Community is what we make it.

If there is one question that stands out since I started publicly identifying as atheist, this has to be it: “What about the community?”. Church binds us together, it ensures that no-one is passed over or falls through the cracks. That’s the kind of community we want our children to grow up in. And if it doesn’t come from Church, how are we supposed to build a community? How are we supposed to make sure it takes care of everyone?

It’s a nice question. Genuinely difficult. How do we build a community like that if we can’t invoke the divine? The difficulty of the question hides the irrelevance of the conditional. Let me put the fallacy into more obvious form: How do we live on Mars if we can’t paint the turnips blue? It is plainly the case that I do not know how to live on Mars, so I cannot answer the question. It is, however, equally plain that my ignorance does not justify painted turnips.

Put bluntly, belief in gods is not reliably associated with prosocial behavior. Religion as a moral framework for social interactions strikes me as frighteningly unstable. And when (not if) it fails, it crushes people. Every. Damn. Time.

An anonymous letter cites your mother’s obituary listing you and your partner to out your sexuality after 19 years of service to the school where you teach. What kind of reaction do we expect of a good community- the kind we want to raise our children in- when confronted by this new information?

In their doubtlessly profound wisdom, the Columbus Diocese decided not to ignore the cowardly troll and not to burn zir nasty letter. Instead, a teacher of 19 years was unceremoniously shown the door: “I turned to the principal and I said, ‘Are we talking like immediately? Am I supposed to leave the building?’ And she just, she said, ‘Yes.’”

That’s what I think of when I hear churches referred to as communities. That and the dozens of times that I have watched family or friends in similar situations. To be honest, after 18 years of inclusion in Catholic communities, the above strikes me as fairly tame.

I don’t know how to do better. But when I read about something like this, I like to think I would have the grace to be ashamed if I didn’t want to try.

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Papal Resignation

There has been some coverage of Benedict’s resignation suggesting that the controversy surrounding his tenure has been due to his adherence to traditional Church teachings. While I certainly would see his record in that regard as grounds for resignation, that’s not really why he gets the hate. It is important to remember that he had to earn that hate, not for some boldly anachronistic theology, but for the lasting damage he has caused to actual people.

Under Benedict’s illustrious leadership, the Vatican cracked down on American nuns for caring too much about poor people and not enough about making gay people feel unwelcome/preventing women from accessing healthcare:

The Vatican also rebuked the nuns for spending too much time “promoting issues of social justice” while failing to speak out often enough about “issues of crucial importance to the life of the church and society,” such as abortion and gay marriage.

The man himself stated that condom use increases HIV, undercutting lifesaving efforts to stem the spread of the disease:

HIV/Aids was, he argued, “a tragedy that cannot be overcome by money alone, that cannot be overcome through the distribution of condoms, which can even increase the problem.”

When he has walked such positions back, it has been a matter of outside public pressure, not a matter of growing ethical understanding.

And, of course, when confronted with instances of child abuse and rape, his first reaction was to protect the rapist, not the child:

A canonical trial authorised by Cardinal Ratzinger’s deputy was halted after Fr Murphy wrote to the future pope asking that proceedings be stopped, despite objections from a second archbishop.

The man was an absolute monster. That’s why we hate the bastard and are glad to see him go.

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How do you science?

I got a question from my family that’s a little more complicated than a quick blurb.  Instead I put a more detailed response here.

I’m curious, how do you decide on which Hypothesis or Experiment to begin with in your work? Do you use any models to weigh impact, risk and learning?

First, working on a particular hypothesis is very different from working on a particular experiment.  A hypothesis can be small scale, but the best ones address a lot of different things at once.  Ideally, these are big picture sorts of things which make a number of testable predictions that you then check by experiment.

How you decide what to do next depends heavily on the kind of work you are doing. If you are in a field that is well developed and has established models, then you can work with a real theory instead of a hypothesis.  If there is an established theory, often when you read the literature there are obvious next steps; the prevailing theory implies x, y and z; both x and z have been confirmed so it’s time to work on y.

Alternately, if you’re in a newish field or a field undergoing a paradigm shift, it’s common to just try established techniques that you know well and see what happens. Once you have some of that data you try to put together a model for how things might work and shift back to the other mode.

Impact is something that we try to weigh for grants and such, but often it is a waste of time to guess at impact. There’s an Asimov quote “The most exciting phrase to hear in science, the one that heralds new discoveries, is not ‘Eureka!’, but ‘That’s funny …’”.  If you know too much about the impact of what you are doing in advance, it’s probably boring.

Risk isn’t typically a consideration unless there is some rare material or a live animal involved in the experiment. Generally the analogous consideration is resource allocation- time, materials, etc. vs. interest in the experiment. Typically we try to keep working on a few things at once so that if one set of experiments stops working there is something else to push forward on and minimize time lost on a project that needs troubleshooting. Mostly this isn’t rigorously modeled (again, if you know too much about how interesting your experiment is, it’s probably boring) but a rough intuition.

There is an interesting temporal aspect to how a lot of us weigh our own interest in a project vs. other people’s interest. Peer review usually leads us to weigh things that we are personally interested heavily early in a project. As a project progresses, colleagues’ interest is weighed more heavily in anticipation of reviewer objections. At the same time, projects nearing completion get more weight relative to other projects so that they can be published.

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Pop science and the basis of life

There is a… thing.

An exhaustive critique would be… exhausting.  But I can’t let this go completely untouched either.  So I’ll compromise with highlighting some of the most egregiously wrong parts.

Living systems are uniquely characterized by two-way flows of information…

Well, no. First of all, computers are also characterized by two-way flows of information, so the word ‘uniquely’ is incorrectly used. Second, life is well characterized in simpler terms by negentropy, or the ability to use energy to transfer entropy from itself to the surroundings and maintain a net negative entropy balance.

But since then, scientists aren’t much further along in understanding how simple amino acids could have eventually morphed into simple, and then complex, living beings.

The reason this field has not advanced in a while is because currently nobody really thinks that amino acids morphed into living beings. We have thought for some time that nucleic acids are more plausible candidates for early life. Nucleic acids have more plausible self-replicating mechanisms and are known to be capable of catalyzing chemical reactions just like protein enzymes. The field of RNA life, incidentally, has made substantial progress since the Miller-Urey experiments.

“Usually the way we identify life on Earth is always by having DNA present in the organism,” Walker told LiveScience. “We don’t have a rigorous mathematical way of identifying it.”

It’s possible that rigor is in the eye of the beholder here, but negentropy is a mathematical way of identifying life, and the presence of DNA is not considered indicative of life on earth since this would include the DNA viruses.

Using a chemical definition of life — for instance, requiring DNA — may limit the hunt for extraterrestrial life, and it also may wrongly include nonliving systems, for instance, a petri dish full of self-replicating DNA, she said.

If you had a sequence of DNA that could self-replicate (although RNA is more plausible for this), why would it be wrong to conclude that it is a living system? It’s definitely a grey-zone, but it’s more solidly on the life side than DNA viruses, for example. They complain about definitions of life that are too stringent, but if their definition really rules out something that faithfully self-replicates, I don’t think they have a leg to stand on in that regard.

Another hallmark of living beings is that they have different physical locations for storing and reading information. For instance, the alphabet of letters in DNA carries the instructions for life, but another part of the cell, called the ribosome, must translate those instructions into actions inside the cell, Davies told LiveScience.

Wildly unjustified criterion. Also- the catalytic site (read as- the business end) of the ribosome is composed entirely of nucleic acid (RNA- the same kind nucleic acid as the ‘instructions’ it reads).

But then, that article about chemistry they criticize is almost equally bad, talking about phosphorus with what I can only describe as reverence.

The evidence that phosphorus plays a unique role in the complex chemistry of life? Phosphorus comes in at #6 in the human body composition, but at a bare 17th in the elemental composition of the solar system. Lets look at the more abundant competition for a moment-

Noble gases: He, Ne, Ar

Metals: Mg, Fe, Al, Ca, Na, Ni, Cr

Forms only 1 covalent bond: H

Forms multiple covalent bonds: O, C, N, Si, S

Noble gases generally will not form any bond with anything. The metals on the list can contribute electrons to a bond, but they will happily float away after doing so. Sometimes hydrogen will do this, too. But even when it doesn’t, it can only form one bond- so it can terminate a polymer, but not continue it. Five of those elements can form a covalent bond with more than 1 other atom at a time- and so could participate in forming a polymer.

Yeah.  I really see what they mean… there are a whopping 5 possible polymer backbone elements more abundant in the solar system than phosphorus (two of which are also present in the phosphorus based backbone of DNA)- and yet phosphorus is the… 4th most abundant of those elements in the human body. And the ones more abundant than it all match abundance order in the solar system to abundance order in the human body. Yes. Clear evidence for the privileged role of phosphorus in the rise of life.

The phosphate (PO4) works as a kind of “super glue,” since it has three oxygen atoms that will carry charges in solution. Two of these oxygen atoms form ionic bonds with two neighboring sugars…

No. Stop. Find the closest chemistry textbook. It will tell you the ribose-phosphate bonds are covalent. Not ionic. You should have done this before writing anything. Also, the ‘super glue’ phosphate-ribose bonds are actually the easiest link in the nucleic acid backbone to break.

Not many molecules could perform this three-charge juggling act. Arsenate is one possibility.

Again, since it is not an ionic bond, charge has nothing to do with anything. Phosphate can bind up to 3 things covalently. Nitrogen can also do this. Carbon can also do this. Both of those elements do this in the context of life on earth.

Because of its vital role, all organisms on Earth must find a source of phosphorus.

This is true of every element in your body. No known organism can perform nuclear reactions, therefore all known organisms must have a source of every element of which they are made.

‘Reduced phosphorus is more chemically reactive than phosphate,’ Pasek said. This extra reactivity could have helped phosphorus sneak its way into the game of life billions of years ago.

Except that reduced phosphorus compounds don’t actually participate in the polymers or metabolic pathways that we use phosphorus for. Also, extra reactivity isn’t useful in a general sense- it can be useful for specific things, but ‘extra reactivity could have helped’ is utterly vacuous without proposing a some chemical pathway or other in which it could be useful. In fact, figuring out what to do with highly reactive compounds are one of the biggest problems your cells face on the molecular level and managing them improperly quickly kills the cell in question.

I’m not being hyperbolic when I say these articles contain more misinformation than information. And the most advanced criticisms above require no more than 1 chemistry class beyond basic high-school proficiency. Some of it is grade-school level. Experts at that level are not hard to find.

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Scarlet A Plus

A+ logo by a Blag Hag commenter.

Growing up, I was exposed to very few atheists. Most of the atheists I was exposed to were either poor role models or sufficiently ambiguous that you wouldn’t guess they were atheists unless you were really looking. I’m not certain if this was due to coordination in the effort to keep me religious or genuine ignorance. Regardless, it left me without the impression that atheism and social justice could be related.

It is an easy impression to get, and many atheists continue to maintain that failure to believe in the supernatural is as far as atheism goes. In a strict sense, this is perfectly reasonable. I hate to think anyone would accuse me of failing to harp on semantics. Nevertheless, as I started to read more atheist/skeptical material, it got to be pretty clear that atheism could be more. Greta Christina’s Litany of Rage (rightly) springs to mind most readily, but she is not alone.

Social justice is a reasonable conclusion to reach if you start from atheism and work your way toward community. Of course, there is no guarantee that is where you will end up, and not everybody who starts from atheism even wants to work toward community. So atheism, both as the set of people who meet the technical definition and as a movement (or, perhaps, as a cat herd) remains full of people who think that atheism neither can nor should be about anything but trying to break the hold of religion. There is even substantial reason to say that we, the atheist community, have achieved worse than would be expected by garden-variety human capacity to be assholes in terms of alienating, devaluing or even outright threatening our most vulnerable allies. But even if it were not the case that we have been particularly bad- the fact that a substantial part of the atheist community that seems to take the position that protecting the most vulnerable members of our community distracts us from the message is weird and that the idea is often framed as a vicious attack is scary.

Never mind that the fact that positive aspects of atheism in regard to social justice and community were entirely absent from my education growing up. Never mind that this fact left me afraid of being an atheist while I was deconverting. Never mind that philosophical counters to arguments for god have been done to death and that, even in the event that we get off that message for five fucking minutes to do a little community building, the material is still going to be right there on the internet, waiting for people who ask those questions. Never mind that my fears in this seem to be the absolute vanilla norm (people considering deconverting/coming out are more often than not afraid to lose community) and that visible, diverse and open communities can go a long way to fix that problem. It’s a distraction. It hurts the movement by getting atheists off message. Or by making old white men feel unwelcome. Or by admitting our weaknesses publicly. Or whatever.

So I have a bit of a problem with this. This might seem a bit odd, but I don’t actually want you to be an atheist. This is not to say that I want people to be religious- I don’t. I simply have no serious desires for other people’s beliefs about the supernatural. Not all atheists are like me but, at the very least, I am. What I do want you to be, at least in some sense, is a secularist and a humanist. I want you to make your decisions that affect the world we share (and the other people in it) based on considerations of the way they will affect the world that we share and the people that we share it with rather than considerations of how they will affect your imaginary friends. I want to know that if tomorrow your deity of choice manifested before you and demanded a platter of human hearts you would side with humanity and tell your deity to fuck off and damn the torpedoes.  If I somehow convinced you to be an atheist but the heart platter issue was still on the table, I would consider myself to have failed in some way.

How, then, do I get behind a movement that sees skeptical examination of (or even basic consideration for) the way our actions affect other people as a distraction? I don’t. Fortunately, I don’t have to. There is (only?) one nice thing about having a movement held together by a shared dictionary entry that nobody even reads anyway. It’s super easy to cut bait and go build your own community; at least when compared to doing the same when there is a patriarchy telling people they aren’t meeting their hellfire quota.

And that’s what seems to have happened. Go Jen. I like this. I like this because one of the most important sources of rage that pushes be to identify publicly as an atheist is that religious communities fail to protect (if not outright attack) children who are atheists. I like this because what I really want from the atheist movement is that those kids or anyone else who deconverts know they have a place to land that doesn’t include threats of rape or other violence.  I like this because when friendly fire didn’t fix the problem, Jen wasn’t disempowered; she was motivated to do more.

I realize this is isn’t huge (yet?). But I find it heartening to see atheist communities built at least partly around social justice. Even if this is just on the internet (or judging by my adolescent experiences- especially if it is on the internet), community matters.

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The Privilege of Reality

I’ve been kicking this one around in my head for a while. People who bring me woo accuse me of all sorts of character traits/behaviors when they find that I am not supportive. Some of these accusations are false; some of them are true but irrelevant; some of them are, doubtless, genuine character flaws; and some of them are not only true but intentional. Regardless, my point here is not to defend the attitude I take when people bring me woo but to explain it. It’s hard to do the latter without slipping into the former. I’m pretty sure I have failed to do so, but I still think it might be useful for people who wonder why I can be so damn rude.

There is alot of woo in the world. Most of us, however skeptical, have some irrational habits or superstitions; we are only human. I say this, not only as fair warning that if you name the Scottish Play in my presence I might spit and throw salt at you, but also because it is important to understand generally. Some of the things that you, personally, believe are wrong.

Many of us humans find this to be deeply troubling. Sometimes we (each and every one of us) seek out validation rather than taking the time to educate and correct ourselves. In some cases this is legitimate- we cannot all be experts on everything. In other cases this is laziness. I’m not trying to judge which is which for particular cases just now, merely stating that both categories are possible and most cases are somewhere in between.

For whatever reason, some people have come to regard me as a source of scientific legitimacy. In some ways this is reasonable and in some ways it is not but it has the effect that people frequently bring their woo (or woo that they find elsewhere) to me for validation. I should clarify that there is a difference between asking honest questions (which I typically enjoy) and asking me to back up your idea to generate infinite free energy. Or asserting that I believe in spirits/ghosts (news to me). Or expecting me to back a university alt-med center because I can’t prove it doesn’t work right now.

With that clarification in mind, when I am presented with theological, spiritual or otherwise supernatural ideas and told either that I don’t understand the experiences or ‘science’ that proves them or that ‘science can’t understand’ them, I am inclined to be dismissive. This is often perceived as rude. I don’t want to do anything which would damage that perception in any way, since it is an honest reflection of such interactions in many cases (see point four). Nevertheless, there are a few points which might be useful in understanding my position.

1) Demanding that you justify an assertion is fundamentally different from dismissing it. I certainly don’t mean to say that I never dismiss people out of hand when they demand that I pay attention to them. In fact, I rather enjoy doing so at times. But that’s not the only way I ever respond to people who try to change my opinion. If you really want to change my mind, it might be worth your while to think about what I actually said to you and determine if I am actually being dismissive or if I have simply failed to agree with you. I do this rarely, but if I tell you to make an argument, then I am giving you my attention. If your response to receiving my attention is to complain that I don’t take you seriously, then I have no reason to take you seriously.

2) Dismissing claims presented without evidence is perfectly reasonable, even if you use ‘dismissive’ as an epithet or claim that it demonstrates arrogance. Hell, I’ll freely stipulate to being arrogant in all kinds of ways if you like. But if you want to make an argument that means something, demonstrating that I am personally arrogant is pointless.

3) I care deeply about all sorts of things that have no extension in the real world. I care about Darth Vader. I care ever so slightly about the gods and legends of old. I care significantly more about the impending zombie apocalypse. I care about Middle Earth enough that in undergrad I wrote a ~20 page analysis of the parallels between the One Ring and the Ring of Gyges. In fact, the number of fictional things about which I care enough to engage in protracted arguments is likely greater than the number of real ones. The fact that I dismiss your particular not-real ideas is not necessarily because they are not real. You should consider the possibility that I am being dismissive because your idea is deeply and fundamentally uninteresting.

4) I am not required to justify basic tenets of physics, chemistry or biology to anyone seeking to convince me of something. Which is not to say that I am never amenable to explaining high-school level science to people. I simply mean that if you come to me wanting to change my mind about homeopathy or some such, it is out of line to expect me to do your homework for you. Nobody is paying me to be a tutor. When I do take the time to educate someone in science, it’s pro-bono. Sometimes I enjoy it. Not always. In any event, it is not only impractical to assume that I could bring everyone up to speed on all the science that I know; it is rude to demand that I do so for the sake of your argument. Doubly so if I happen to know that you have taken the relevant coursework and are failing to apply what you have learned.

5) Ideas that explain and predict reliable, measurable effects in the world are privileged in my priorities. I live in the world. I interact with the world. I interact with other people (including you) through the world and through no other medium. I will continue to do so until I die, which I hope to be some significant amount of time from now. Ideas about other things that interact with the world that I live in have a head-start when I decide what to care about. This is eminently reasonable.

That last one is important. Really important. Frankly, the idea that it should be otherwise strikes me as insane. Sure, you are free to make an argument that I should care about more about some idea which shows no evidence of relating to the actual world I live in than those which do- I might even agree. But probably not. So don’t expect it.

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Not helping

There is not alot to say about this. It is flat out wrong, and stupid to boot. I mention it only for two reasons.

First, because it deserves unequivocal condemnation and because friendly fire is the most important (and effective) kind.

Second, because the Friendly Atheist has set up a donation pool to benefit a charity determined with the pastor. If you’re of a mind to heal damage caused by destructive idiots, details may be found here.

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