, and he showed how these arose from the same forces as act on all animals, from the pigeons outside his window to the fish of coral reefs".
Cymothoa exigua is a crustacean parasite that eats the tongue of the host fish and then attaches itself to the mouth of the fish and functions as the tongue would have, sharing in the food that the fish brings in.
According to paleontologist Gareth Dyke, "fossil evidence that [predatory] dinosaurs were feathered is now 'irrefutable'". Digitally remastered Jurassic Park can't be too far down the road.
Daniel Dennett on why intelligent design isn't science. "Evolutionary biology certainly hasn't explained everything that perplexes biologists. But intelligent design hasn't yet tried to explain anything."
A small ocean microbe called Pelagibacter has the smallest genome of any self-sufficient organism with 1,354 genes. It also doesn't appear to have any extra DNA...no junk or redundant copies of genes.
Interview with Frans de Waal about his work with primate behavior and politics. "I call the human species the most bipolar ape, meaning that we go beyond chimps in our violence, which is systematic and often results in thousands of dead, and we go beyond the bonobo in our empathy and love for others, so that human altruism is truly remarkable."
Biologists are beginning to simulate living things by computer, molecule by molecule. They're starting with E. coli, but they've still got a long way to go.
The club-winged manakin sings by playing its feathers like a washboard. Crickets do this, but the manakin is the first vertebrate observed to do it.
Butterfly team colors may discourage inter-species mating and pave the way for the development of separate species. "This process, called 'reinforcement', prevents closely related species from interbreeding thus driving them further apart genetically and promoting speciation."
Robotics research suggests that Lucy walked upright like humans. Lucy, discovered in 1974 in Ethiopia, is a 3.2 million year old Australopithecus afarensis skeleton.
Male and female fire ants maintain their own independent gene pools. "The sperm of the male ant appears to be able to destroy the female DNA within a fertilized egg, giving birth to a male that is a clone of its father. Meanwhile the female queens make clones of themselves to carry on the royal female line."
The Economist reports of the current state of biomimicry. Includes information about "biological patents", which I'd never heard of before.
Researching quantum honeybees. Can bees detect quantum fields and use them to find food?
Biologically odd people are pushing the limits of what the human body is capable of. "In 2002, Lynne Cox swam to Antarctica, withstanding 32-degree water in only a swimsuit."
Advancing scientific research means that chimeric animals are on the way. "In the case of human cells' invading the germ line, the chimeric animals might then carry human eggs and sperm, and in mating could therefore generate a fertilized human egg. Hardly anyone would desire to be conceived by a pair of mice."
Scientists at Princeton have made a crude computer out of bacteria. Earlier work showed "they could insert DNA into cells to make them behave like digital circuits [and] perform basic mathematical logic. The latest work expands this concept to vast numbers of bacteria responding in concert."
Life's top ten greatest inventions. Includes the eye, sexual reproduction, photosynthesis, and language.