Lineage-Enders

WaterMother

Teddy Wayne recently wrote a piece for the Sunday New York Times called “The Childless Life” (the digital version is titled “No Kids for Me, Thanks”) which at face value was a discussion of the individual choice to go vocally, self-righteously extinct. In it, he reviewed a recent collection of essays written by persons who will leave behind no descendants, on purpose. “Selfish, Shallow, and Self-Absorbed” is an anthology, the collected expressions of a group of 16 authors, all of whom have chosen both to remain childless and to write about that fact. The Venn diagram of scientists and writers should have some modest overlap, but apparently not in the case of these Lineage-Enders.

In fairness, it was @HollyDunsworth who first suggested the title “Lineage-Enders” in a tweet that anticipated someone might be reading the NYT article and wonder why it seemed so utterly uninformed by Darwinian thought. We complain a lot in America because numerous opinion surveys show a majority of us do not believe or understand the theory of evolution. Responsibility for that seems to extend to the literati, as it’s basically nonsense to write about the self-selected infertility of the educated elite without gazing through evolution’s eyepiece. So with your indulgence, I will discuss the evolutionary implications of Lineage-Enders (LE).

BadParents

One need not read every word of the childless to come to an overarching theme: Children bother these people. They resent that children are loud with unstructured lives that interrupt what adults would be doing if left alone. Lineage-Enders as a group resent sharing of space, patience, silence, and resources with small and uncivilized toddlers. They complain loudly that, when burdened by childcare responsibility, they as adults are not as completely happy and fulfilled as they imagine they otherwise might be. They are basically bad parents, and many admit as much. There have always been “bad parents,” but it is important to separate the pejorative from the shrewd life strategy trajectory.

Hands_Plant        womanwithgoat

Just for argument’s sake, let’s propose that two distinct parenting behavioral strategies resting on separately heritable genetic foundations arose in early hominids. The first we will call Ultra-Nurtures (UN) and although the genetics of this condition are not certain, the phenotype is well understood. Everyone knows a UN human being, and it might be argued that this behavior is the more prevalent human pattern. Being UN allowed us to be farmers and to treat all manner of non-human things as we would treat our own children. Thus, helpless wolf cubs were coddled and fed, turning them into dogs instead of small bite-sized breakfasts. Tiny sprigs of green were watered, sheltered, and turned into wheat and corn. The same for small, orphaned foals, who most likely would have required the milk of a human female to survive long enough to begin to eat grass and start the long journey to domestic horses. Ultra-Nurture humans are both male and female, but the endlessly cheerful daycare lady sitting on the floor with kids piled around her lap is a good icon.

ultra_nurturing

(There exist already long and contentious threads of discussion about behaviors and their heritability as well as their teachability. There isn’t any question that there are environmental inputs that act on underlying, genetic predispositions to act out behavioral programs of activity. Those include reproductive life strategy activities. For the rest of this essay, I will refer to the LE and the UN behaviors as being enabled by a small number of discrete and identifiable genetic elements, full stop. This is not a nature/nurture debate.)

The second group is the one we are now calling Lineage-Enders (LE), but for millions of years they were anything but—it is more accurate to call them parental resource hoarders and to recognize that they had a robust reproductive strategy that exploited the weaknesses of their UN relatives. As soon as early hominids were living in cohesive, complex social groups of cousins, grandparents, and other close relatives, abandonment of one’s own toddler at an early age into the arms of a more devoted aunt, sister, or other relative would have enabled the child-intolerant (LE) female to engage again in sex and speed her own re-entry into the reproductive cycle. On the other hand, the indulgent, patient, Ultra-Nurturing adoptive parents of these abandoned infants probably shared many genes in common with them and so continued to enhance their own Darwinian fitness through proxy reproduction of close kin. Aggressive, child-intolerant males could devote themselves to building alliances of dominance instead of building toys and teaching life skills to children. That works especially well if they are able to mate with a number of females, preferably from both LE and UN backgrounds. With the right fractional survival of each type of offspring, the coexistence of LE and UN fractions within human society is evolutionarily stable. It does give rise to the occasional pejorative, as earlier noted, and so we have “bad parent,” “loose woman,” “ladie’s man,” and a host of others, as each judgmentally examines the behaviors of the other and looks for exploitation.

Prior to the transition to eusociality, LE genes would have been catastrophically disadvantaged. But I would argue that cognitive patterns that typify LE parenting styles are also fundamental to our explosion of intellect. It’s not hard to conceptualize that the urge to study intently, to concentrate, and to think carefully and methodically might have some conflicts with the typical modern parenting experience. Still, the genes underlying LE behavior have probably been under positive selection for millions of years.

This equilibrium was demolished by the molecule norethynyl estradiol, invented in 1951 by Carl Djerassi and now universally known and understood as The Pill.

ThePill     Carl_Djerassi

This earthshaking chemical advance enabled women for the first time to be absolutely in control of their fertility, while simultaneously opening the door of extinction to the Lineage-Enders. Prior to effective, cheap birth control, the LE fraction of humanity was reproducing fitfully, if distastefully. Their lack of interest in caring for children did not preclude an avid interest in the activity, sex, that produces them, and so were born countless under-parented, neglected, and sometimes abandoned small people who made their own selfish way in the world the best they could. Most of them who survived and even thrived did so because the other important group of humans, the Ultra-Nurtures, took pity on these children and made sure they were fed and well cared for. But for the last several generations of man, the desire not to reproduce could be acted upon in an executive manner by any woman with LE inclinations. Those unwanted children would no longer be born—but why?

The widespread human predilection to adopt and care for unrelated children is anticipated by sporadic cases of infant adoption in social, non-human primates. There is no such biological precedent for the Lineage-Enders, so their motivations must be taken at face value. An attenuated gag reflex can be helpful here. Much has been written, in addition to the above mentioned anthology. Sezin Koehler is a Lineage-Ender, and she writes about that here. So pleasant to know that all this hyperbole is just a few decades from dying out.

The poster child for LE humans is probably @Ericholthaus, the “sniveling beta-male” ridiculed by Fox News for his labored public weeping over the multiple challenges of humanity and the gratuitously self-indulgent idea that his own personal vasectomy might have such an impact as to represent a turning point for mankind. Even more hilariously, he then squelched, backed out of the sterilization, and got his partner pregnant—the rationalization being that this made him feel “hopeful.” Never has there been a person more in need of a gentle reminder of his own inconsequentiality. And although he has blurred the line demarcating his own extinction by a generation, he does bring to mind a salient point: If Mr. Holthaus had the intellectual capacity of a fig tree, he would recognize that he is currently living in a period of rich and plentiful food and resources. If the dreaded future that he envisions is really just a generation to come, then his most viable and Darwinian reproductive strategy would be to produce as many babies with as many women as physically possible and distribute them far and wide, the better to insure that some fraction of them actually pull through his imaginary, upcoming human population bottleneck. That is—he would be masting.

Neuroscience has discovered interesting discontinuities between what we actually do and how we describe why we took these actions once we become aware that they have happened. The rationalizations of LE humans ramble with hand wringing piousness over carbon footprints, disease, malnutrition, and the peculiarities of their personal psychoanalysis with repetition of terms like fulfillment, actualization, achievement, and etc. (gag). I would argue instead that they are LE because this is their genetically predisposed reproductive strategy, and their verbalizations are all just window dressing to try to spin up their self-induced extinction to a crowd of inquisitive onlookers.

I am not a Lineage-Ender. In typical UN fashion, I have raised to maturity 3 unrelated stepdaughters who share no immediate genetic relationship to me, although they now share 25% of their genes with four of my children. I have raised two millennial males to adulthood (well, not quite, but to that amorphous near-adult state that is specific to this generation), and I have three more kids not yet out of high school. As a semen donor when a younger man, I donated my genes and any inclusive parenting predisposition to many dozens of women who lacked only male gametes in their profound desire to reproduce and have a baby for themselves. My kind will go forth and multiply, exponentially.

In closing, I have only some final thoughts for the Lineage-Enders. The first is that no one will notice. The freeways will be just as jammed in 2040 despite the absence of your un-offspring and their un-purchased automobiles. Other campers will still beat me to the signup counter in Yellowstone Park, making me wait an additional day to go with my grandkids to my favorite campsite at Black Tail Deer Creek. Airlines will still manage to cram 300 people onto an airplane when tickets have been sold to 320 and the plane was designed for 288. Atmospheric carbon dioxide concentration will still march forward in its inexorable grandeur, and will not twitch in the slightest 0.0000000001 ppmv due to anything either of us has done.

But what will change is something called the allele frequency, ƒ, for any unique genes that you may be carrying on your chromosomes, versus the ones on my chromosomes. For your genes, you are placing an a=0 value in the equation ƒ=a/n*N. For myself, I am placing a large integer value in the place of a, probably about 400. There is no implication that those particular genes unique to me, or to you, are also advantageous. Sometimes I think some of mine may be detrimental, or in the case of my null mutant KCNQ3 ion channel, perhaps responsible for some really intractable insomnia. But this is not for me to judge—it is for the viability of future generations to establish by that most Darwinian process called survival of the fittest. For you, the process is done. You are completely unfit. Oral contraceptives have been the undoing of your reproductive strategy. And do you remember that annoying woman stuck in the elevator with Tom Hanks in “You’ve Got Mail,” so anxious to get out so she could have her eyes lasered?  Future humans may notice a few less of those.

Posted in Environment, Genetics, Natural History, Science, Sperm donation | Tagged , , , , | Leave a comment

Of Mice and Men, and Cats and Women

 Wookie Bear

WookieeBeah

Wookie Bear is a facultative guest parasite of humans. She receives grooming, medical care, treatment for her own parasites (mostly worms and arthropods), shelter, heat, and all her food requirements from her host. She uses large, expressive eyes and a cry that mimics a human infant in order to insinuate herself into the host living space. Her host also disposes of her fecal waste and urine.

I am infested with parasites. My entire house is lousy with them—the word lousy is derived from the singular form for lice, a particular small mammalian ectoparasite. We categorize our parasites by where they live—the endoparasites like ascarid worms and nematodes,  giardia, and strange things ingested in bad sushi live in our bowels. The ectoparasites (fleas, ticks, bedbugs, lice, etc.) expose themselves on our surface. They crawl in our pubic hair. They get us sent home from school with red faced parents who stop at the pharmacy for foul smelling shampoos and fine-toothed egg combs. 100% of humans tested at age 18 by Dr. Michelle Trautwein carry the ectoparasitic facial skin mite Demodex folliculorum or its close relative Demodex brevis. These mildly disgusting little arachnids live inside your hair follicles and sebaceous glands, respectively, and cause very little harm because this living space provides room for only a few milligrams of total parasitic load per human.

Demodex folliculorum

An example of a human ectoparasite. The facial mite (Demodex folliculorum) at high magnification.

The hookworm is a good example of the typical endoparasite. Hookworms such as Necator americanus attach to the epithelial lining of the small intestine where they munch on the intestinal villae, cause bleeding, and then drink the leaking blood.

Hookwormshookworms08 An 8 ounce load of intestinal hookworms is a severe infestation and will result in weight loss, anemia, malabsorption, and other overt symptoms of chronic illness. An amount of hookworms equal to the weight of a single house cat, perhaps 10 pounds, would eventually prove fatal. A link to a nice review of these conventional parasites (PDF) in human evolution was recently posted on Twitter by Jennifer Wagner @DNAlawyer. Like most modestly hygienic Americans, I have very small whole-body burdens of both exoparasites and endoparasites. But when it comes to social guest parasites, I’m suffering from an acute infestation.

Social parasitism is a unique parasitic niche, inhabited by creatures specifically adapted to exploit the complex living spaces, communication channels, and behaviors of social animals. While many species of animals form groups and have some social structure, highly social (eusocial) species are restricted to humans, ants, bees, termites, and wasps. (See E.O Wilson, The Insect Societies for many hours of reading about the latter four of those.) Entomologists have long studied the parasitic insects that live in close relationships with the social insects, as I will expand on below, and often give them the euphemistic name of guest. On further reading, one sees that they behave very badly as guests, if that is their status. Almost all of them end up consuming the eggs and young of their social insect host, which is fairly rude. I think “social guest parasite” is a more fitting term. Hosts usually mount some sort of immune or behavioral defense against their conventional parasites. The distinguishing feature of a social guest parasite is that the host actively coddles and protects it, most often mistaking it for its own kind.

The two main human social parasites are Felis silvestris catus the house cat, and Canis Canis the dog. I have the former. I am supporting at least 10 cats or about 120 pounds of parasites. This is not a survivable parasite load for any of the common intestinal worm infestations that I’ve taken care to avoid. Fortunately for me, my social guest parasites live on the couch, not in my bowels.

Three young adult Felis silvestris catus parasites occupy a living space within the home.

Three young adult Felis silvestris catus parasites occupy a living space within the home.

There is considerable argument whether the dog should be considered a human social symbiont or commensual and not a parasite, as the cat clearly is. Dogs work for humans and shoulder large labor burdens for them, as can be seen by Googling “Inuit sled dog” or “Irish border collie.” Cats, on the other hand, do not even listen to their human hosts, much less perform any chores for them. Dogs also are eaten as food in many cultures, making them livestock, while cats are not.* When humans keep, feed, and shelter a dog, the dog thinks the human is God and serves him faithfully. When humans keep, feed, and shelter a cat, the cat understands that it is God and expects the human to serve him faithfully. So we will leave dogs out of the current discussion as possibly still man’s best friend, and concentrate on cats, who are not.

Assisted by the spread of mankind, cats have extended their population from a small area of North Africa and the Middle East to the entire habitable area of the world. There are about 200 million of them in the US alone, evenly split between the parasitic niche (domesticated) and the feral state (in between hosts). An estimated $30 billion is spent each year by American hosts sustaining this parasite load of about 3 cat pounds per person. Even with the ever increasing cost of raising children, the amount of resources  currently diverted to pet cats would raise an additional 3 million Americans to adulthood every year.

Our human social history is very short, but exactly how short is hard to say, as behaviors leave no fossils. Our entire genus goes back no more than 2.5 million years, and it is reasonable to think that when the human lineage split from that of chimps and bonobos, we had a rudimentary social system similar to theirs today. Chimps do not have pets; they do not have any affinity for cats or dogs, and so they have no guest parasites that exploit their sociality. Homo sapiens has been attended by guest parasites that exploit our unique and robust sociality for a very brief evolutionary interval, perhaps between 10,000 and 20,000 years. In that perspective, we are just seeing the nascent glimmerings (as in oncoming headlights) of the possible exploitation that is yet to come.

To get a better view of what can happen to hosts and guests locked in social parasitism, it is informative to look first at ants and termites. Their own sociality both predates ours by many tens of millions of years, and their social guest parasites are much more refined than our own. There are many forms of social parasitism in insects we can look at, including an advanced social parasite of ants, the Large Blue butterfly Phengaris arion. Life Cycle A

ant1

After hatching from its egg and feeding for a time on plant material, the caterpillar of P. arion drops to the ground and wanders aimlessly until approached by an ant.

The caterpillar hunches into a contorted posture while releasing pheromones. Together, the behavioral cue and chemical message informs the ant that it has found one of its own larvae, and it gently picks up the guest parasite and carries it back to the brood chamber of the ant colony. Here the butterfly larva slaughters and eats the ant brood while soliciting tropholaxis (demanding vomited food) from the nurse ants until it matures and undergoes pupation. Hatching of the adult butterfly completes the cycle.

The extremes to which evolution has selected features of guest parasite anatomy is exemplified by the termitophilous staphylinid beetles, guest parasites of African termites, shown below. The abdomen of the beetle has been distended and projected back over the dorsum of the insect, so that its anus sits directly above the head. Curious worker termites who approach the beetle actually interact with the anus and false appendages, rather than the actual head of the beetle hidden below. Pheromones secreted by perianal glands mimic those of worker termites. Exudatoria, or fake legs, dangle from the sides, making this a termite version of a human adult blow up doll. Following the lead of the Great Blue, staphylinid larvae become large consumers of termite eggs and larvae.

ant6

C. ovambolandicus shows an extreme level of physogastry (abdominal hypertrophy) believed to enable it to represent its distal abdomen and anus to worker termites as a false surrogate for its actual head.

Back to the Future…

It is interesting to speculate as to how evolution will shape this emerging guest parasitism by cats of humans. If we learn anything from the study of insects, it should teach us that social guest parasites gravitate towards exploitation of the brood. House cats have eaten the fingers of babies in the past, but this isn’t a behavior that is likely to be widely tolerated. Instead, just as the staphylinid beetle A. Pubicollis induces regurgitation by its Myrmica hosts, it is possible that cats will learn to accost babies in their cribs, licking and pawing the oropharynx in a surreptitious manner to induce vomiting, then quickly consuming the regurgitated milk before a defensive response can be mounted by the human host parent.

baby_cat_bugs

A. Pubicollis, above right, uses its antennae and front legs to tap, stroke, and induce the regurgitation of food from its host ant. A human infant host could be relieved of its stomach contents by similar feline behaviors, leading to the nutritional disparity seen at left.

The passing of human breast milk from the mother to the guest parasite cat via an infant intermediary could be exactly the break another emerging parasite has been waiting for. Toxoplasma Gondii is a protozoan obligate intracellular parasite with a variety of intermediate hosts, such as mice, rats, swine, cattle, and (yes) humans, but only one definitive host: the domestic house cat. T. gondii and F. sylvestris have accommodated well to each other, in that the parasite inflicts no apparent harm or damage to the cat, and the cat in turn provides ample resources in its intestine for the production of millions of parasite oocysts, which are shed in cat feces. Sporulation of the oocysts a few days or as much as a year after defecation produces the virulent form of the parasite, which can be ingested by any of the intermediate hosts. The state of diplomacy between T. gondii and the intermediate hosts, particularly mice and humans, resembles more of a smoldering insurgency. Unable to form its egg stage in these hosts, the parasite instead forms dormant cysts or bradyzoites in the host brain and muscle tissue. Famously, it alters the behaviors of the parasitized mice, causing them to lose their instinctive fear of cats and to expose themselves to easy predation. Consumption of the deranged mouse allows ingestion of the cysts and completion of the T. gondii life cycle.  More controversially, latent cerebral T. gondii infection in humans has also been linked to an increase in suicidal and high-risk behaviors. But the suicide of the human fails to close the life cycle loop of the parasite since cats are generally prevented from consuming the brain or muscle of deceased persons. Meanwhile, toxoplasmosis exacts a small but continuous health toll on the  human host, causing a low grade, flu-like illness in many and catastrophic birth defects when an active maternal infection is transmitted to the growing human fetus.

The next emerging zoonosis might not be an offshoot of ebola or malaria, but simply a small redirection of the human T. gondii tropism from muscle and placenta to breast tissue, where the active tachyzoite stage of the parasite would be secreted directly into human breast milk. Toxoplasmosis transmitted via breast milk has been documented in mice in controlled experiments**, but such data in humans is absent. Transfer of the partially digested milk from the infant stomach to the social guest parasitic house cat would complete the protozoal life cycle with some enormous new advantages. First, the cat would not have to kill and eat the intermediate host, but simply rob it of its stomach contents. Rather than a single transfer of protozoan back to cat, there could be hundreds of transfers over many months, with the human breast recruited as a factory for the production of T. gondii parasites. T. gondii could also use its well documented ability to influence host brain function by inducing pregnant human females to desire and to tolerate cats, especially around their nursery room. In this way, the protozoan would suddenly have full access to exploit the human as a definitive host, rather than as a biological dead end.

Humans will play more than a passive role in the evolution of this relationship. Cats currently face an exceptional negative selection pressure from their human hosts, who tend to restrain, sedate, and sterilize their guest parasites. Pet sterilization increases with household income, rising to 93% of all cats in homes with more than $35,000 in annual income. Only those individual cats who can somehow evade this ongoing mass culling will provide the genes and characteristics that typify the cat species of the future. For a cat in a wealthy American household, the best choice may be simply to get out—to flee the initial host and join the 100 million feral cats, only 3% of whom have been neutered. In this scenario, parasitism of a human household would be a transitional step in the development of cats, employed by kittens that gain an advantage over feral-raised kittens by way of the food and vaccinations they obtain from the humans. Those prompted to escape before neutering would become the dominant individuals in the feral population that breeds relatively freely. A queen cat would be a female who insinuates herself into the household just around the time the woman is pregnant, in order to establish the lucrative co-parasitism of the expected infant. By timing her own pregnancy to coincide with that of her human host, the cat could take advantage of the general chaos that surrounds the human neonatal period, increasing the odds that she would not be spayed because the overwhelmed hosts simply forgot to do it.

Cats living in the developing world and in the poorer households of wealthy countries still face a 50/50 chance of being neutered before they can reproduce. Accelerated sexual maturation and precocious mating has been observed in many species, including overexploited populations of fish, in response to this sort of inescapable early mortality.***

Kirk M Maxey with a juvenile social guest parasite who is soliciting grooming, heat transfer, and protection from the host.

* Yes, they do eat cats in parts of China, but they eat everything in China, including the civet cats that first introduced the SARS virus into the world. As noted above, eating cats is probably a very bad idea in the first place, considering their close affiliation with toxoplasmosis.

** Am.J.Dis.Chld. Eichenwald, H. p307, 1948 (I was unable to read this 1948 reference without feeding money to the JAMA Paywall, which you, kind reader, will not have to do. The full PDF is available in the Reference section of my blog. After 67 years, it’s about time it became public knowledge.

*** Spayed and neutered cats do not actually die, but live on for as long as 20 years in the host living space, consuming host resources. Since these individuals are already dead in a Darwinian sense, it would be highly adaptive for the cat to develop mutations that actually kill it during or immediately after such a surgical operation. That would free the host living space for another cat, which would likely be sourced from the same breeding population as the original, now deceased neutered one. The host human would be less likely to insist on sterilizing each subsequent pet, as humans tend to grieve the loss of their guest parasites in the same manner as the actual human offspring that the cats are replacing.

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Yeitse

DNA1

This post was inspired by Michael Eisen (@mbeisen), who innocently asked about the DNA content of various foods on Twitter a few days ago. As expected, the responses were mostly the rantings of idiots, all sound and fury, signifying nothing. Michael Eisen also brought my attention to a recent Oklahoma State University survey that returned the surprising result that 80% of Americans don’t understand the difference between DNA itself and genetically engineered DNA. Although, there’s some debate about the veracity of the survey, as Ben Lillie (@BenLillie) points out that previous research doesn’t back the claim that Americans are so dense, but I’ve shown before that survey design can alter the outcome.

Due to this cacophony, I remembered an old post I’d abandoned about eggs, or yeitse. (Yeitse is the Russian word for egg. It helps if there is one cool fact that you can take home from any blog post. :-) In it, I noted that eggs are virtually DNA-free. So I spruced up the old text and hope that Michael will find it more informative than the usual 140 character Twitter snark.

An egg weighs about 57 grams and contains 213 milligrams of cholesterol. It is about 80% water, and the rest of the weight is evenly split between protein and fat. Eggs have been appreciated as a great source of concentrated nutrients for thousands of years, except for perhaps the last 50. It has been proposed that the building of the pyramids was enabled by the prior domestication of the chicken. Chickens permitted the pharaohs to set up massive, mobile protein manufacturing plants (chicken coops) in any area, immediately adjacent to new construction sites, and thus feed the manual laborers that were their primary source of motive power.

Eggs, as I mentioned, are a rich source of cholesterol. Humans first began to badly misunderstand the egg at the same time that they began to associate, but not fully comprehend, cholesterol and atherosclerosis. When they examined the diseased blood vessels of well fed men suffering from heart attacks, they found disgusting, yellowish gobs of material distorting the walls of these vessels. The material was mostly cholesterol. Not recognizing (or perhaps forgetting) that cholesterol makes up about 35% of every membrane in every cell in the body, and that most of the cholesterol in the human is made especially for this purpose by the liver—they decided that eating cholesterol caused heart disease.

So they took an animal that does not normally eat eggs, and they fed them eggs anyway. They also picked an animal that does not make cholesterol in its liver, like people, but gets it by eating plants. This animal, the white rabbit, developed really bad atherosclerosis when overfed with eggs. So forgetting that people are not rabbits, it was announced that atherosclerosis is caused by the eating of eggs. And most people believed it, and tried to stop eating them.

MINOLTA DIGITAL CAMERA

An egg is just a single cell. You tend to forget that, holding one in your hand and tossing it up into the air. If you were holding an onion of about the same size, you would be holding several million cells. There are other differences between an egg and an onion, but one that really stands out is the amount of DNA. It takes about 30 times more DNA to make an onion than a chicken. That is, the chicken genome contains about 1.8 billion bases, but the onion genome contains more than 70 billion. It’s not entirely clear why an onion takes such a detailed instruction manual, while a chicken can be made using an IKEA version. An egg that you buy in the store usually isn’t fertilized, so it contains only one single copy of the chicken genome. Even if the chicken had sex and the egg was fertilized, there would be only two copies. In an onion, you get millions of copies of the onion genome. None of this would really matter, except that about the same time humans began to misunderstand eggs, they also began to get some funny ideas about DNA.

For as long as humans have been eating, they have been eating DNA. Whether from chickens, or onions, or goose liver—if you eat a cell, you eat DNA. Eating the DNA of another organism isn’t dangerous. Since it occurred commonly prior to January 1, 1958, the government considers it to be GRAS—or Generally Recognized As Safe. GRAS is a technical term used by health regulatory officials. It means, literally, that if a substance has been consumed by people for as long as anyone can remember, then it can’t hurt you. Seems like an odd concept, when you think about alcohol, which has a long history of human consumption and isn’t very good for you… but anyway, DNA falls into this category.

Very soon after people began to be fearful that their heart disease was being caused by eggs, they also began to be fearful of eating DNA, but not all DNA, or at least not most of it. They were specifically worried about recombinant DNA. Now, every time an organism reproduces, the DNA recombines, so all DNA is recombinant, by definition. But still, there was DNA out and about starting in the later part of the twentieth century that had been helped to recombine just the way some human scientists wanted it to. This came to be known as genetically modified, or GM. Again, that’s bad terminology, because DNA is constantly being modified. As stable as it is, DNA is continually damaged, cut, and locally annihilated by reactive chemicals and radiation. So all DNA is GM. Some very special DNA is GM at the behest of humans, and the rest is randomly and senselessly GM at the behest of entropy. So the intelligently modified DNA could be called genetically engineered, or GE.

Someone mentioned to me that it might be particularly risky to eat human genes. Jeffrey Dahmer did it. Not to say that makes what he did OK, but I think something altogether different was responsible for his lack of health and sanity. Likewise, there was the Argentine soccer team who got stranded in the Andes and had to eat each other to stay alive. Then again, there are certain sexual practices that culminate in one or the other of the participants getting a mouth full of semen. I think this was already happening in 1958, so it just might be GRAS. Some people swallow, and some don’t. As far as I know, there is no alleged health difference between these groups. What I do know for sure—one swallow like that contains more human DNA and protein than… well, that’s probably enough said about that.

Admittedly, people who eat human genes sometimes die, but I don’t think it is a causal relationship. It seems to me that eating human DNA can be associated with a risk of infectious disease, and a risk of incarceration, depending on how exactly it is done. In talking with people who fear recombinant DNA, it dawned on me that they were not well informed. They do not realize that when they catch a virus, it inserts copies of its own DNA right into theirs. Often, the genes the virus inserts are clever and malevolent, capable of deprogramming their cells and forcing them to make cloned copies of the virus. That’s quite scary, compared to just making a healthy nutrient as in golden rice or other GM,GE improved foods. It turns out that the genes of biotechnology critics are themselves genetically modified and perverted in ways that ought to induce an acute self-loathing. Perhaps it’s not possible to be virulently opposed to molecular biotechnology and still fully educated about the types of DNA modification and gene swapping routinely indulged in by bacteria and viruses, inside your own body, 24/7.

Addendum

I notice the government has chimed in, and they are almost certainly wrong, because plant genomes run 3-50 times bigger than most animal genomes. That is because plants bear a heavy load of parasitic retrotransposons—bits of old jumping DNA, like the ones that make corn colorful.

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When is a Survey not a Survey?

One of the great things about Twitter is that it alerts you to new papers and discussions of those papers that you’d otherwise not be privy to. Sadly, the 140 character limit badly stunts those discussions just when they are really warming to a good topic, as happened here:

Twitter_Conv

Since I found this paper very interesting and applicable to my professional experience and personal experience as a participant in the Personal Genome Project, I read it—and then I personally took the survey on which it was based.

Unfortunately, about 5 minutes into the exercise, I was surprised when the “survey” actively challenged one of my answers. That is, it attempted to caution me that what I was in favor of, and I quote, “…is likely to be very expensive and time consuming. This may mean that the research is compromised.”

Maybe I have some assumptions with respect to the use of scientific surveys that form the basis of publications in peer reviewed journals that are a bit old-fashioned, but it seems obvious to me that this survey instrument is not really a survey at all if it seeks to guide the responder’s choices by 1) supplying added information that may change a response and 2) making claims that suggest there will be negative consequences because of a response.

Imagine for a moment that this survey was about diet and not about the incidental findings of genomics research. And suppose it asked the respondent how many servings of “crisps” (I just love sticking with the very British tone of this thing) they ate? Imagine, if after admitting to eating 8 servings of crisps each day, the survey instrument then prompted, “Eating that amount of crisps is unhealthy and is likely to make you very obese. Are you sure that you really eat that much?” The psychology of this situation is very well understood—a substantial percentage of people will slant their responses in order to seem to be good, normal persons as opposed to bad, unhealthy persons. Or in the case of genomics research, one certainly would try to avoid having an opinion that causes things to become very costly and time consuming, compromising genomics research.

Not only does this survey seek to instruct and then query, but I question very much the accuracy of the information it provides. There is free software available on the internet that can easily be used to call every SNP in the human genome. Or more to the point, to identify every known disease-associated mutation in the Online Mendelian Inheritance in Man (OMIM) which will supply more than 10,000 possible incidental findings. It is actually NOT very costly or time consuming to supply this information to each participant in a genomics research study, and a system could be established to automatically deliver boilerplate explanations and followup recommendations for these disease associated mutations, which brings us to the really relevant point of this all.

Any participant, in almost any medical research study of any kind, is going to receive a hands-on physical examination by a physician. This exercise is as old and stereotypical of anything in medicine today. Such an examination certainly has costs, but we recognize those as essential costs of conducting proper medicine and patient care. Further, we would never have a discussion as to whether any abnormalities that were unexpectedly observed during that exam should be shared with the patient—of course they should be shared. Those that seem to have some risk should be actively followed up.

Examining a patient’s genome is not really any different—it is simply a matter of volume. While a physical exam could return perhaps 100 findings, a genomic exam will return tens of thousands. By quickly sieving those through the available software mentioned earlier, it is not costly or burdensome to supply the patient with a brief written summary of what is known about the genetic findings that have been made, ranked in their order of importance or actionability. The idea that a genomics researcher could just decide not to do that is very irresponsible. But then, so is constructing a survey that seems to actively go fishing for a set of opinions that will justify this lazy attitude that there is no expectation on the part of the patient to ever be told this information either.

It is my experience that patients want to be told every important medical observation that could have an impact on their health and well being. The fact that this may need to be presented on a CD—that’s just how it is with genomic medicine.

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Re: Will a return of rising temperatures validate the climate models?

Instability is the first thing that one will notice if presented with climate data, on almost any scale. That is why the flat-line in global surface air temperature that began in 1998 is so unexpected. The debate over climate change is largely partisan, unscientific, acrimonious, and unyielding to moderation. But both sides in this political trench warfare seem to quietly admit that this stability cannot last, and that they’d better be prepared with spin pre-packaged when it comes undone.

From the perspective of alarmists, the longer we go without managing even 0.01 °C of warming, the further off their “drop dead limit” of 2° C gets. So predictably, a comment recently appeared in Nature written by David Victor and Charles Kennel (PDF) urging everyone to just forget about that 2° C thing. Like hurricanes that fail to appear and sea levels that don’t rise, surface air temperature is losing favor as a motivational factor. Climate alarmists are now searching for a “thing” to keep fighting, even if their main thing, which is warming, drops out on them.

In the other camp, climate realists are also taken somewhat aback by the duration of this stability, and readily admit that surface air temperature can’t be predicted in advance and may go in any direction, up or down. The problem for them comes if it starts back up. Does that mean that all of the failed climate models that blundered so badly for the last 20 years will be rehabilitated? Again, to get in ahead of the data, a recent post on the blog Climate etc. throws a preemptive strike at the possibility that the next flip of the global climate coin comes up heads – for Hotter:

The coincidence of the current plateau in global surface temperatures with the continuing rise in the atmospheric concentration of carbon dioxide has raised many questions about the climate models and their forecasts of serious anthropogenic global warming.

Or as Clint Eastwood said, “A man’s got to know his limitations.”

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Run

Pleistocene horse race. The three coat colors depicted in this video all predate the domestication of the horse around 10,000 years ago.

 

 

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Saving Mallet’s Creek

Public institutions, many of them with specific missions to preserve nature, are the biggest impediment to conservation in suburban America. Together with other governmental agencies with no conservation mandate, they effectively prevent any meaningful remediation unless you are willing to wade through their red tape for dozens of years.

Mallet’s Creek is an urban waterway that originates in a marsh near the Ann Arbor airport, winds its way for a few miles through the southeastern part of the city, and then empties into the Huron River. Concrete walls and riprap dominate much of the stream bank, and the invasive, European strain of Phragmites australis chokes the rest of it. In heavy rainstorms, its flow increases more than one hundred fold as the runoff from many acres of adjacent parking lots and flat roofs suddenly pours in. In the winter, its salinity surpasses that of the Great Salt Lake as concentrated brine seeps into it from heavily salted roadways. This event sterilizes the creek of all living organisms below the waterline.

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Mallet’s Creek before reclamation efforts

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Mallet’s Creek after reclamation efforts

 The stream emerges from a concrete pipe and flows for 87 feet across the campus of Cayman Chemical in Pittsfield Township, exiting into another pipe under Ellsworth Road as it enters into the City of Ann Arbor. When my company bought the property in 1997, the creek was a sludge-filled dead zone of decaying plant material and roadside trash. Its fate was mediated by the conflicting authorities of the Pittsfield Township Zoning Authority, the Washtenaw Country Road Commission, the Washtenaw County Drain Commission, the Michigan Department of Natural Resources, the City of Ann Arbor, and the US Environmental Protection Agency. In 2001, we began the application process required in order to enter into this “wetland” to remediate its degradation. We started the work three weeks ago, and we finished it yesterday.

MalletsCreekBefore

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Our reclamation project was sharply constrained by the unusual ecology of this waterway. We had to plan for flow conditions of essentially zero for several months at a time, increasing to more than two cubic meters per second in three to four annual flooding events. The mid-winter brine catastrophe had to be contained within the smallest possible volume at the bottom of the stream bed and refugia for plants and invertebrates created so that the lifeless bottom could be quickly re-colonized in the spring.

Our vision was to recreate, in this short section of creek, an ecosystem more reflective of the pre-human conditions about 10,000 years ago, at the end of the last glaciation. The overall flat and anaerobic bottom profile was re-sculptured into a narrow V-shape. This was lined with a mixture of rocks and boulders taken from local glacial moraines now mined as gravel pits. The sand and gravel was layered over the underlying muck providing a well drained, but relatively nutrient poor substrate for native plants. Some of the larger boulders weighing between five to seven tons were placed by heavy equipment, in a random pattern typical of glacial erratics.

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The Black Curtain of Death (BCD) that we erected for a few days to mollify one of the local authorities. See additional post.

To address the winter die off and spring re-population, we created a refuge wetland running to the east along Varsity Drive. A dam of boulders about 18” high creates a lip that prevents the road brine from backing up into this side channel, which is spanned by a pre-stressed monolith concrete bridge to accommodate the sidewalk.

MalletsCreekBeforeAndAfter3

This refuge wetland extends more than 200 yards along the road, where it reaches a deep, permanent fresh water pond. The entire watershed for this pond consists of the lawn and sidewalks of Cayman’s main 1180 research building. That is important, because by instituting a minimal salting policy on our own property, we can insure that this body of water retains a normal pH and conductivity throughout the winter. Each spring, we can flood both the refuge wetland and our newly reclaimed creek with fresh water, arthropods, and all of the normal inhabitants that have not survived the harsh roadside conditions.

Over the course of the next 12 months, we will steadily re-introduce native plants, while we monitor for the inevitable return of Phragmites. A big bottle of Roundup is an essential when the creek in both directions is a monoculture of this invasive reed. Active management is the keyword when working to maintain a diverse ecology in these difficult circumstances.

Conservation boils down to an issue of trust. When we entrust conservation to a single public entity, like the National Park Service, it works in many cases because there is only one executive agent at the table. The Park Service has numerous failings, as I outlined here in my book, but in general they have kept large tracts of public land in a relatively clean and unspoiled condition. When multiple public entities claim jurisdiction of increasingly small tracts of land, as was true in this case, the result is complete paralysis and degeneration of the resource to its worst possible condition. A monoculture of invasives is tolerated as the status quo. Road salting, which has never had and would never pass an environmental impact study, is allowed to kill off entire ecosystems wholesale. Completely failed and ineffective practices (please see “Rant”) continue for years because they give a theatre effect of seeming to do something.

Private citizens and corporations like Cayman should be likewise entrusted to be the single entity empowered to improve their own “sensitive” environmental properties. When only remediation without concurrent development is proposed, all of the red tape and regulations we waded through should simply be waived, and each public body claiming jurisdiction reduced to the equivalent of cc status on an email. They should be copied on the work plans as they progress, but should be rendered powerless to obstruct them until the work is complete. At that time, they can either sign off and approve the remediation as completed, ask to have further improvements made, or file a lawsuit if they feel there has been gross misconduct and unlawful activity.

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What did all this cost? 

I will close with a photo of  Mallett’s Creek where it emerges from our project and courses into Ann Arbor. There’s still a lot left to be done. L3 Communications is the next good steward of the land in line. This photo speaks for itself.

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As Mallet’s Creek Continues…

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