kottke.org posts about biology
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.
(via waxy)
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.
(via clusterflock)
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.
(via rw)
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.
(thx, anne)
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.
(thx, flip)
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.”
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