At last, you’ll learn how to pronounce “Leeuwenhoek”!
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Pharyngula
Evolution, development, and random biological ejaculations from a godless liberal
Get in the mood for this bit of news, the synthesis of an artificial organism by Craig Venter’s research team.
Here’s the equivalent of that twitching hand of Frankenstein’s monster:
Those are two colonies of Mycoplasma mycoides, their nucleoids containing entirely synthesized DNA. You can tell because the synthesized DNA contained a lacZ gene for beta-galactosidase, making the pretty blue product. That’s one of the indicators that the artificial chromosome is functioning inside the cell; the DNA was also encoded with recognizable watermarks, and they also used a cell of a different species, M. capricolum, as the host for the DNA.
The experiment involved creating a strand of DNA as specified by a computer in a sequencing machine, and inserting it into a dead cell of M. capricolum, and then watching it revivify and express the artificial markers and the M. mycoides proteins. It really is like bringing the dead back to life.
It was also a lot more difficult than stitching together corpses and zapping it with lightning bolts. The DNA in this cell is over one million bases long, and it all had to be assembled appropriately with a sequencing machine. That was the first tricky part; current machines can’t build DNA strands that long. They could coax sequences about a thousand nucleotides long out of the machines.
Then what they had to do was splice over a thousand of these short pieces into a complete bacterial chromosome. This was done with a combination of enzymatic reactions in a test tube, and in vivo assembly by recombination inside yeast cells. The end result is a circular bacterial chromosome that is, in its sequence, almost entirely the M. mycoides genome…but made from a sequence stored in a computer rather than a parental bacterium.
Finally, there was one more hurdle to overcome, getting this large loop of DNA into the husk of a cell. These techniques, at least, had been worked out last year in experiments in which they had transplanted natural M. mycoides chromosomes into bacteria.
The end result is a new, functioning, replicating cell. One could argue that it isn’t entirely artificial yet, since the artificial DNA is being placed in a cell of natural origin…but give it time. The turnover of lipids and proteins and such in the cytoplasm in the membrane means that within 30 generations all of the organism will have been effectively replaced, anyway.
It’s a very small cell that has been created — the mycoplasmas have the smallest genomes of any extant cells. It’s not much, but this is a breakthrough comparable to Wöhler’s synthesis of urea. That event was a revelation, because it broke the idea that organic chemicals were somehow special and incapable of synthesis from inorganic molecules. And that led to the establishment of the whole field of organic chemistry, and we all know how big and important that has become to our culture.
Venter’s synthesis of a simple life form is like the synthesis of urea in that it has the potential to lead to some huge new possibilities. Get ready for it.
If the methods described here can be generalized, design, synthesis, assembly, and transplantation of synthetic chromosomes will no longer be a barrier to the progress of synthetic biology. We expect that the cost of DNA synthesis will follow what has happened with DNA sequencing and continue to exponentially decrease. Lower synthesis costs combined with automation will enable broad applications for synthetic genomics.
We should be aware of the limitations right now, though. It was a large undertaking to assemble the 1 million base pair synthetic chromosome for a mycoplasma. If you’re dreaming of using the draft Neandertal sequence to make your own resynthesized caveman, you’re going to have to appreciate the fact that that is a job more than three orders of magnitude greater than building a bacterium. Also keep in mind that the sequence introduced into the bacterium was not exactly as intended, but contained expected small errors that had accumulated during the extended synthesis process.
A single transplant originating from the sMmYCp235 synthetic genome was sequenced. We refer to this strain as M. mycoides JCVI-syn1.0. The sequence matched the intended design with the exception of the known polymorphisms, 8 new single nucleotide polymorphisms, an E. coli transposon insertion, and an 85-bp duplication. The transposon insertion exactly matches the size and sequence of IS1, a transposon in E. coli. It is likely that IS1 infected the 10-kb sub-assembly following its transfer to E. coli. The IS1 insert is flanked by direct repeats of M. mycoides sequence suggesting that it was inserted by a transposition mechanism. The 85-bp duplication is a result of a non-homologous end joining event, which was not detected in our sequence analysis at the 10-kb stage. These two insertions disrupt two genes that are evidently non-essential.
So we aren’t quite at the stage of building novel new multicellular plants or animals — that’s going to be a long way down the road. But it does mean we can expect to be able to build custom bacteria within another generation, I would think, and that they will provide some major new industrial potential.
I know that there are some ethical concerns — Venter also mentions them in the paper — but I’m not personally too worried about them just yet. This cell created is not a monster with ten times the strength of an ordinary cell and the brain of a madman — it’s actually more fragile and contains only genes found in naturally occurring species (and a few harmless markers). When the techniques become economically practical, everyone will be building specialized bacteria to carry out very specific biochemical reactions, and again, they’re going to be poor generalists and aren’t going to be able to compete in survival with natural species that have been honed by a few billion years of selection for fecundity and survivability.
Give it a decade or two, though, and we’ll have all kinds of new capabilities in our hands. The ethical concerns now are a little premature, though, because we have no idea what our children and grandchildren will be able to do with this power. I don’t think Wöhler could have predicted plastics from his discovery, after all: we’re going to have to sit back, enjoy the ride, and watch carefully for new promises and perils as they emerge.
Gibson et al. (2010) Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science Express.
Lartigue et al. (2009) Creating Bacterial Strains from Genomes That Have Been Cloned and Engineered in Yeast. Science 325:1693-1696.
We’re hearing the first stirrings of a big story: Craig Venter may have created the first organism with an artificially synthesized genome. Conceptually, building a strand of DNA and inserting it into a cell stripped of its genome is completely unsurprising — of course it will work, a cell is just chemistry — but it is a huge technical accomplishment.
Carl Zimmer has more background. I want to see the paper.
This essay on the accommodationists vs. the ‘new atheists’ gets off to a bad start, I’m afraid, and I had some concern it was going to be another of those fuzzy articles.
There is a new war between science and religion, rising from the ashes of the old one, which ended with the defeat of the anti-evolution forces in the 2005 “intelligent design” trial.
That’s incorrect. The anti-evolutionists have not been defeated — they got smacked in the nose with a rolled-up newspaper, and that’s about it. The creationists are still thriving, and in some places (like Texas) getting even bolder and noisier.
It gets better from there, though. It’s a polite framing of the arguments between the apologists for religion and the opponents of religion, and the author favors the latter.
You don’t have to tell me, I know I’m late to the party: the news about the draft Neandertal genome sequence was announced last week, and here I am getting around to it just now. In my defense, I did hastily rewrite one of my presentation to include a long section on the new genome information, so at least I was talking about it to a few people. Besides, there is coverage from a genuine expert on Neandertals, John Hawks, and of course Carl Zimmer wrote an excellent summary. All I’m going to do now is fuss over a few things on the edge that interested me.
This was an impressive technical feat. The DNA was extracted from a few bone fragments, and it was grossly degraded: the average size of a piece of DNA was less than 200 base pairs, much of that was chemically degraded, and 95-99% of the DNA extracted was from bacteria, not Neandertal. An immense amount of work was required to filter noise from the signal, to reconstruct and reassemble, and to avoid contamination from modern human DNA. These poor Neandertals had died, had rotted thoroughly, and the bacteria had worked their way into almost every crevice of the bone to chew up the remains. All that was left were a few dead cells in isolated lacunae of the bone; their DNA had been chopped up by their own enzymes, and death and chemistry had come to slowly break them down further.
Don’t hold your breath waiting for the draft genome of Homo erectus. Time is unkind.
We have to appreciate the age of these people, too. The oldest Neandertal fossils are approximately 400,000 years old, and the species went extinct about 30,000 years ago. That’s a good run; as measured by species longevity, Homo sapiens neandertalensis is more successful than Homo sapiens sapiens. We’re going to have to hang in there for another 200,000 years to top them.
The samples taken were from bones found in a cave in Vindija, Croatia. Full sequences were derived from these three individuals, and in addition, some partial sequences were taken from other specimens, including the original type specimen found in the Neander Valley in 1856.
The three bones used for sequencing were directly dated to 38.1, 44.5, and 44.5 thousand years ago, which puts them on the near end of the Neandertal timeline, and after the likely time of contact between modern humans and Neandertals, which probably occurred about 80,000 years ago, in the Middle East.
Just for reference: these samples are 6-7 times older than the entire earth, as dated by young earth creationists. The span of time just between the youngest and oldest bones used is more than six thousand years old, again, about the same length of time as the YEC universe. Imagine that: we see these bone fragments now as part of a jumble of debris from one site, but they represent differences as great as those between a modern American and an ancient Sumerian. I repeat once again: the religious imagination is paltry and petty compared to the awesome reality.
A significant revelation from this work is the discovery of the signature of interbreeding between modern humans and Neandertals. When those humans first wandered out of the homeland of Africa into the Middle East, they encountered Neandertals already occupying the land…people they would eventually displace, but at least early on there was some sexual activity going on between the two groups, and a small number of human-Neandertal hybrids would have been incorporated into the expanding human population—at least, in that subset that was leaving Africa. Modern European, Asian, and South Pacific populations now contain 1-4% Neandertal DNA. This is really cool; I’m proud to think that I had as a many-times-great grandparent a muscular, beetle-browed big game hunter who trod Ice Age Europe, bringing down mighty mammoths with his spears.
However, it is a small contribution from the Neandertals to our lineage, and it’s not likely that these particular Neandertal genes made a particularly dramatic effect on our ancestors. They didn’t exactly sweep rapidly and decisively through the population; it’s most likely that they are neutral hitch-hikers that surfed the wave of human expansion. Any early matings between an expanding human subpopulation and a receding Neandertal population would have left a few traces in our gene pool that would have been passively hauled up into higher numbers by time and the mere growth of human populations. In a complementary fashion, any human genes injected into the Neandertal pool would have been placed into the bleeding edge of a receding population, and would not have persevered. No uniquely human genes were found in the Neandertals examined, but we can’t judge the preferred direction of the sexual exchanges in these encounters, though, because any hybrids in Neandertal tribes were facing early doom, while hybrids in human tribes were in for a long ride.
Here’s the interesting part of these gene exchanges, though. We can now estimate the ancestral gene sequence, that is, the sequences of genes in the last common ancestor of humans and Neandertals, and we can ask if there are any ‘primitive’ genes that have been completely replaced in modern human populations by a different variant, but Neandertal still retained the ancestral pattern (see the red star in the diagram below). These genes could be a hint to what innovations made us uniquely human and different from Neandertals.
There’s good news and bad news. The bad news is that there aren’t very many of them: a grand total of 78 genes were identified that have a novel form and that have been fixed in the modern human population. That’s not very many, so if you’re an exceptionalist looking for justification of your superiority to our ancestors, you haven’t got much to go on. The good news, though, is that there are only 78 genes! This is a manageable number, and represent some useful hints to genes that would be worth studying in more detail.
One other qualification, though: these are 78 genes that have changes in their coding sequence. There are also several hundred other non-coding, presumably regulatory, sequences that are unique to humans and are fixed throughout our population. To the evo-devo mind, these might actually be the more interesting changes, eventually…but right now, there are some tantalizing prospects in the coding genes to look at.
Some of the genes with novel sequences in humans are DYRK1A, a gene that is present in three copies in Down syndrome individuals and is suspected of playing a role in their mental deficits; NRG3, a gene associated with schizophrenia, and CADPS2 and AUTS2, two genes associated with autism. These are exciting prospects for further study because they have alleles unique and universal to humans and not Neandertals, and also affect the functioning of the brain. However, let’s not get confused about what that means for Neandertals. These are genes that, when broken or modified in modern humans, have consequences on the brain. Neandertals had these same genes, but different forms or alleles of them, which are also different from the mutant forms that cause problems in modern humans. Neandertals did not necessarily have autism, schizophrenia, or the minds of people with Down syndrome! The diseases are just indications that these genes are involved in the nervous system, and the differences in the Neandertal forms almost certainly caused much more subtle effects.
Another gene that has some provocative potential is RUNX2. That’s short for Runt-related transcription factor 2, which should make all the developmental biologists sit up and pay attention. It’s a transcription factor, so it’s a regulator of many other genes, and it’s related to Runt, a well known gene in flies that is important in segmentation. In humans, RUNX2 is a regulator of bone growth, and is a master control switch for patterning bone. In modern humans, defects in this gene lead to a syndrome called cleidocranial dysplasia, in which bones of the skull fuse late, leading to anomalies in the shape of the head, and also causes characteristic defects in the shape of the collar bones and shoulder articulations. These, again, are places where Neandertal and modern humans differ significantly in morphology (and again, Neandertals did not have cleidocranial dysplasia — they had forms of the RUNX2 gene that would have contributed to the specific arrangements of their healthy, normal anatomy).
These are tantalizing hints to how human/Neandertal differences could have arisen—by small changes in a few genes that would have had a fairly extensive scope of effect. Don’t view the many subtle differences between the two as each a consequence of a specific genetic change; a variation in a gene like RUNX2 can lead to coordinated, integrated changes to multiple aspects of the phenotype, in this case, affecting the shape of the skull, the chest, and the shoulders.
This is a marvelous insight into our history, and represents some powerful knowledge we can bring to bear on our understanding of human evolution. The only frustrating thing is that this amazing work has been done in a species on which we can’t, for ethical reasons, do the obvious experiments of creating artificial revertants of sets of genes to the ancestral state — we don’t get to resurrect a Neandertal. With the tools that Pääbo and colleagues have developed, though, perhaps we can start considering some paleogenomics projects to get not just the genomic sequences of modern forms, but of their ancestors as well. I’d like to see the genomic differences between elephants and mastodons, and tigers and sabre-toothed cats…and maybe someday we can think about rebuilding a few extinct species.
Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PL, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. (2010) A draft sequence of the Neandertal genome. Science 328(5979):710-22.
Years ago, when the Trophy Wife™ was a psychology grad student, she participated in research on what babies think. It was interesting stuff because it was methodologically tricky — they can’t talk, they barely respond in comprehensible way to the world, but as it turns out you can get surprisingly consistent, robust results from techniques like tracking their gaze, observing how long they stare at something, or even the rate at which they suck on a pacifier (Maggie, on The Simpsons, is known to communicate quite a bit with simple pauses in sucking.)
There is a fascinating article in the NY Time magazine on infant morality. Set babies to watching puppet shows with nonverbal moral messages acted out, and their responses afterward indicate a preference for helpful agents and an avoidance of hindering agents, and they can express surprise and puzzlement when puppet actors make bad or unexpected choices. There are rudiments of moral foundations churning about in infant brains, things like empathy and likes and dislikes, and they acquire these abilities untaught.
This, of course, plays into a common argument from morality for religion. It’s unfortunate that the article cites deranged dullard Dinesh D’Souza as a source — is there no more credible proponent of this idea? That would say volumes right there — but at least the author is tearing him down.
A few years ago, in his book “What’s So Great About Christianity,” the social and cultural critic Dinesh D’Souza revived this argument [that a godly force must intervene to create morality]. He conceded that evolution can explain our niceness in instances like kindness to kin, where the niceness has a clear genetic payoff, but he drew the line at “high altruism,” acts of entirely disinterested kindness. For D’Souza, “there is no Darwinian rationale” for why you would give up your seat for an old lady on a bus, an act of nice-guyness that does nothing for your genes. And what about those who donate blood to strangers or sacrifice their lives for a worthy cause? D’Souza reasoned that these stirrings of conscience are best explained not by evolution or psychology but by “the voice of God within our souls.”
The evolutionary psychologist has a quick response to this: To say that a biological trait evolves for a purpose doesn’t mean that it always functions, in the here and now, for that purpose. Sexual arousal, for instance, presumably evolved because of its connection to making babies; but of course we can get aroused in all sorts of situations in which baby-making just isn’t an option — for instance, while looking at pornography. Similarly, our impulse to help others has likely evolved because of the reproductive benefit that it gives us in certain contexts — and it’s not a problem for this argument that some acts of niceness that people perform don’t provide this sort of benefit. (And for what it’s worth, giving up a bus seat for an old lady, although the motives might be psychologically pure, turns out to be a coldbloodedly smart move from a Darwinian standpoint, an easy way to show off yourself as an attractively good person.)
So far, so good. I think this next bit gives far too much credit to Alfred Russel Wallace and D’Souza, though, but don’t worry — he’ll eventually get around to showing how they’re wrong again.
The general argument that critics like Wallace and D’Souza put forward, however, still needs to be taken seriously. The morality of contemporary humans really does outstrip what evolution could possibly have endowed us with; moral actions are often of a sort that have no plausible relation to our reproductive success and don’t appear to be accidental byproducts of evolved adaptations. Many of us care about strangers in faraway lands, sometimes to the extent that we give up resources that could be used for our friends and family; many of us care about the fates of nonhuman animals, so much so that we deprive ourselves of pleasures like rib-eye steak and veal scaloppine. We possess abstract moral notions of equality and freedom for all; we see racism and sexism as evil; we reject slavery and genocide; we try to love our enemies. Of course, our actions typically fall short, often far short, of our moral principles, but these principles do shape, in a substantial way, the world that we live in. It makes sense then to marvel at the extent of our moral insight and to reject the notion that it can be explained in the language of natural selection. If this higher morality or higher altruism were found in babies, the case for divine creation would get just a bit stronger.
No, I disagree with the rationale here. It is not a problem for evolution at all to find that humans exhibit an excessive altruism. Chance plays a role; our ancestors did not necessarily get a choice of a fine-tuned altruism that works exclusively to the benefit of our kin — we may well have acquired a sloppy and indiscriminate innate tendency towards altruism because that’s all chance variation in a protein or two can give us. There’s no reason to suppose that a mutation could even exist that would enable us to feel empathy for cousins but completely abolish empathy by Americans for Lithuanians, for instance, or that is neatly coupled to kin recognition modules in the brain. It could be that a broad genetic predisposition to be nice to fellow human beings could have been good enough to favored by selection, even if its execution caused benefits to splash onto other individuals who did not contribute to the well-being of the possessor.
But that idea may be entirely moot, because there is some evidence that babies are born (or soon become) bigoted little bastards who do quickly cobble up a kind of biased preferential morality. Evolution has granted us a general “Be nice!” brain, and also that we acquire capacities that put up boundaries and foster a kind of primitive tribalism.
But it is not present in babies. In fact, our initial moral sense appears to be biased toward our own kind. There’s plenty of research showing that babies have within-group preferences: 3-month-olds prefer the faces of the race that is most familiar to them to those of other races; 11-month-olds prefer individuals who share their own taste in food and expect these individuals to be nicer than those with different tastes; 12-month-olds prefer to learn from someone who speaks their own language over someone who speaks a foreign language. And studies with young children have found that once they are segregated into different groups — even under the most arbitrary of schemes, like wearing different colored T-shirts — they eagerly favor their own groups in their attitudes and their actions.
That’s kind of cool, if horrifying. It also, though, points out that you can’t separate culture from biological predispositions. Babies can’t learn who their own kind is without some kind of socialization first, so part of this is all about learned identity. And also, we can understand why people become vegetarians as adults, or join the Peace Corps to help strangers in far away lands — it’s because human beings have a capacity for rational thought that they can use to override the more selfish, piggy biases of our infancy.
Again, no gods or spirits or souls are required to understand how any of this works.
Although, if they did a study in which babies were given crackers and the little Catholic babies all made the sign of the cross before eating them, while all the little Lutheran babies would crawl off to make coffee and babble about the weather, then I might reconsider whether we’re born religious. I don’t expect that result, though.
The discussion is interesting. Sam Harris recently and infamously proposed that, contra Hume, you can derive an ‘ought’ from an ‘is’, and that science can therefore provide reasonable guidance towards a moral life. Sean Carroll disagrees at length.
I’m afraid that so far I’m in the Carroll camp. I think Harris is following a provocative and potentially useful track, but I’m not convinced. I think he’s right in some of the examples he gives: science can trivially tell you that psychopaths and violent criminals and the pathologies produced by failed states in political and economic collapse are not good models on which to base a successful human society (although I also think that the desire for a successful society is not a scientific premise…it’s a kind of Darwinian criterion, because unsuccessful societies don’t survive). However, I don’t think Harris’s criterion — that we can use science to justify maximizing the well-being of individuals — is valid. We can’t. We can certainly use science to say how we can maximize well-being, once we define well-being…although even that might be a bit more slippery than he portrays it. Harris is smuggling in an unscientific prior in his category of well-being.
One good example Harris uses is the oppression of women and raging misogyny of the Taliban. Can we use science to determine whether that is a good strategy for human success? I think we can, but not in the way Harris is trying to do so: we could ask empirically, after the fact, whether the Taliban was successful in expanding, maintaining its population, and responding to its environment in a productive way. We cannot, though, say a priori that it is wrong because abusing and denigrating half the population is unconscionable and vile, because that is not a scientific foundation for the conclusion. It’s an emotional one; it’s also a rational one, given the premise that we should treat all people equitably…but that premise can’t claim scientific justification. That’s what Harris has to show!
That is different from saying is is an unjustified premise, though — I agree with Harris entirely that the oppression of women is an evil, a wrong, a violation of a social contract that all members of a society should share. I just don’t see a scientific reason for that — I see reasons of biological predisposition (we are empathic, social animals), of culture (this is a conclusion of Enlightenment history), and personal values, but not science. Science is an amoral judge: science could find that a slave culture of ant-like servility was a species optimum, or that a strong behavioral sexual dimorphism, where men and women had radically different statuses in society, was an excellent working solution. We bring in emotional and personal beliefs when we say that we’d rather not live in those kinds of cultures, and want to work towards building a just society.
And that’s OK. I think that deciding that my sisters and female friends and women all around the world ought to have just as good a chance to thrive as I do is justified given a desire to improve the well-being and happiness of all people. I am not endorsing moral relativism at all — we should work towards liberating everyone, and the Taliban are contemptible scum — I’m just not going to pretend that that goal is built on an entirely objective, scientific framework.
Carroll brings up another set of problems. Harris is building his arguments around a notion that we ought to maximize well-being; Caroll points out that “well-being” is an awfully fuzzy concept that means different things to different people, and that it isn’t clear that “well-being” isn’t necessarily a goal of morality. Harris does have an answer to those arguments, sort of.
Those who assumed that any emphasis on human “wellbeing” would lead us to enslave half of humanity, or harvest the organs of the bottom ten percent, or nuke the developing world, or nurture our children a continuous drip of heroin are, it seems to me, not really thinking about these issues seriously. It seems rather obvious that fairness, justice, compassion, and a general awareness of terrestrial reality have rather a lot to do with our creating a thriving global civilization–and, therefore, with the greater wellbeing of humanity. And, as I emphasized in my talk, there may be many different ways for individuals and communities to thrive–many peaks on the moral landscape–so if there is real diversity in how people can be deeply fulfilled in life, this diversity can be accounted for and honored in the context of science. As I said in my talk, the concept of “wellbeing,” like the concept of “health,” is truly open for revision and discovery. Just how happy is it possible for us to be, personally and collectively? What are the conditions–ranging from changes in the genome to changes in economic systems–that will produce such happiness? We simply do not know.
The phrase beginning “It seems rather obvious…” is an unfortunate give-away. Don’t tell me it’s obvious, tell me how you can derive your conclusion from the simple facts of the world. He also slips in a new goal: “creating a thriving global civilization.” I like that goal; I think that is an entirely reasonable objective for a member of a species to strive for, to see that their species achieves a stable, long-term strategy for survival. However, the idea that it should be achieved by promoting fairness, justice, compassion, etc., is not a scientific requirement. As Harris notes, there could be many different peaks in the moral landscape — what are the objective reasons for picking those properties as the best elements of a strategy? He doesn’t say.
I’m fine with setting up a set of desirable social goals — fairness, justice, compassion, and equality are just a start — and declaring that these will be the hallmark of our ideal society, and then using reason and science to work towards those objectives. I just don’t see a scientific reason for the premises, wonderful as they are and as strongly as they speak to me. I also don’t feel a need to label a desire as “scientific”.
This is the first I’ve heard of this, but there is a devastating disease called Plum Pox Virus that kills trees bearing stone fruits, like plums and peaches, and the only way to deal with infected plants is to rip them out of the ground and destroy them. There has been a recent outbreak in Pennsylvania; don’t rush out to buy the last of the fruits in an apocalyptic terror, it’s just a hint of a potential problem for the future, but you can worry a little bit. And maybe you can promote some science that will help.
A new variety of plum called the Honey Sweet has been genetically engineered that is completely resistant to the virus. It is just now in the process of being deregulated by the EPA, and they’re looking for public comment (it’s a confusing site: look for “Public Participation for Coat Protein Gene of Plum Pox Virus”, and “Comment Due”; click on it and you can tell the government what they should do).
Work fast, this is the last day for input. For the plums!
If you’ve ever invited me out to give a science talk, you know that what I generally talk about is this concept of deep homology: the discovery that features that we often consider the hallmarks of complex metazoan life often have at their core a network of genetic circuitry that was first pioneered in bacteria. What life has done is taken useful functional elements that were worked out in the teeming, diverse gene pools of the dominant single-celled forms of life on earth and repurposed it in novel ways. The really interesting big bang of life occurred long before the Cambrian, as organisms evolved useful tools for signaling, adhesion, regulation, and so forth — all stuff that was incredibly useful for a single cell negotiating through space and time in a complex external environment, and which could be coopted for building multicellular organisms.
But if you don’t feel like flying me out to tell you all about it, Carl Zimmer has an excellent article on deep homology in the NYT, and he uses a new example I’ll have to steal: a genetic module that we use to regulate blood vessel growth that can also be found in yeast cells, where it is used to maintain cell walls.
For many years, the NSF has been producing a biennial report on American attitudes (and many other statistics) about science called Science and Engineering Indicators. This year, as they have every year, they got the uncomfortable news that a majority of our compatriots reject human evolution and the Big Bang (that last one might have been partly because of the dumb way the question is phrased). What’s different, though, is that for the first time the NSF has decided to omit the fact.
This is very strange. It is a serious problem in our educational system that so much of the public is vocal in their opposition to a well-established set of ideas — these ought to be relevant data in a survey of national attitudes towards science. Why were they dropped? It isn’t because of an overt whitewash to hide our shame away, it seems — instead, it sounds like it’s an accommodationist’s discomfort with highlighting a conflict between religion and science. At least, that’s how I read the excuses given. John Bruer, a philosopher who led the review team on this section of the report, is open about his reasoning.
Bruer proposed the changes last summer, shortly after NSF sent a draft version of Indicators containing this text to OSTP and other government agencies. In addition to removing a section titled “Evolution and the Big Bang,” Bruer recommended that the board drop a sentence noting that “the only circumstance in which the U.S. scores below other countries on science knowledge comparisons is when many Americans experience a conflict between accepted scientific knowledge and their religious beliefs (e.g., beliefs about evolution).” At a May 2009 meeting of the board’s Indicators committee, Bruer said that he “hoped indicators could be developed that were not as value-charged as evolution.”
Bruer, who was appointed to the 24-member NSB in 2006 and chairs the board’s Education and Human Resources Committee, says he first became concerned about the two survey questions as the lead reviewer for the same chapter in the 2008 Indicators. At the time, the board settled for what Bruer calls “a halfway solution”: adding a disclaimer that many Americans didn’t do well on those questions because the underlying issues brought their value systems in conflict with knowledge. As evidence of that conflict, Bruer notes a 2004 study described in the 2008 Indicators that found 72% of Americans answered correctly when the statement about humans evolving from earlier species was prefaced with the phrase “according to the theory of evolution.” The 2008 volume explains that the different percentages of correct answers “reflect factors beyond unfamiliarity with basic elements of science.”
George Bishop, a political scientist at the University of Cincinnati in Ohio who has studied attitudes toward evolution, believes the board’s argument is defensible. “Because of biblical traditions in American culture, that question is really a measure of belief, not knowledge,” he says. In European and other societies, he adds, “it may be more of a measure of knowledge.”
I’ve emphasized the key phrases in that summary, and actually, I rather agree with them. These are issues in which ignorance isn’t the fundamental problem (although, of course, ignorance contributes), but in which American culture has a serious and active obstacle to advancing scientific awareness, the evangelical stupidity of religion. That is something different from what we find in Europe, and it’s also something more malevolent and pernicious than an inadequate educational system.
It seems to me, though, that that isn’t a reason to drop it from the survey and pretend it doesn’t exist and isn’t a problem. Instead, maybe they should promote it to a whole new section of the summary and emphasize it even more, since they admit that it is an unusual feature of our culture, and one that compels people to give wrong answers on a science survey.
Maybe they could title the section, “The Malign Influence of Religion on American Science Education”.
I also rather like the answer given by Jon Miller, the fellow who has actually conducted the work of doing the survey in the past.
Miller believes that removing the entire section was a clumsy attempt to hide a national embarrassment. “Nobody likes our infant death rate,” he says by way of comparison, “but it doesn’t go away if you quit talking about it.”
Exactly right. But if we do talk about it, we end up asking why it’s so bad, and then we make rich people squirm as we point fingers at our deplorable health care system. And in the case of the question about evolution, we make religious people, and especially the apologists for religion, extremely uncomfortable, because they have been defending this institution of nonsense that has direct effects on measurable aspects of science literacy.
Unfortunately, Bruer has also been caught saying something very stupid.
When Science asked Bruer if individuals who did not accept evolution or the big bang to be true could be described as scientifically literate, he said: “There are many biologists and philosophers of science who are highly scientifically literate who question certain aspects of the theory of evolution,” adding that such questioning has led to improved understanding of evolutionary theory. When asked if he expected those academics to answer “false” to the statement about humans having evolved from earlier species, Bruer said: “On that particular point, no.”
What was he thinking? The question on the NSF survey is not asking about details of the mechanisms of evolution, so his objection is weirdly irrelevant. I don’t know if he’s hiding away any creationist sympathies (that phrasing is exactly what I’ve heard from many creationists, after all), but it does reveal that he’s not thinking at all deeply about the issue. And for a philosopher, shouldn’t that be a high crime?
Bhattacharjee Y (2010) NSF Board Draws Flak for Dropping Evolution From Indicators. Science 328(5975):150-151.
