Archive for the ‘biology’ Category


Darwinism proven by Bible Code methods

November 10, 2007

Some years ago, actually, but I just caught up with it. We have Noam Elkies, number theory maven at Harvard, to thank for the discovery.

If God weren’t an evolutionist, he would never have allowed “Ape’s son, IMHO” to be an anagram for homo sapiens.


Mirkwood comes to Midland

September 1, 2007

The New York Times reports that a state park in Texas has become home to a spider web several acres in size.

Sheets of web have encased several mature oak trees and are thick enough in places to block out the sun along a nature trail at Lake Tawakoni State Park, near this town about 50 miles east of Dallas.
The gossamer strands, slowly overtaking a lakefront peninsula, emit a fetid odor, perhaps from the dead insects entwined in the silk. The web whines with the sound of countless mosquitoes and flies trapped in its folds…
Mr. Dean and several other scientists said they had never seen a web of this size outside of the tropics, where the relatively few species of “social” spiders that build communal webs are most active…

The Times doesn’t mention the possibility, but one predicted consequence of global warming is that tropical species will extend their ranges northward. Maybe the spiders have congregated to reward all those Texas oilmen for providing them with new habitat.

The Grey Lady is also mum on the explanation I find most likely: once both Tom DeLay and Karl Rove headed back to the Lone Star State for good, word went out on the grapevine that the nucleus had formed for a creepy crawler flash mob.


The Kandy Kolored Citronella Flaked Slimelined Baby

June 9, 2007

nudibranch cuthona behrensi

You can talk about your Amazonian butterflies, your Cuban hummingbirds, your Costa Rican poison tree frogs. But for sheer variety in bejewelled unearthly beauty, give me sea slugs every time.

The more polite name for them is nudibranchs, and they’re seemingly endless in their variety. My attention was drawn to them again when the Smithsonian Tropical Research Institute announced the discovery of five nudibranch species at a whack. One of them was Cuthona behrensi, pictured above. (Click here for the larger original, and here for a pdf file including medium sized pics of all five.)

While trolling the net for that pic, I stumbled across the delightful, and in particular its Opistobranch of the week gallery. Take a leisurely browse, and you’ll be looking at those plodding plug uglies in your garden with a new respect. They may be poor relations, but they come from a royal family.


Your garden is full of quantum computers

April 24, 2007

It hasn’t made a big splash in the media, but the revelation about photosynthesis in Nature two weeks ago might be the sleeper science story of the year. (You’ll need a subscription or an academic account to follow the link.)

Photosynthesis has always posed a conundrum. It’s unreasonably efficient. While materials scientists struggle to get solar cells up to 30% efficiency, green plants everywhere chug happily along, converting photons to bound chemical energy with effiiciencies topping 95%.

How on earth do they manage it? That solar cell just converts a photon’s energy to charge, in a single step, and then drains off the charge. But in the light-eating organism, the photon excites an electron in one atom, and the excitation goes through a long cascade of other atoms in a complex molecule like chlorophyll, presumably losing energy all the way, until it finally creates a high-energy bond in a carbohydrate at the other end.

In a world run according to classical physics, not much energy could trickle through that whole process. But direct measurements have now indicated that what passes through the photosynthesizing molecule isn’t a series of distinct particles. It appears to be a single quantum wave, which doesn’t lose its coherence.

Let me unpack that just a bit more. In the two-slit experiment, the textbook example of a quantum process, an electron passes through a shield with two openings to land on a target plane. And what we learned in the ’20s and ’30s is that the electron will act like a wave which passes through both slits at once. The peaks and troughs of the wave passing through one slit will intefere with those of the wave passing through the other slit. At some points on the target plane the two parts of the wave will reinforce each other – the electron will be more likely to show up at those places – and at some they’ll cancel each other out, so the electron can’t show up there at all. Until the rest of the world interacts somehow with the electron, forcing the wave to collapse into a particle, it will retain this wavy character. The wtave state is said to be “coherent”, until such time as a collapse makes it decohere.

What Nature tells us is, that the excited electron at one end of the photosynthetic complex remains coherent, taking all possible paths through the molecule to the other end. And it appears that the complex is so cunningly arranged, that the inefficient, energy-losing paths cancel each other out, while the efficient paths enhance one another. As a result, hardly any energy is lost. It’s a process analogous to the “try all possible answers” method by which quantum computers are expected to filter out all but the right answer to a difficult factorization problem.

Such sustained coherence isn’t supposed to be possible very far from absolute zero. Thermal disturbances ordinarily force decoherence. But it seems that evolution, that clever artificer, has found some way to fend it off.

What does all this signify?

Weird as it is, quantum mechanics really does undergird the seemingly solid physical world. Over the years, we’ve grown used to quantum effects, whether we know it or not, since transistors – and with them our whole panorama of blinking, beeping, mousing, clicking, vlogging consumer electronics world – would be so much dead silicon in a classical Newtonian world.

Every so often some maverick will come along (Roger Penrose being the most credentialed) to suggest that something about our mental lives, from free will to consciousness itself, rests in some vaguely defined fashion on quantum strangeness. And those mavericks are generally laughed out of court, with very little hearing. Brains, neurons, proteins, are so big, and quanta are so small!

Now, the likes of Frank Capra may not deserve much hearing. But the bald assertion that quantum effects can’t figure in to the workings of the brain, because neurons, and even neural synapses, are several orders of magnitude larger than elementary particles, never really made sense. Geiger counters are several orders of magnitude larger still, but their macroscopic behavior will differ, depending on how the Schroedinger wave cookie crumbles.

Thanks to this article, the notions that free will, or consciousness itself, might be quantum-generated effects within the brain, have instantly become orders of magnitude more respectable.

In amore practical terms, the new result raises the faint possibility that plants and microbes may eventually teach us how to triple the efficiency of our solar systems. Why faint? Precise calculation of the quantum states of something as simple as a lithium atom push the limits of today’s supercomputers. To model the green sulphur bacterium’s “Fenna-Matthews-Olsen antenna complex” , its chlorophyll cradled by the attendant chromophores that maintain its subtle balances, would push the limits of Douglas Adams’ Deep Thought.

Some enterprising bioengineer may find an ingenious workaround to avoid brute force calculation. But unless she does, chlorophyll will keep most of its quantum secrets until long after we humans have either solved our CO2 problems by other means, or brought our own quantum computer technology into its full maturity , or descended into barbarism.


Strange Seas and Shores

November 24, 2006

Politically, sure, it’s been a nightmare. But sometimes I just love the 21st century.

Every issue of Science or Nature these days includes an article or two spelling out how some enzyme or bit of RNA expression machinery does its thing: clarifying how it hooks or snips or binds or stretches some other bit of the machinery, or perhaps just drafting a megamolecule’s shape precisely enough that some future article can suss out the ways that shape can bend and move.

This is what it looks like when biologists and 3-D graphics professionals put a big fat stack of those brain-numbing articles together with meticulous accuracy, a good sense of space and color, and loving care. These are the dances that are going on in every one of your cells, every minute. It’s a journey that puts that dear old chestnut Fantastic Voyage to shame.

Here the animation team describes how the 3 minute clip was created. And here is a summary of the plotline, from a biologist’s point of view.


Jesus wants me for a snowflake

July 19, 2006

Today George W. Bush proudly vetoed a stem cell research bill. The debates on this are old and tired now; everybody knows everybody else’s talking points, everybody has seen everybody else’s dog and pony shows.

For opponents of embryonic stem cell research, the cutest puppies and the high-steppingest colts are photos of the “snowflakes” – embryos scheduled for discard, who have been “adopted” by right-to-lifers, implanted in the adoptive mother’s womb, and in the (thereafter) natural course of things, turned into post-born babies.

Like all babies, they are of course cute as the dickens. But it’s hard to see exactly what that’s supposed to prove. They are no cuter than the already post-born babies, languishing in orphanages and crying out for homes, whom those same eager parents decided to shove aside in order to make a space in their lives for the “snowflakes.”

That’s not the only thing that bugs me about the phenomenon. The theory upon which this callous disregard of the already post-born in favor of the single frozen cell is justified has been clearly articulated: each frozen egg is already a full human person in every sense, and it would be murder to discard it with the rest of the day’s medical waste.

Okay, then – why not “adopt” the frozen egg, and never implant it? After all, there’s a reason why all those extra fertilized eggs are lying about in fertility clinics. The reason is that each infertile couple needs several eggs to work with since, once implanted, most of them fail to come to term. Less gently put, the process of implantation kills most of them.

You see where this is going. According to their own logic, the “snowflake” parents have been murdering children. On average, murdering several children to produce each bouncing, cooing child that is displayed before the Senate cameras. By their lights, how could that ever be justified? Especially when they could “adopt” dozens and dozens of frozen eggs, and keep them alive forever, just by maintaining the lab fees, for far less effort than it took them to kill several eggs, and shepherd one to adulthood.

Yes, each “snowflake” that survives the uterine gauntlet gets to do things like breathe, sleep, eat, gurgle, things it could never have done back in the petri dish. But that scarcely makes it right to kill its siblings off to give it the luxury of experiencing those things. After all, it was already a full and complete human being back in the freezer. These little add-ons are merely the kind of “quality of life” trappings that the right to life movement is always telling us pale into insignificance beside the stark difference between preserving life, and committing murder.

While I wait for those happy adoptive parents to grasp the logic of what they’ve done, and spend the rest of their natural lives curled up in a ball of horrified remorse – no doubt a very long wait – let’s turn to the latest scientific breakthrough.

Another staple of opponents of embryonic stem cell research has been the flatly false canard that adult stem cells can do anything that embryonic stem cells can do. (In reality, some kinds of adult stem cells are multipotent, coaxable into forming several kinds of tissue, but none are pluripotent as embryonic stem cells are.) But of course every gene that’s in an embryonic stem cell is present in an adult stem cell – and for that matter, present in every adult cell. Pluripotency should be a simple matter of turning on the embryonic genes that got turned off as pluripotency was lost. If only one could determine which set of genes that is.

At the end of last month, Shinya Yanamaka of Kyoto University announced the production of “embryonic-stem-cell-like cells” from adult mouse cells. They are capable of generating some tissues from each body layer (ecto-, meso-, endoderm), and pump out at least one of the proteins that appears only in embryonic stem cells. It takes a concoction of just four enzymes to pull it off. Considerable work remains to be done to double check all this, and then to try it out with human cells.

The hope is of course that, several years down the road, stem cells from this new process could replace embryonic ones, and cut the Gordian knot of the current stem cell debate. And that would be great. Stem cell research is a fine wedge issue for the left, but I’d rather see the wrangling end, and the medical miracles begin to roll in.

But would it really stop there? If there’s a magic formula for making an adult cell revert to a pluripotent form, there’s probably another magic formula that goes all the way. By providing the right nutrient bath, an adult cell could probably be made to revert to totipotent form – to the precise equivalent of a fertilized egg, capable of generating not just arbitrary tissues, but the whole organism.

Voila! – the Gordian knot retied. All that keeps a frozen embryo from becoming a baby is the lack of a nurturing environment. And at that point all that would keep any adult cell from becoming a baby is the lack of a (slightly enhanced, by a handful of extra chemicals) nurturing environment. It therefore becomes immoral, under the axioms of the Right To Life movement, not to preserve every cell of flaked skin or fallen hair root, every cell of every biopsy or excised tumor, so that the life all those pre-born babies will not be lost.

When that Rubicon of knowledge is crossed, Jesus will not just want you for a snowflake. He will want you for thousands and thousands of them.


Calico Women and Larry Summers: part deux

July 18, 2006

Okay, so assuming I haven’t been tarred, feathered, and defenestrated: Where do calicos come into it?

This is the fun part. Calicos explain why males enjoy a standard of deviation that makes them more deviant and less standard than their opposite numbers.

As you probably already know, all calico cats are female. No toms ever sport that colorful patchwork fur. What you may not know is that all female mammals, including all women, are calicos. Here’s how it works.

Most chromosomes come in two copies. The copy from Dad will differ in minor ways from Mom’s copy, but they code for pretty much the same genes. A certain amount of that gene’s product, not too much and not too little, is needed for the proper functioning of the cell. So all of the cell’s deliriously complicated little gene expression mechanisms work together to guarantee that each chromosome pumps out enough messenger RNA to get half of the optimal amount of the protein in question built. Jointly, they fill the quota.

But when it comes to the sex chromosomes, there’s a snag.

The Y’s all right. Nobody, in the ordinary course of things, has more than one copy. Anything it produces, it will have to produce all of, so the gene activation machinery just doubles the order. But what to do with the X?

Sometimes (in girls) there’ll be two copies of the X, sometimes (in boys) there’ll be only one. But most of the X genes (unlike Y) have nothing to do with sexual characteristics. A protein that functions well at one concentration will starve or overwhelm its target process at half or double that concentration. It wouldn’t do to have all the guys spending their lives in hypoglycemic shock, or all the girls with blood sugar counts off the charts. (Just a for instance, the gene for insulin lies elsewhere.)

Evolution’s solution to the problem was to set the gene expression thermostat at male levels. And then, in the females, to turn off one X chromosome in every cell, so that its genes never get expressed. As it happens, it doesn’t get around to doing this until the fertilized egg cell and its daughters have divided quite a few times. And then it picks at random which X chromosome to turn off. Half the cells will now express Dad’s X genes, half will express Mom’s. The embryo has become what’s called a “chimera”: its body is composed of two kinds of cells, which are genetically different. Two intermingled and interspersed parts of its body have, in effect, become fraternal twins.

The choices of X are frozen. As the cells divide and the embryo grows, each Daddy-X cell produces only Daddy-X daughters, and each Mommy-X cell only Mommy-X daughters. The fetus, and eventually the infant, is patched together from big clumps of cells of one kind or the other. How big are those clumps? Look at the coat of a calico cat, and you’ll see the patches written out on her fur.

In humans, skin and hair color aren’t coded on the X chromosome, sparing girls some serious wardrobe compatibility headaches. What has emerged from the human genome project, though, is the fact that X contains a higher than usual density of genes which are expressed only in neural tissue. Brain genes. Consequently, while a man’s brain runs on only one parent’s X-genes, a woman’s contains regions expressing her mother’s X-genes, and other regions expressing her father’s. You could say that women have twice the brains.

One would expect this to have a smoothing effect. Any brain protein from the X that makes her brother particularly smart, or dumb, or impulsive, or cautious, would have its effects moderated in her case by the version of the same protein she inherited from her other parent. Presto! The lower standard of deviation, in IQ and what have you, among females.

Last I heard, they’d pinned down which X proteins are expressed only in nerves. Learning the functions of them all is going to be a long hard piece of gumshoeing. So my previous graf’s final sentence is just speculation at this point. The rest is solid.