Sneaking political commentary into science papers? Glorious!

Via Jonathan Eisen, a simple exercise.

Please take a minute to experience for yourself one of the greatest scientific Easter eggs in a long time.

Step 1: download the PDF of this paper: https://www.nature.com/articles/s41598-018-20427-9

Step 2: Go to Page 3.

Step 3: Zoom way way in on the turd in Figure 1.

Step 4: Enjoy and share.

The article is titled “Methylation-based enrichment facilitates low-cost, noninvasive genomic scale sequencing of populations from feces”, in case you’re interested.

For those of you who don’t want to take the trouble, I’ll put the illustration of a baboon turd below the fold. You never know, someone might decide to insist on having it redrawn.

[Read more…]

Everything is a religion, according to Andrew Sullivan

I’m away. I’m on a break. I’m distracted by an adorable baby granddaughter. But even with those diversions, the stench of Andrew Sullivan’s latest column has disturbed my rest. It is just too stupid. I was stunned by the first paragraph, staggered a little further, and collapsed in defeat.

Everyone has a religion. It is, in fact, impossible not to have a religion if you are a human being. It’s in our genes and has expressed itself in every culture, in every age, including our own secularized husk of a society.

I’ve seen this a thousand times before, and I know what will follow. Sullivan is going to give us his own, personal, idiosyncratic definition of “religion” that he has made so broad and nebulous that he can assign it to everyone, no matter how godless they might be, and he’s going to rely on general human properties that he can then interpret as “religious”.

By the way, no genes for religion have been identified. Not one. He’s lying, unsurprisingly for someone who liked The Bell Curve. He links to a book by some guy named Dominic Johnson, who does have a degree in evolutionary biology, and from what I can see relies entirely on bullshit evolutionary psychology to make his claims.

Here comes his redefinition:

By religion, I mean something quite specific: a practice not a theory; a way of life that gives meaning, a meaning that cannot really be defended without recourse to some transcendent value, undying “Truth” or God (or gods).

I see that he has also redefined the word “specific”, because that is broadly vapid nonsense, not specific at all. A “practice”? So is writing garbage for NYMag his religion? Appearing on Bill Maher’s show is a religion? Except that it is specifically not a theory, but at the same time it requires a “transcendant value” that gives “meaning”. This is such a muddled mess of contradictions and immeasurable assertions that it in itself gives the lie to the idea that it could be based on something as concrete as a gene. He really wants us to believe that this wobbly bullshit is a load-bearing pillar…of jello. And it’s all set up to support this groaner of a familiar assertion by theists.

Which is to say, even today’s atheists are expressing an attenuated form of religion.

If your definition of religion is so amorphous that you can claim everything is a religion, then you’ve said nothing useful. You’ve turned religion into white noise. Religious people ought to find that as offensive as atheists do.

Their denial of any God is as absolute as others’ faith in God,

Wait. I thought religion was a practice, not a theory. But now he’s including “faith” and ideas about a hypothetical concept. He can’t even stick to his own definition!

…and entails just as much a set of values to live by — including, for some, daily rituals like meditation, a form of prayer.

So now it’s defined by daily rituals? I get up in the morning, brush my teeth, have a cup of coffee…this is now, in the mind of Andrew Sullivan, a religion. Hey, if I didn’t get out of bed, my life would be meaningless, if I never brushed my teeth, I’d be disgusting and would die of dental disease, and no coffee…that would be an unimaginable hell.

Also, my spiders spend their days in the endless ritual of maintaining their webs, and their lives would end without them. Therefore, spiders are religious. Maybe they don’t have a concept of a god (which I don’t know for sure), but remember…religion is a practice that gives meaning to life. And is genetic. If you can claim that atheists who explicitly reject gods and religion are religious, we’re at the point where you can’t stop me from claiming spiders are religious.

…(There’s a reason, I suspect, that many brilliant atheists, like my friends Bob Wright and Sam Harris are so influenced by Buddhism and practice Vipassana meditation and mindfulness. Buddhism’s genius is that it is a religion without God.)

OK, I’m done. I can read no further than the point where he claims Sam Harris is a brilliant atheist because he follows some Buddhist practices.

When will NYMag wake up to the fact that they’ve got a columnist who writes drivel? Probably never, since the NY Times has a similar problem, and will never change.

A solution to the “Baby It’s Cold” problem

This is the question that is dominating social media right now. Should it be banned? But that’s censorship! And then the usual free-speech babble is combined with terrible in depth, word by word analyses of the lyrics to show the interpretation is malleable, depending on the views of the analyzer. I hate it all. I hate the song.

The only fair thing to do is ban all Christmas carols. Use objective methods to measure the frequency of play of certain songs, and if they show an unusual annual peak, no matter when, they are clearly not good enough to be enjoyed except in very narrow contexts, and therefore are abominations that should be prohibited. If you don’t want to hear it in July, why do radio stations think it’s desirable to inflict them on us in December? Just kill all the mediocre music.

I’m also considering a prohibition on all media that has “cold” in the title, which seems to be a cause of serious conflict. This would have the benefit of also abolishing all those endless arguments about Tom Godwin’s “The Cold Equations”, which used to take over certain nerd conversations, once upon a time.

The problem of homology

We don’t get to see our granddaughter this morning — she’s getting her pediatric checkup today — so while sitting on my thumbs in my hotel room this morning, I threw together a video on the problem of homology, as misrepresented by Jonathan Wells and Paul Nelson. Seriously, they get it all wrong with tendentious misrepresentations.

There is a real problem of homology, because homology is rendered difficult to see by standard, naturalistic evolutionary processess. Wells and Nelson get it all exactly backwards. That homologies are obscured by the nature of evolutionary change is what we’d expect from evolutionary theory. It’s like how bioinformaticians will talk about the problem of long branch attraction; it’s a real problem, but it doesn’t imply that evolution is wrong, because it’s an expected effect of evolutionary change.

Likewise, evo-devo people will write long papers about the problem of homology, because the action of evolution obscures homologies and we have to struggle to see beyond it. Only a pair of buffoons would argue that it means evolution is false.

I don’t have a script for this one, because it’s just me talking extemporaneously in a dull hotel room, sorry. But I do have a good quote from Mary Jane West-Eberhard, and that’ll have to do if you don’t have the patience to listen to some geezer talking at a camera.

Changing characters do not march ever outward along the branches of a phylogenetic tree. While homology, parallelism, and convergence remain useful conceptual guides, they need to be seen against a background of continual reshuffling with a particulate, mosaic phenotype that renders linear terms like parallelism and convergence only approximate, and potentially misleading, descriptions of evolution.

Does a concept of mixed or partial homology just make a mess of homology? In fact, evolution makes a mess of homology.

Mary Jane West-Eberhard

Old encyclopedias are informative in new ways

The National Library of Scotland has made available to the public digitized versions of all 3 volumes of the 1771 edition of the Encyclopædia Brittanica. I’ve been browsing through it, and it’s a fun read — it doesn’t seem to be able to make up its mind about whether it’s a dictionary or an encyclopedia, but it does have long sections on 18th century agriculture, algebra, and chemistry, so if you ever want to know what people actually thought about those subjects over 200 years ago, you can look them up.

There isn’t much on the stuff I study though — biology hadn’t been invented yet, so you’ll search through the “B”s fruitlessly. I thought maybe there’d be something on embryology, but no, this is it, and it’s rather brutal. They were straightforward about abortion back then.

There is a substantial illustrated section on midwifery, though, so if you ever need to deliver a baby without anesthesia or sterile technique, but you do have a great big handy pair of kitchen tongs, this section will do it for you.

Clenched fist salute to Eric Sprankle of Minnesota State University

We Minnesota professors have to stand together in solidarity, and Dr Sprankle spoke truth in a way that got attention.

He wrote: “The virgin birth story is about an all-knowing, all-powerful deity impregnating a human teen. There is no definition of consent that would include that scenario. Happy Holidays.”

He later added: “The biblical god regularly punished disobedience. The power difference (deity vs mortal) and the potential for violence for saying ‘no’ negates her ‘yes.’ To put someone in this position is an unethical abuse of power at best and grossly predatory at worst.”

Yes! The gods are abusers!

Best of all, he roused the ire of that popular dimbulb, Tucker Carlson, who thought this was a statement significant enough to require repudiation. How shallow of him, said the king of shallowness, and used it as an excuse to berate the dire state of the academy (I thought it was a good insight. Yes, we should think about how our culture has glorified the misuse of power, especially at the expense of women, and consider that this kind of story is the foundation of a lot of patriarchal attitudes). The only sense in which it is shallow is that it is trivially and obviously true. Then it gets weird.

The host interjected that religious critics never target the owners of technology companies.

It’s not even brave, Carlson responded. They never criticize Jeff Bezos, the richest man in the world. Or Apple. Tim Cook. Or Google. They suck up to people in power and then beat up on evangelicals and call themselves, you know, countercultural. I mean, it is pathetic.

Wait, what? He thinks lefty atheists don’t criticize billionaires?

If I had the power, I would strip Bezos of most of his wealth and use it for more worthy causes. Apple has obscene amounts of money sequestered away in tax havens. There are libertarian atheists who might think excessive wealth is a sign of virtue, but a great many of us disagree and will happily criticize all of those people and organizations.

But then, Carlson has consistently demonstrated that he’s the dumbest man on Fox News, and I’m comparing him even to those morning pundits that Trump adores.