Bdelloid Rotifers: Amazing.

This is a short piece about bdelloid rotifers, which are absolutely amazing little animals. For the more scientifically literate of you, I'll point you right here, which is a paper about what I'm explaining below. Somebody on reddit asked me to please "translate that page into idiot for me," which turned into a fairly long explanation of the basic concepts involved that hopefully explain why they're amazing. And so we begin.

Basically, rotifers are tiny animals that live in pretty much every watery environment on the planet. If you've ever accidentally swallowed some lake or river water, congratulations, you've eaten some. Bdelloids are a special group even beyond their ancient asexuality, because they can survive dessication - complete dryness - at any life stage.

Many organisms can do this at certain periods in their life, like some plant seeds can lie in a dry desert for months or years and suddenly start growing when water shows up. But remove all water from the environment of a grown plant, or any animal, and they die extremely quickly. All the water evaporates, their cell membranes fracture and break open, exposing the cell interiors to the environment. And DNA tends to crack and break apart, too.

Well, bdelloid rotifers routinely survive the complete absence of water for long periods of time. Years. Decades. You surprise them at any stage of their life cycle by drying them out, and they go dormant. You then let them sit there for basically as long as you want. Then you pour water back on them and BAM - little bastards spring back to life like nothing happened. It's incredible.

One of the things you need to survive this kind of damage is DNA repair mechanisms - something to take the fractured and broken DNA and stitch it all back together. Now, this is done in basically every living organisms, but bdelloid rotifers are just really, really good at it. An undergrad in my lab did some radiation testing on rotifers, which causes various types of DNA damage, and bdelloids can survive MASSIVELY higher radiation doses for much longer periods of time than...basically anything else. But these rotifers don't live in particularly radioactive environments, so it's odd that they seem well-adapted to survive lots of radiation. Luckily for them, the same kind of DNA repair you need to survive drying out is the same kind of repair mechanism you need to survive radiation. This DNA repair is actually really interesting for a lot of reasons, including human medical conditions like cancer and aging.

Well, they took a close look at bdelloid rotifers for various reasons, and sequenced the genome. Then they compared the genetic sequence - the literal order of GATCs in the DNA - to other creatures. And what they found was astonishing. They found plant genes. And bacterial genes. Now, it's important to note that all living organisms share some ancestral genes, like some involved in DNA replication. But the amazing part about genetics today is that we can tell the difference. Give me the sequence of a shared gene and, with some freely-available online databases, I can probably tell you whether it's most closely related to a plant, animal or bacteria. Even if it's a gene that does close to the same thing in every living organism on the planet.
So they didn't find a gene that had the same function in rotifers and other animals and plants. They found a gene whose nearest match was found in a modern plant. They found another gene whose nearest match was in e. coli bacteria. This...shouldn't happen. It basically makes no sense. But even beyond that, the e. coli gene was extra weird. It was clear that the rotifer was actually using the gene.

I'm not sure if you'll have an understanding of introns and exons but, without getting into it, think of bacteria genes like a text file. It just reads beginning to end. Higher-order creatures like plants and animals - rotifers - use "junk" sections inserted in the middle of the genes (for various reasons). Think of it like encryption - bacteria genes are not encrypted, but rotifer genes are. If you stick a rotifer gene in a bacteria, the bacteria will make garbage. If you stick a bacteria gene in a rotifer, though, it will work just fine.

But here's the crazy part - the e. coli bacteria gene in the rotifer? It was "encrypted." The rotifer had taken this bacteria gene and inserted an intron garbage section (that has to be removed to make a proper protein). But if you ignore the inserted section, the gene is an excellent match to a bacteria. Additionally, the rotifer had added some very specific sequences to the front end of the gene that helps the rotifer find and start producing protein from the gene.

So this is just batshit. What they think is happening is pretty cool, though. These bdelloids get dried out, and they crack open. Eventually, water rushes back over them and they start up their life cycle again. But when they are first exposed to water, they're actually cracked open. They think that, basically, DNA from other, dead creatures that's just floating around in the water flowed INSIDE these rotifers as they woke up. The rotifers begin stitching all the DNA that's broken apart. But for reasons I won't go into, the DNA repair mechanisms can't tell the difference between the rotifer's own DNA and the DNA that came from the environment. It just stitches the foreign DNA right in next to the regular DNA, and the rotifer starts life again, not even caring.

So at some point in the past, there were bdelloid rotifer ancestors that were dried out and had sections of DNA from plants or bacteria washed into them, which they took up and kept around. But not only that, they started actually using some of those genes from other creatures. It's as if you put a bunch of tiny animals and some algae into a blender, hit puree, and hybrids came out. Well, that's overstating it, but still.

THAT is why bdelloid rotifers are absolutely crazy. And, if you're a biology nerd like me, completely awesome.


Religion and Politics - My response to a lecture by George Will

My friend Charlie sought my input regarding a speech he read regarding religion and its place in politics. Here I post the link and, following it, my response.


I find it unconvincing and there are multiple points I find objectionable. Perhaps most important of them is the characterization of the fascism and communism as THE forms secular government has taken. I appreciate that it is his meaning that American democracy has been infused by religious feeling from its very inception, but both it and many other democratic governments have been at their heart secular. Remind me when the Scandinavians slaughtered millions of people, theirs being countries approaching 90% irreligion. Tell me how, despite its various unacceptable actions and treatments, modern communist China is not the most powerful anti-poverty, suffering-lessening engine in world history. Certainly it could not do so with such drive without the advancement of the Western world before it, but that does not mean that a Communist nation is completely and inerrantly destined for nothing but suffering and slaughter (It should be noted here, if for no other reason than to avoid derailing the subject, that I still have very strong objections to much about China in multiple ways and I do not propose to hold them up as a model of human decency).

As for the bloodshed supposedly caused by the meaninglessness of certain states in the 20th century, it's important to remember that, despite those conflicts, the 20th century is currently second only to the 21st as the LEAST violent century in human history, when adjusted for the percentage of humans killed by other humans. The only reason the bloodshed of the 20th century was possible was because there were just so damn many of us married to the birth of weapons of mass killing, but we still killed a lower percentage of the global population of ourselves than in the previous 100 years. Of course it was unprecedented, but any conflict in that time would be similarly so, lest one think that one thinks a nation-state with the ideology of the modern Iranian theology dropped into 1930's Europe with Germany's industry, weapons technology, population and power would result in less bloodshed.

Ultimately, he comes off as a snob, as arrogant. I have seen this among my fellow atheists, and I suspect it resided in some measure in the mind of George Washington himself. It's the opinion that society isn't decent enough, people aren't good enough to be decent and good people without religion. It's saying, "*I* don't need God to find my moral compass, but look at all these mongrels about me. They're so numerous and so low that without the Fear of God to keep them in line, there's no hope that they'd be anything more than murderous, savage mob out for blood." I have a higher opinion of humanity than that.

Putting aside the question of whether religion in general or any particular version of religion is true, religion was likely necessary, or at least very important, in the childhood and adolescence of human civilization, at a point where human culture had to overcome millennia of tribalism, conflict and distrust to forge the earliest associations of large groups of humans. But I think that time is over. There are more, healthier humans than have ever existed on the planet, even when measured by percentage, and more of them are irreligious than ever before. The happiest, safest and, by nearly every reasonable measure, best nations and societies on the planet are also the least religious. The only anomaly to the general trend is the United States of America...except that the trend is restored when you break the US up into constituent states. I won't claim to know the causative factor, but I believe it puts the lie to the proposition that irreligion somehow dooms us to meaninglessness and abject despair, a state from which we can accomplish only malice.

I believe something quite different. Many humans will find meaning in many human things. For many, for a very long time and for a long time to come, a major source has been religion. I have no intention of forcibly taking that away from anyone. But I also believe that religion's gradual decline is not leading to a malaise of meaning, but instead, to finding meaning elsewhere, with a multitude of sources of transcendence. I found it in gazing into the depths of the universe on a cold night, in the astonishing intricacies of the most basic living organisms and in the realization that even if some religion is true, the only way humans can truly be certain of changing the world is by changing it themselves. There are too many driven, passionate atheists, many of whom I have met myself, for there to be a dearth of meaning and motivation in a world without religion.

And so I find George Will's treatment to be unconvincing, wrongheaded and arrogant. I neither begrudge my fellow humans to worship as they will nor fear their behavior if they cease that worship.

Incongruity in Animal Suffering

This thought originally came to me some weeks ago in the midst of an impromptu, informal, semi-moderated discussion with friends about the nature of vegetarianism, animal cruelty and a variety of other related issues. I have spent some time rolling it around since, likely mostly in the depths below conscious thought, as when it occurred to me again it had much firmer structure and stronger lines than the halting genesis of the half-formed argument in the midst of a much larger discussion. Though I don't think it could ever amount to anything approaching a substantive argument on the subject at large, I believe it to be an ethical misstep.

The basis of the argument goes like this. Many vegans and vegetarians do not consume meat products due to the cruelty and suffering caused to the animals raised and slaughtered for human consumption. Certainly there are other reasons, but that is a big one and I want to concentrate exclusively on it here. So the opposition to consuming meat is often based on a moral opposition to the slaughter and suffering of food animals raised exclusively for human consumption. Videos of animal cruelty and heartless beatings were cited in argument and I don't disagree - such treatment of animals is abhorrent and intolerable.

I agree. Animal suffering should be lessened to the largest degree possible, particularly where humans have absolute control over these animals from conception to slaughter. I don't accept the argument that nature is cruel and therefore we should have no concern about domesticated animal suffering; that a larger percentage of humans died due to violence done by other humans 60,000 years ago is no reason not to do everything we can to lessen human violence and suffering today. I have never found the uncaring nature of the cosmos to be a particularly convincing reason that humans shouldn't care. As such, I support the lessening of animal suffering wherever possible, though I am unwilling, at this point, to forgo eating meat. Part of the reason is that I do not accept that meat consumption and prevention of animal suffering is a zero-sum game. It is possible, I believe, to have both, although we clearly have a long way to go. In this particular argument, I cited the work of Temple Grandin's slaughter facilities as among the ways that we can reduce animal suffering, and I support the expansion of such efforts. I should note here that I will be an eager supporter and consumer of lab-grown meat, when we get that worked out. It's really the best compromise I can at this point imagine.

Yet here we come to a rub. It was stated by someone who does not consume meat that while they oppose large-scale slaughter facilities, they don't have a problem with individuals hunting, killing and consuming wild animals for food, so long as they hunt at least in part for food. I have heard this argument before from hunting advocates or otherwise used in defense of hunting as somehow more acceptable than a meat slaughter facility, and I have a problem with this argument. To put it bluntly, there is no reasonable way to judge that being shot and killed amounts to less suffering than a standard cattle stunner. A deer is optimally shot with a firearm of varying destructive force (depending on location and weapon season) somewhere in the anterior chest cavity or neck and dies over the course of minutes or longer. This says nothing of the far lower killing power of bows and arrows. By contrast, a properly-administered high-powered electrical shock or captive bolt knocks the animal unconscious prior to the kill. Personalize it, if that makes it easier to envision. In a circumstance where either injury will inevitably lead to your death, would you rather be shot randomly in the chest so that you can limp and stumble away only to eventually lose strength, fall to the ground and bleed out, or be subject to a sudden shock that knocks you unconscious before your brain could even register the event, let alone injury or pain, before you are fatally injured? For me, this would be an easy decision.

I think it is beyond question of which instance of death is less traumatic for an individual animal. Keep in mind that up to this point, I have discussed the fatal injury only.

I believe part of the issue here is that of volume. Hunting has become romanticized in some sense, even among many otherwise in favor of gun control and ethical treatment of animals. It is in many ways the last remaining domain of the hunter-gatherer in our society. Somehow it evokes a sense of a contest between man and beast, the ingenuity of man against the faster, stronger denizens of the wild. But I believe that to be a lie. Hunted animals are completely outmatched in every sense of the word. Humans have had intelligence and technology outmatching whatever animal it was most expedient to kill for probably a hundred thousand years. In today's world of high-powered rifles and pheromone attractants it is delusional to think any animal any human seriously wants to kill has a real chance. The only thing that prevents the wholesale slaughter of animals is hunting licenses and restrictions put in place by government agencies tasked with preserving some part of the environment that existed before the United States moved from sea to shining sea. And if you want to cite deer overpopulation and the necessity of killing off some of them, I will remind you of the 100,000,000 buffalo that roamed the Great Plains 200 years ago as an example of what happens with unrestricted human hunting.

And yet modern meat consumption allowed by the current meat industry dwarfs even that number, with billions of animals slaughtered every year to supply meat consumed. But the question is not whether there are more animals killed or more total suffering caused by one method or the other. The question is whether there would be more or less suffering if one method were completely exchanged for the other. That is, would there be less suffering if billions of animals were hunted and shot in semi-open preserves rather than slaughtered in the current method? No.

Now there are other arguments here. Individuals hunting for their meat would probably lessen overall meat consumption and might reduce total suffering by reducing total animals killed. The lives of food animals may be distressing and uncomfortable for their entire lives up to the point of the kill (although I have a hard time thinking, absent deliberate human cruelty, the life of even a feedlot animal is substantially worse than, for instance, a deer experiencing winter food scarcity, disease, injury and substantial risk of being hit by a car). But the fact is that people are eating meat, they will continue to eat meat and I believe the best approach is a balanced one that includes efforts to lessen suffering of animals rather than simply writing off the meat industry as an incurable machine of cruelty more deserving of rank castigation and demonization instead of real efforts of compromise and incremental animal welfare improvements.

But my main point here is this. If there are 12.5 million hunters in the US (2007) and they each manage to kill only one animal, can we really say that those 12.5 million animals suffer less than if they were killed in a modern meat slaughter facility specifically designed for their humane destruction? I think they suffer substantially more, and I think the acceptance of hunting as somehow better than modern, humane animal slaughter is a mistake in ethical judgment. Usually, probably, because people just don't think about it that much.


To each according to what he needs. From each according to the benefits he gleans.

Ok, it's not as snappy as the traditional (and much-maligned, in the United States) socialist mantra.

What follows is the very first development of an idea that occurred to me tonight, so certain deficits of argument are to be expected. With awareness and adjustment, I hope they can all be remedied, but comment and counter-argument will be appreciated, so that I can find these errors and attempt the repair.

For a while now, I have been rolling around the idea that rich people ought to pay a disproportionately higher amount of taxes than the average person because they disproportionately benefit from the system set up by society. As they benefit out of scale, they should pay out of scale to maintain that which provides them the benefits. It is also the case that the rich tend to use the resources of society more than the poor. The poor person may use food stamps or housing subsidies or other benefits, but it is the rich who rely on public infrastructure to move the goods and services they produce and bring their workers to the place of business, who rely on public education to train the highly-skilled workers they employ and who engage in lawsuits that commandeer outrageous resources from the public justice system in order to protect their intellectual property. There is much more to be said on that topic, and I believe it stands as a compelling argument for a progressive tax system that takes an increasingly high percentage in taxes from the upper echelons of society, but it is not what I am writing about tonight.

What came to me this evening is the other side of this argument. Society is structured so that some benefit far above the scale of most others. But that is only at the top. What about the bottom? Society is also structured so that some at the far bottom will benefit far below the scale of most others. Part of our society wants to label these people as lazy or stupid and blame them for their own misfortune. Many of us recoil against that notion and refuse to think of the poor as losers. But I will not attempt to argue that the poor are not stupid or lazy. I absolutely do not believe the poor to be stupid or lazy as a rule (I think they are stupid and lazy in precisely the same proportion as trust-fund babies who get life on easy mode thanks to some predecessor's success), but I believe that stupidity and laziness are irrelevant to the argument:

As a society, we have structured the world we live in such that it is impossible for some people to thrive in it. Whether they are the victims of genetics or experiences incompatible with today's society, there are at least some percentage of people who absolutely cannot succeed in today's society. Incontrovertible examples include intellectual disabilities or severe mental illness. But I believe it goes further, into categories like severe substance abuse, extreme attention disorders and "anti-social" behaviors (generally these categories allow others to feel superior to the sufferer out of the amazingly arrogant assumption that the mere application of will would allow these people to turn their lives around). It is as unreasonable to expect some people to thrive in our society as it is to expect some people living today to survive being magically dropped into the African Serengeti 60,000 years ago. While all of our genes were shaped in hunter-gatherer societies and it presents challenges to all of us on occasion, the reality is that some people get dealt a genetic hand or grow up in an environment that makes them summarily unfit for a successful life in modern society. The very characteristics that would allow them to survive as a hunter thousands of years ago - or survive horrible conditions as a destitute child today - make it virtually impossible for them to succeed on the terms the rest of us demand. And it's not their fault, no more than an heir who inherits millions from a successful relative is responsible for that windfall.

The fault lies on society. We have built a system that works for a great many of us. It is, in sum, a good system (though by even making this argument I obviously think it stands ready for improvement). But it does not benefit all equally. Some at the top disproportionately benefit and some at the bottom disproportionately suffer. This is the result of the rules we have built. We have, collectively, constructed a society that locks some out by its very nature. There may be many reasons one cannot thrive in this society and why expecting that one succeed on his or her own without assistance is unreasonable. Whether it is someone prone to addiction and feeling far stronger urges to chase a chemical substance or particular activity than show up to work or the powerful sexual urges that make expecting teenagers to not have sex a complete fantasy, some will not be able to hold down a job or will become pregnant or suffer from another medical condition that render them unemployable. We recognize some of these barriers to normal life, those that we collectively consider to be beyond the fault of the affected individual - severe injury, paralysis, disease, etc. - and we have put in place some level of support in the case of their occurrence.

Other barriers, however, many of us assume are mere failings of character and expect one to be able to will themselves out of trouble; to be able to effectively think one's way out of obsessions and compulsions: just have the strength of will to not take drugs or not have sex or not gamble and your life will turn around. I find this to be an extremely uncharitable opinion and also one completely devoid of an understanding of the sheer reality of human biology. For one thing, it may be that some of the very deficits that separate someone from success in our society would have enabled their wild success (compared to other humans) in other times and other places. It is these cases that I argue for here. Persons against whom the rules of society are stacked, who have little reasonable chance of succeeding in this world. As they suffer more because the structure the more-numerous rest of us have constructed locks them away from success, it is incumbent upon us to create a minimum reasonable standard below which we let no person fall. I believe it to be morally requisite that we provide all people with some portion of the benefits the rest of us glean from our society, even those who contribute nothing to society in return. Where this level lies will always shift over time as we move the bar to balance costs and benefits, but I think it is rightly substantially higher than it is now. Universal health treatment at a strong level of care is an absolute requirement under this obligation of society to its lesser members, for instance.

Do not mistake this for opposition to programs to break addictions, train job skills and empower people to take care of themselves and join in the benefits most of us enjoy. Do not mistake this for blanket approval for the creation of welfare dependency cycles, which do exist. Do not mistake this for a full indictment of capitalism nor an endorsement for unfettered socialism. Do not mistake this for willingness to blindly dump money into social programs with no oversight or objective assessment of benefits.

Take what I have said here for what it is: a recognition that the society we have created guarantees that some will greatly benefit and some will greatly suffer. It is effectively the duty of those who benefit more to pay a higher portion of the cost of the society than those who benefit less. And there are some who will not benefit at all, unless we undertake to grant them an explicit minimum level of benefits with no requirement or expectation of their contribution back to society in return. I consider this undertaking to be morally requisite upon society, because, by its very nature, our society itself prevents some from achieving any level of success at all. As we have effectively destroyed, or failed to provide, any trace of an environment they can thrive in, it is our duty to ensure they can survive in what we have created.


The Christian Right Enters its Epilogue

One of the major themes I see in this year's election result is the absolute destruction of the Conservative Christian agenda. Much of this overlaps with hard-line Catholics as well, but in general it is the domain of white evangelical churches that has been resoundingly crushed. What agenda is that? It's the one that died everywhere it was contested, all across the country, in the course of a single day. From Maine to Washington, voters soundly rejected the old-school Christian doctrine.

What issues were these? There are three.

First, gay marriage. Four states had measures that had the capability to grant or restrict gay marriage, and in four states, our LGBT citizens won. Maine, Maryland and Washington legalized gay marriage. Same-sex marriage is flat-out legal in those states. It was the first victory for same-sex marriage in any popular vote, and it won in three states on the same day. In Minnesota, the vote was reversed. A proposition aimed to amend the Minnesota Constitution to specifically restrict marriage to one man and one woman. In another first, voters rejected this amendment.

Second, abortion and the rape exception. For a long time, there has been tip-toeing around abortion in the form of opposing abortion except in the cases of rape and incest, as it seems particularly cruel to force abused women to go through further torment and agony. So it has seemed relatively safe to allow for these exceptions and appear to occupy something of a middle ground. And yet, as the Republican party has skewed incredibly, wildly to the right in order to appease the increasingly panicked Christian Ultra-Right, candidates who firmly avow that rape and incest exceptions are just as wrong - being against the Will of God - have come out of the woodwork. While two years ago this was safe territory amidst the explosion of the fanatic Tea Party, the relentless assault against women's rights finally saw the counter-stroke, as every major candidate who came within a mile of saying abortion shouldn't be allowed if a woman becomes pregnant from a rape was defeated. Every. One.

Third, the rise of the non-religious voting bloc. According to the Public Religion Research Institute's latest American Values survey, among President Obama's supporters, the single-largest religious category is "none." 23% of Obama's supporters self-identify as having no religion (which does not mean atheist or agnostic, simply not practicing an organized religion). That is a higher percentage than any other faith group, once further subdivided into the racial categories that often show up strongly in many congregations. But even if one wishes to quibble over whether Christian sects should be divided by race, more than 1 in 5 Americans who support Obama are unaffiliated with any religious group.

As an aside, while these issues have long been associated with the Republican Party, it should be noted that while the Christian Right lies within the Republican Party, there is more to the GOP than just these issues, no matter how hard it has had to pander to the Christian Right in recent years.

These results are a potent boot on the neck of social conservatism. Right-to-Life proponents are definitively losing ground if they remain hard-line on rape and incest exceptions. Gay marriage is still a very hard sell in some areas of the country, and there are many battles to be fought before all of the prior damage to the cause is removed from state constitutions around the country. Yet I think it is fair to say that the tide has definitively turned, and we will see more Same-Sex Marriage legalization in northern states, although it will likely be a while before the south comes around unless compelled by a national mandate.

Abortion hardliners lost. The gays won. The non-religious turned out in droves to support the winner of the election. Frankly, it should be an evangelical's nightmare. The Christian Right is in what I expect to be a permanent decline. With the ultra-conservative agenda unable to win nationally, more and more state and local areas will fall to the evils of liberal Christianity and irreligion as time goes on, eventually to sputter into irrelevance. Don't expect it to be quiet or quick, though. Just inevitable.