Dec 09 2013
Dec 09 2013
Secular Humanists want to abort the Christ child so they can snort drugs and have gay sex on its corpse!
I think we’re all tired of the War on Christmas. The atheists have won; it’s officially a secular, federal holiday, the capitalists promote it as a consumerist orgy of mass consumption, most people see it as a nice time of year to get together with friends and family, and this Jesus guy, as always, is superfluous. But like the Japanese soldiers occasionally found holed up on remote Pacific islands, there’s Bill O’Reilly, dug in and flailing. Apparently, we have some grand plan to destroy Christmas so we can win entitlements and get gay married and have lots of abortions.
Give it up, O’Reilly. You’re just sounding increasingly deranged. War’s over.
I quite like this sentiment:
But of course, Bill O’Reilly would see that as oppressive and atheistic, because it doesn’t elevate his “Judeo-Christian” values to an exalted position.
Just to spite O’Reilly, this year I’m going to have two Christmases, one with the youngest daughter and middle son in Boulder, and another with the oldest son in St Cloud. Nyah.
Dec 09 2013
I’ve been distracted lately — it’s end of the
world semester time — and so I didn’t have time to comment on this recent PNAS paper that reports on dramatic sex differences in the brains of men and women. Fortunately, I can just tell you to go read Christian Jarrett, who explains most of the flaws in the study, or you can look at these graphical illustrations of the magnitude of the differences. I just want to add two lesser points.
First, let’s all be really careful about the overselling of fMRI, ‘k? It’s a powerful tool, but it’s got serious spatial and temporal resolution limitations, and it is not, as many in the public seem to think, visualizing directly the electrical signaling of neurons. It’s imaging the broader physiological activity — respiration, oxygen flux, vascular changes — in small chunks of the brain. If you’re ever going to talk about fMRI, I recommend that you read Nick Logothetis’s paper that cooly assesses the state of affairs with fMRI.
The limitations of fMRI are not related to physics or poor engineering, and are unlikely to be resolved by increasing the sophistication and power of the scanners; they are instead due to the circuitry and functional organization of the brain, as well as to inappropriate experimental protocols that ignore this organization. The fMRI signal cannot easily differentiate between function-specific processing and neuromodulation, between bottom-up and top-down signals, and it may potentially confuse excitation and inhibition. The magnitude of the fMRI signal cannot be quantified to reflect accurately differences between brain regions, or between tasks within the same region. The origin of the latter problem is not due to our current inability to estimate accurately cerebral metabolic rate of oxygen (CMRO2) from the BOLD signal, but to the fact that haemodynamic responses are sensitive to the size of the activated population, which may change as the sparsity of neural representations varies spatially and temporally. In cortical regions in which stimulus- or task-related perceptual or cognitive capacities are sparsely represented (for example, instantiated in the activity of a very small number of neurons), volume transmission— which probably underlies the altered states of motivation, attention, learning and memory—may dominate haemodynamic responses and make it impossible to deduce the exact role of the area in the task at hand. Neuromodulation is also likely to affect the ultimate spatiotemporal resolution of the signal.
Just so you don’t think this is a paper ragging on the technique, let me balance that with another quote. It’s a very even-handed paper that discusses fMRI honestly.
This having been said, and despite its shortcomings, fMRI is cur- rently the best tool we have for gaining insights into brain function and formulating interesting and eventually testable hypotheses, even though the plausibility of these hypotheses critically depends on used magnetic resonance technology, experimental protocol, statistical analysis and insightful modelling. Theories on the brain’s functional organization (not just modelling of data) will probably be the best strategy for optimizing all of the above. Hypotheses formulated on the basis of fMRI experiments are unlikely to be analytically tested with fMRI itself in terms of neural mechanisms, and this is unlikely to change any time in the near future.
The other point I want to mention is that there’s a lot of extremely cool data visualization stuff going on in fMRI studies, and also that what you’re really seeing is data that has been grandly massaged. Imagine that I take a photo of my wife’s hand, and my hand. If I just showed you the raw images, the differences would be obvious, and you’d probably have no problem recognizing which was the man’s and which was the woman’s. This is not true of the raw data from two brain scans from a woman and a man — without all kinds of processing and data extraction (legitimate operations, mind you) it would look like a hash of noise. But do we look at two people’s hands, with obvious differences, and announce that we’ve made a dramatic discovery that sex differences are hardwired? So why do scientists get away with it if it involves sticking heads in a very expensive machine that makes funny noises?
Furthermore, the processing done in this distance was designed to abstract and highlight the differences, amplifying their perception. Take the photos of my wife’s hand and mine, and now do some jazzy enhancement to subtract out anything that is the same, so the bulk of the images are erased as unimportant, and then pseudocolor the remainder into neon reds and blues, and display it in 3 dimensions, rotating. That would be a weird, complex image far removed from the mundane familiarity of the shape of the hand, but it would emphasize real differences to an extraordinary degree, while obscuring all of the similarities, and give a false impression of the magnitude of the differences.
Let’s not assign all the differences to something genetic, either (although of course, some are modulated by biological — but not really genetic — differences). If you were to do the same comparison of my hand to my father’s, you’d see much grander differences than between mine and my wife’s. He was a manual laborer and mechanic, and I recall doing the comparison myself: his hands were muscular, powerful, calloused, deeply lined. I should have gotten a photo while he was alive so I could publish it in PNAS, touting significant biological differences between father and son.
Logothetis NK (2008) What we can do and what we cannot do with fMRI. Nature 453(7197):869-78. doi: 10.1038/nature06976.
Dec 09 2013
Jonny Scaramanga has posted a sampling of quiz questions from Accelerated Christian Education. Take a look, and ask yourself, “Am I smarter than a fundamentalist Christian taught from a home-school curriculum developed by fanatics in Texas?”
You will be reassured by the fact that yes, you are. Much smarter. Although after reading the questions, you might be a little less smart than you were five minutes before.
You’ll need all your smarts when you face the truly terrifying question: who thinks the ACE curriculum is an acceptable educational standard for the 21st century?
In the United Kingdom, UK NARIC has deemed qualifications based on ACE to be comparable to A-level. Ofsted routinely whitewashes ACE schools in reports, and ACE nurseries teaching creationism receive government funding.
In New Zealand, ACE qualifications are accepted for university entrance.
In the USA, ACE’s Lighthouse Christian Academy is accredited by MSA-CESS. The curriculum is used in givernment-funded creationist voucher programs in eleven states.
In South Africa, based on HESA’s recommendation, a number of universities have signed up to accept ACE graduates.
ACE says its curriculum is used in 192 countries and 6000 schools worldwide. This is happening nearer than you think.
They want to dumbify everybody.
Dec 07 2013
Would I watch this? Probably. Would I hate myself for it? Certainly.
Dec 07 2013
Salon has published another of those articles — you know, the ones where some clueless ignoramus presents his biased interpretation of what atheism means and then proceeds to flog the New Atheists for their imagined sins. This time, it’s Sean McElwee bashing away at What Hitchens got wrong: Abolishing religion won’t fix anything. And here’s his premise:
The fundamental error in the “New Atheist” dogma is one of logic. The basic premise is something like this:
1. The cause of all human suffering is irrationality
2. Religion is irrational
3. Religion is the cause of all human suffering
The “New Atheist” argument gives religion far, far too much credit for its ability to mold institutions and shape politics, committing the classic logical error of post hoc ergo propter hoc — mistaking a cause for its effect.
Tellingly, he can’t quote any prominent New Atheist say any such thing — or for that matter, any atheist at all — but he does quote a reporter from the Independent, Bernard Lewis, and Terry Eagleton on the wickedness of Hitchens, and of course Hitchens himself was rather bellicose and I concede that he might have promoted some hyperbole…but I don’t know of any specific quotes, and certainly no one I know follows that illogical chain of reasoning above.
I’d also agree that abolishing religion (wait, does any reasonable atheist propose abolishing religion?) would not fix everything, but educating people away from irrationality would certainly fix some things. We have a more moderate vision of the affliction that is religion than McElwee credits us with, but at least we can still recognize some legitimate distinctions, unlike him.
The impulse to destroy religion will ultimately fail. Religion is little different from Continental philosophy or literature (which may explain the hatred of Lacan and Derrida among Analytic philosophers). It is an attempt to explain the deprivations of being human and what it means to live a good life. Banish Christ and Muhammad and you may end up with religions surrounding the works of Zizek and Sloterdijk (there is already a Journal of Zizek Studies, maybe soon a seminary?). Humans will always try to find meaning and purpose in their lives, and science will never be able to tell them what it is. This, ultimately is the meaning of religion, and “secular religions” like philosophy and literature are little different in this sense than theology. Certainly German philosophy was distorted by madmen just as Christianity has been in the past, but atheists fool themselves if they try to differentiate the two.
So religion is just like philosophy and literature, and philosophy and literature are just instances of this peculiarly vague monstrous amalgam McElwee wants to call “religion”? Do science, philosophy, and literature have at their heart an unevidenced concept that defies everything we know of reality, an elaborate and ultimately nonsensical premise around which theologians build intricate fantasies that contradict one another and all human experience?
The man libels philosophy and literature, and puffs up myths and lies with a credibility they do not deserve. For shame.
Dec 07 2013
Razib Khan poked me on twitter yesterday on the topic of David Dobbs’ controversial article, which I’ve already discussed (I liked it). I’m in the minority here; Jerry Coyne has two rebuttals, and Richard Dawkins himself has replied. There has also been a lot of pushback in the comments here. I think they all miss the mark, and represent an attempt to shoehorn everything into an established, successful research program, without acknowledging any of the inadequacies of genetic reductionism.
Before I continue, let’s get one thing clear: I am saying that understanding genes is fundamental, important, and productive, but it is not sufficient to explain evolution, development, or cell biology.
But what the hell do we mean by a “gene”? Sure, it’s a transcribed sequence in the genome that produces a functional product; it’s activity is dependent to a significant degree on the sequence of nucleotides within it, and we can identify similar genes in multiple lineages, and analyze variations both as a measure of evolutionary history and often, adaptive function. This is great stuff that keeps science careers humming just figuring it out at that level. Again, I’m not dissing that level of analysis, nor do I think it is trivial.
However, I look at it as a cell and developmental biologist, and there’s so much more. That gene’s transcriptional state is going to depend on the histones that enfold it and the enzymes that may have modified it; it’s going to depend on its genetic neighborhood and other genes around it; it’s not just sitting there, doing its own thing solo. And you will cry out, but those are just products of other genes, histone genes and methylation enzymes and DNA binding proteins, and their sequences of nucleotides! And I will agree, but there’s nothing “just” about it. Expression of each of those genes is dependent on their histones and methylation state. And further, those properties are contingent on the history and environment of the cell — you can’t describe the state of the first gene by reciting the sequences of all of those other genes.
Furthermore, the state of that gene is dependent on activators and repressors, enhancer and silencer sequences. And once again, I will be told that those are just genetic sequences and we can compile all those patterns, no problem. And I will say again, the sequence is not sufficient: you also need to know the history of all the interlinked bits and pieces. What activators and repressors are present is simply not derivable from the genes alone.
And I can go further and point out that once the gene is transcribed, the RNA may be spliced (sometimes alternatively) and edited, processed thoroughly, and be subject to yet more opportunities for control. I will be told again that those processes are ultimately a product of genes, and I will say in vain…but you don’t account for all the cellular and environmental events with sequence information!
And then that RNA is exported to the cytoplasm, where it encounters other micro RNAs and finds itself in a rich and complex environment, competing with other gene products for translation, while also being turned over by enzymes that are breaking it down.
Yes, it is in an environment full of gene products. You know my objection by now.
And then it is translated into protein at some rate regulated by other factors in the cell (yeah, gene products in many cases), and it is chaperoned and transported and methylated and acetylated and glycosylated and ubiquitinated and phosphorylated, and assembled into protein complexes with all these other gene products, and its behavior will depend on signals and the phosphorylation etc. state of other proteins, and I will freely and happily stipulate that you can trace many of those events back to other genes, and that they respond in interesting ways to changes in the sequences of those genes.
But I will also rudely tell you that we don’t understand the process yet. Knowing the genes is not enough.
It’s as if we’re looking at a single point on a hologram and describing it in detail, and making guesses about its contribution to the whole, but failing to signify the importance of the diffraction patterns at every point in the image to our perception of the whole. And further, we wave off any criticism that demands a more holistic perspective by saying that those other points? They’re just like the point I’m studying. Once I understand this one, we’ll know what’s going on with the others.
That’s the peril of a historically successful, productive research program. We get locked in to a model; there is the appeal of being able to use solid, established protocols to gather lots of publishable data, and to keep on doing it over and over. It’s real information, and useful, but it also propagates the illusion of comprehension. We are not motivated to step away from the busy, churning machine of data gathering and rethink our theories.
We forget that our theories are purely human constructs designed to help us simplify and make sense of a complex universe, and most seriously we fail to see how our theories shape our interpretation of the data…and they shape what data we look for! That’s my objection to the model of evolution in The Selfish Gene: it sure is useful, too useful, and there are looming barriers to our understanding of biology that are going to require another Dawkins to disseminate.
Let me try to explain with a metaphor — always a dangerous thing, but especially dangerous because I’m going to use a computer metaphor, and those things always grip people’s brains a little bit too hard.
In the early days of home computing, we had these boxes where the input to memory was direct: you’d manually step through the addresses, and then there was a set of switches on the front that you’d use to toggle the bits at that location on and off. When a program was running, you’d see the lights blinking on and off as the processor stepped through each instruction. Later, we had other tools: I recall tinkering with antique 8-bit computers by opening them up and clipping voltmeters or an oscilloscope to pins on the memory board and watching bits changing during execution. Then as the tools got better, we had monitors/debuggers we could run that would step-trace and display the contents of memory locations. Or you could pick any memory location and instantly change the value stored there.
That’s where we’re at in biology right now, staring at the blinking lights of the genome. We can look at a location in the genome — a gene — and we can compare how the data stored there changes over developmental or evolutionary time. There’s no mistaking that it is real and interesting information, but it tells us about as much about how the whole organism works and changes as having a readout that displays the number stored at x03A574DC on our iPhone will tell us how iOS works. Maybe it’s useful; maybe there’s a number stored there that tells you something about the time, or the version, or if you set it to zero it causes the phone to reboot, but let’s not pretend that we know much about what the machine is actually doing. We’re looking at it from the wrong perspective to figure that out.
You could, after all, describe the operation of a computer by cataloging the state of all of its memory bits in each clock cycle. You might see patterns. You might infer the presence of interesting and significant bits, and you could even experimentally tweak them and see what happens. Is that the best way to understand how it works? I’d say you’re missing a whole ‘nother conceptual level that would do a better job of explaining it.
Only we lack that theory that would help us understand that level right now. It’s fine to keep step-tracing the genome right now, and maybe that will provide the insight some bright mind will need to come up with a higher order explanation, but let’s not elide the fact that we don’t have it yet. Maybe we should step back and look for it.
Dec 06 2013
Dec 06 2013
Gwen Pearson makes a really good point about the Ark Park: there has been virtually no thought put into animal care, and it’s an abuse scene waiting to happen.
I’ve helped manage and care for a wide assortment of wild and domestic animals, big and small, over the course of my career. There is a HUGE amount of paperwork, documentation, and inspections involved in having captive animals. It is, frankly, a gigantic pain in the ass, and the animals are healthier and receive better care because of all the annoying, complex rules. That’s why the Ark project set off all sorts of alarm bells in my head.
Keeping animals in captivity is really, really difficult. By gathering animals together in an artificial environment you concentrate all the poop and pee, and just make it easier for diseases to rapidly spread. (Got a kid in daycare? You know exactly what I’m talking about.)
As caretakers we have an ethical duty to provide captive animals with the food and environment they need to stay healthy. Doing that takes specialized knowledge. If you have raptors or game birds, they can get bumblefoot just from the wrong kind of perches. Feeding an imbalanced diet, or just not noticing a raptor is off its food, can tip a bird into a metabolic crash. Ducks can get a fatal type of herpes.
And they’re doing everything backwards! They originally planned to stock their fake ark with a menagerie, and are now backing off and plan to use some live animals and a mix of animatronic and stuffed animals now, but this is exactly the reverse of what you do in setting up a facility that will contain live animals:
Those were some early ideas about how we’re going to lay things out, and we are going to fine tune those as we get the final plans back from the architects. The architects are planning the building, lighting, air conditioning, ventilation. Once that is done, then our display design team will take those plans… we have 132 bays that we’ll have available for exhibits.
Wait…they’re planning the ventilation first, and then they’ll think about how to shove animals into their 132 bays? How many ways can that go wrong?
I guess it’s only to be expected from idiots so remote from biology that they’ll design a zoo based on a few paragraphs of mythology in a religious text.
For those of you not imbedded in the academic bureaucracy, “IACUC” is “Institutional Animal Care and Use Committee”, an organization that oversees appropriate and ethical care of laboratory animals.