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Jul 23 2014

Botanical Wednesday: Cruel bird

This bird, over many generations, has warped the poor Centropogon‘s flower into that bizarre curve.

Jul 23 2014

They don’t understand allometry!

I think the engineers are just trying to wind me up, again. Joe Felsenstein tackles a paper published in an applied physics journal that redefines evolution and tries to claim that changes in aircraft design are a good model for evolution. It’s a terrible premise, but also, the execution is awful.

But permit me a curmudgeonly point: This paper would have been rejected in any evolutionary biology journal. Most of its central citations to biological allometry are to 1980s papers on allometry that failed to take the the phylogeny of the organisms into account. The points plotted in those old papers are thus not independently sampled, a requirement of the statistics used. (More precisely, their error residuals are correlated). Furthermore, cultural artifacts such as airplanes do not necessarily have a phylogeny, as they can borrow features from each other in massive “horizontal meme transfer”. In either case, phylogeny or genealogical network, statistical analysis requires us to understand whether the points plotted are independent.

The paper has impressive graphs that seem to show trends. But looking more closely we notice that neither axis is actually time. If I interpreted the graphs as trends, I would conclude that birds are getting bigger and bigger, and that nobody is introducing new models of small airplanes.

And they really do redefine evolution.

Evolution means a flow organization (design) that changes over time.

I’m going to redefine bridge construction as gluing together lots of matchsticks. Hire me, everyone, to help fix your infrastructure problems! I can probably underbid everyone!

But it’s just kind of amazing that they’ve defined evolution without any mention of populations or shifting allele frequencies or any of the processes (which don’t include design) that lead to changes in genotype, or even a recognition of how these processes derive from a core unity and lead to diversity. Design done did it.

My big gripe is that they got this paper published that is all about allometry with scarcely any understanding of the concept. Here’s the abstract of The evolution of airplanes.

The prevailing view is that we cannot witness biological evolution because it occurred on a time scale immensely greater than our lifetime. Here, we show that we can witness evolution in our lifetime by watching the evolution of the flying human-and-machine species: the airplane. We document this evolution, and we also predict it based on a physics principle: the constructal law. We show that the airplanes must obey theoretical allometric rules that unite them with the birds and other animals. For example, the larger airplanes are faster, more efficient as vehicles, and have greater range. The engine mass is proportional to the body size: this scaling is analogous to animal design, where the mass of the motive organs (muscle, heart, lung) is proportional to the body size. Large or small, airplanes exhibit a proportionality between wing span and fuselage length, and between fuel load and body size. The animal-design counterparts of these features are evident. The view that emerges is that the evolution phenomenon is broader than biological evolution. The evolution of technology, river basins, and animal design is one phenomenon, and it belongs in physics.

Isn’t it cute how they claim biology as a small subset of physics? Blech.

But they only address a very narrow part of allometry. There is a functional constraint on form: you won’t survive if you have a human-sized body and a mouse-sized heart; if you scale the diameter of your legs linearly with your height, you won’t be able to walk; for a given metabolic rate and mass, you need a certain amount of respiratory surface area. That’s interesting stuff to a physiologist, but it’s also purely defined by necessity.

A developmental biologist might be more interested in how the relative sizes of different body parts change over time. Again, relative growth rates of different parts of your body are not linearly related; imagine being six feet tall with the same proportions as a baby. There are regulatory constraints on development that impose different rates in different areas.

But these guys are talking about evolution and allometry…and they treat it as a simple function of physics, where you need an engine of size X to propel a plane of size Y. Then how come every animal of the same size don’t look identical? Why doesn’t every passenger plane that carries a certain number of customers look the same (well, they do kind of blur together for me, but I’m sure any aerospace aficionado can tell me about all the differences between Boeing and Airbus. But many of these differences in animals are a result of inherited patterns, and phylogeny is essential to understand them.

For example, here’s a plot of brain mass relative to body mass (yeah, ugh, “lower” and “higher” vertebrates; let’s call them anamniotes and amniotes instead).

eq

Notice that there are two lines drawn. Both show an upward trend, with a slope that’s proportional to the 2/3 power of the body size (that N2/3 shows up a lot in allometric growth plots). But given a fish (an anamniote, or “lower” vertebrate) and a mammal (an amniote, or “higher”) of exactly the same body mass, the mammal will have a relatively and absolutely much larger brain.

Explain that, engineer, with nothing but algebra and no concern about phylogenetic relationships. It takes more to understand evolution than physics alone, and you have to take into account history, environment, inherited properties, selection, and chance as important parameters.

Oh, well, I’ve learned that physics must be really simple. I can design a plane from the ground up if I simply postulate a spherical 747. Ha ha, all those fools getting engineering degrees when they could just bring in a clever biologist to solve all their trivial little problems.

Jul 23 2014

Well, I am on a diet and trying to lose weight

So it’s very kind of John C. Wright to assemble a post that completely kills my appetite — in fact, it makes me feel like an inhabitant of the planet Miranda, only I can’t make up my mind whether to just lie down and die or go full Reaver. It’s titled The Secret to the Most Mind-Blowing Sex Ever. Very click-baity. I can only the imagine the disappointment of people searching for “mindblowing sex” and landing on Wright’s article, and feeling their generative organs shrivel.

It’s premise is that there’s more to sex than just the physical — and I’d agree with that. It’s emotional, it’s social, it strengthens the pair bond, it’s fun. But Wright isn’t thinking along those lines, and he also has a peculiar idea of what’s appropriate about the physical side of it.

If the union were physical only, nothing but the physical sensation of the orgasm would matter, and rubbing your penis in an anus, mouth, armpit, elbow, or an elephant’s ear, not to mention the crevasses of mothers and sisters and underage children, convenient animals, and fresh corpses or whatever floats your boat would be called sex just the same as sex is sex. The word sex would refer only to the hunger for the sensation, and not to the sex act.

I’m fine with people who get off on armpits. As long as the two people doing it (and I’m pretty sure that one requires at least two people; if you can do it solo, you must be built like a barnacle) are willing participants who both are enjoying it, why not? And of course I’d be among many agreeing that there’s a difference between sexual interactions and sexual gratification, and that regarding your mother as a collection of crevasses is more than a little icky. It is rather important in long-term sexual relationships that you consider your partner as a human being.

But no, that’s not what Wright is getting at. He has his own definition of the function and purpose of sex.

In order to understand the perfect sexual experience, we first must say what sex is: it is copulation, the process by which two halves of a sexual whole find complement and completion, and reproduce. The sex act is the act of sexual union in sexual reproduction. The sexes, however, are spiritual rather than physical: men are masculine in psychology and mind and soul, masculine in speech and deportment and nuance in all they do just as women are feminine. The sexual union is spiritual, ordered toward the end of reproduction.

That’s it. The whole purpose of sex is making babies. For someone who just lectured on interminably in flowery language about how sex is not physical only, he sure seems focused on the physical process of getting the lady preggers.

Since sex is ordered toward reproduction, anything that hinders it is an imperfection. Prudence, if nothing else, would warn potential mother and potential fathers not to do the act which makes you a mother or a father until you have a household and loving union ready to rear children.

If you are artificially sterile, or using contraception, you are holding back, you are not passionate about the sex, you are trying to use the sex rather than surrender to the sex.

Gosh, is he an evolutionist? Because we’d be the types to say that the only ‘goal’ of evolution, the only measure of success, is sustained maintenance of the species. Of course, we’d also note that it’s a much more complicated process in humans than blindly inseminating random females (that’s more appropriate to sea urchins), and that sex also plays a role in strengthening bonds between people to help with survival, and we’d also note that lots of phenomena in biology have interesting side-effects that can be important in life histories, too. Sex is not exclusively ordered towards reproduction, so his premise is false.

We get to his real deal, at least: he’s against contraception. He doesn’t see any point to any kind of sexual interaction that doesn’t have the possibility of conception. Well, gosh, I’ll have to break the news to my wife that there were only three brief periods in my life when our sex life mattered, and that was when we were trying to have kids. All the rest was frivolity and illusion, and now that we’re all done with the kid stuff, we can stop. Because sex would be pointless.

It just gets worse from here. If you’re just trying to lose a bit of appetite, you can stop just a couple of paragraphs in — proceeding further takes you deeper into bulimia territory, as you discover that sex is also supposed to reinforce very traditional roles for men and women: master and servant.

Since sex is ordered toward reproduction, you have to love the woman first, and want her to be the mother of your children, and want it more than you want life itself. Since sex is spiritual, you have to protect your children and your wife and make them safe. Your wife cannot be made safe if you are allowed to abandon her. Hence, since sex is ordered toward reproduction, you must swear, swear by Holy God and your hope of heaven, never to leave her, but to love and cherish her, in sickness and health, for better or worse, until nothing less than horrid death itself you do part.

For her part, she must vow to love and honor and obey.

And if you do not understand about that obey part, you do not understand women. She wants a leader, an alpha male, a chief, a Christ, and you must be willing to die for her as Christ was willing to die for you, or she will not feel secure in your love. If she does not swear to obey, you are not a couple, not a dyad, not a unit, but are still two sovereigns dealing with each other at arm’s length, not intimate, and she cannot trust you fully, cannot love you fully, not with a divine and self-sacrificing love. And she knows you don’t love her fully, not with a love that is more than madness, more than sense, more than the universe.

So much nonsense. Here’s the real secret to mindblowing sex: each treats the other as a sovereign, intimately. My interactions with my wife are not subservient to praising tropes in a dusty old holy book, nor are they dedicated to creating some third party (yeesh, especially not at our age).

Of course, this is John C. Wright babbling: Catholic, conservative, fan of Vox Day, science fiction writer. And if the puffed-up goofy prose in that column is any example, not a very good writer. Judging by the content, also a dogmatic idiot.

I think it would do him a world of good to go fuck an elbow, actually.

Jul 23 2014

AtheistTV, next week

I hope AtheistTV is good — they’ve announced they’ll be putting 50 years worth of their video archives on there, so I’m hoping for some interesting content. On the other hand, if it’s recycling crap from youtube as a fast way to get lots of noise online, well…it could get embarrassing. There has to be some quality control, somewhere.

I’ll check it out next Tuesday and let you know what’s on.

Jul 22 2014

Big News: God was not a Klingon

Poor Ken Ham: the media has been distorting his words. They claim that he said all the space aliens are damned to hell. He did not! He plainly said:

And I do believe there can’t be other intelligent beings in outer space because of the meaning of the gospel.

See? They aren’t going to hell, because they don’t exist. He continues with a beautiful example of fundagelical creologic:

You see, the Bible makes it clear that Adam’s sin affected the whole universe. This means that any aliens would also be affected by Adam’s sin, but because they are not Adam’s descendants, they can’t have salvation. One day, the whole universe will be judged by fire, and there will be a new heavens and earth. God’s Son stepped into history to be Jesus Christ, the “Godman,” to be our relative, and to be the perfect sacrifice for sin—the Savior of mankind.

Jesus did not become the “GodKlingon” or the “GodMartian”!  Only descendants of Adam can be saved.  God’s Son remains the “Godman” as our Savior.  In fact, the Bible makes it clear that we see the Father through the Son (and we see the Son through His Word).  To suggest that aliens could respond to the gospel is just totally wrong.

An understanding of the gospel makes it clear that salvation through Christ is only for the Adamic race—human beings who are all descendants of Adam.

Now that’s impressive arrogance and delusions of grandeur. So there are 1011 galaxies and almost 1023 stars in the universe, and they’re all entirely empty of intelligent life, and they’re all going to be burned away and discarded when a Magic Jew comes reappears on Planet Earth. We know this because of an ancient book written by people who thought the earth was flat and the sky was held up on pillars.

Ooooookay.

Jul 22 2014

Can someone dig up the corpse of Norman Vincent Peale and drive a stake through its heart?

He’s still stalking about, giving the complacent a lie to shut the dissatisfied up. No, positive thinking doesn’t work; affirmations have no power; The Secret is a scam. The @SciCareer guy put his foot in it again by touting some paper titled “Happy Thoughts May Help Postdocs Handle Stress.” As you might guess, the reactions of young academics aren’t exactly enthusiastic.

Are you for actual serious with this?? The article describes a new study–and I use this word lightly because it’s based on a one-time survey of 200 postdocs–that found less anxiety and depression in folks who self-reported more frequent positive emotions. So, not only do we have a clear correlation vs. causation issue here – who can say that it was the positive emotions that prevented the development of clinical symptoms and not vice versa – but it belittles the many real stressful problems that postdocs face that cannot simply be "thought" away.

The real money quote is this:  "When we suggest that people need more positive emotions in their lives, I know it sounds kind of frou-frou, but it’s actually a very simple practice.” OK. a) I don’t think you know what frou-frou means (frilly or ornamented, not fluffy or insubstantial, which is what you probably mean and you’d be right). b) No, it is not simple. Postdocs have personal, financial, and professional stresses on a daily basis. They are busy as fuck. To suggest that watching a sit-com or going for a run can change that reality not only presumes they have time for something like that, but has very strong undertones of "stop complaining and just change your attitude."

Anger is fuel for change, “positive thinking” is a worthless analgesic for the masses. Get angry, and do something about it.

Jul 22 2014

Commitment

Jonathan Eisen is walking the walk, turning down an endowed lecture opportunity because of their gender imbalance.

Thank you so much for the invitation and the respect it shows to me that I would be considered for this.  However, when I looked into past lectures in this series I saw something that was disappointing.  From the site XXXX where past lectures are listed I see that the ratio of male to female speakers is 14:3.  I note – the XXXX lecture series – also from XXXX – also has a skewed ratio (11:2).  As someone who is working actively on multiple issues relating to gender bias in science, I find this very disappointing.  I realize there are many issues that contribute to who comes to give a talk in a meeting or seminar series or such. But I simply cannot personally contribute to a series which has such an imbalance and I would suggest that you consider whether anything in your process is biased in some way. 

Sincerely, 

Jonathan Eisen

Jul 22 2014

Caricature, corrected

MRA’s have been sending me this video they’re very excited about — it’s done by a pretty young woman who comically repeats every stupid stereotype of feminists by anti-feminists everywhere. Did you know feminists don’t want you to be young and slender and pretty, and you shouldn’t wear makeup or pretty clothes, and most of them hate men, and it’s all about competing to see who is most oppressed? We don’t need feminism any more, because men and women are already equal in all things, and besides, she has never experienced any discrimination, so nobody else can have. It is funny. Funnily bad.

I thought about writing a rebuttal, but shortly I have to go to work, and it would take hours to dismantle it nonsensical misconception by outright flaming stupidity, sentence by sentence. There’s so much of it.

Fortunately, I don’t have to. One of the sensible people who sends me things (They exist! Really, my in-box isn’t just a shitstorm of derp. Usually.) sent me this most excellent common sense general defense of feminism by the Bloggess, so I’ll just tell you all to go read that instead.

Feminism is inherently good.  It’s not even close to perfect and still needs lots of work and sometimes it gets all fucked up and backward and awful but that doesn’t mean it’s not still worth fighting for.  Now go back and replace “Feminism” with “The human race”.  It works, right?.  That’s because feminists are made of human.  Men and women.  In fact, one of my favorite feminists is Sir Patrick Stewart.

Patrick Stewart, feminist. His mother made 3 pounds 10 shillings for working a forty hour week in a weaving shed. She was also an abuse victim and he’s an anti-domestic violence advocate.

Patrick Stewart, feminist. His mother made 3 pounds 10 shillings for working a forty hour week in a weaving shed. She was also an abuse victim and he’s an anti-domestic violence advocate.

I’m not saying you can’t choose to not be a feminist but know what you’re choosing.  Don’t make a decision about a group based on the most radical beliefs of a group.  Don’t get defensive if you get deeper and are exposed to difficult ideas about intersectionality and race and gender and colonialism and patriarchy and male liberation.  Just listen.  Some of it will make sense.  Some of it won’t.  Some of it will later when you’re a different person.  Some of it you’ll change your mind about throughout your life and the world will change too.  Some of it is bullshit.  Some of it is truth.  All of it is worth listening to.

And now you get to decide.  Are you a feminist?  Yes?  No?  Well, don’t worry because tomorrow you get to choose again.  And that keeps happening every day for the rest of your life.

As for me, I am a feminist (among so, so many other things).  I believe in equality and I think we still have work to do.  I’m thankful to the men and women who worked to give me the freedom and rights I have today and I am proud to be a part of a movement that I hope will make the world better and safer for my daughter (and for the men and women she’ll share that world with).  I’m happy we’ve come so far and I’m glad that we’re becoming more aware of feminist issues that don’t just focus on straight, white women, even though confronting those issues is sometimes painful. And I’m happy that the womenagainstfeminism tumblr exists.  Because even though I disagree with most of them I’m glad that those women have a platform on which to speak, and also because if we know what the arguments or misperceptions are against feminism then we can better address them.  Or agree with them.  Or ignore them.  Or discuss them with our sons and daughters so they can make informed decisions for themselves.  It’s up to you.

That pretty young woman’s video? The most important part of the description is that she’s young. I hope she grows up to be just like the Bloggess.

Jul 22 2014

Those sneaky forms of academic bias…

It’s Tuesday…that must mean it’s “Let’s point out flaws in the academic system!” day.

Here’s another example: some investigators did a study of the value of screening cancer patients for distress — they asked whether such screening actually contributed to patient’s feelings of well-being and willingness to follow medical recommendations, and whether it was cost-effective. Their answer was no on all counts. Kudos to the Journal of Clinical Oncology for publishing a negative result.

Raspberries to the Journal of Clinical Oncology for what they did next, though. They brought in a proponent of screening to write a dismissal of the study.

Hollingsworth and colleagues were surely disappointed to discover that their article was accompanied by a negative editorial commentary. They had not been alerted or given an opportunity to offer a rebuttal. Their manuscript had made it through peer review, only to get whomped by a major proponent of screening, Linda Carlson.

After some faint praise, Carlson tried to neutralize the negative finding

despite several strengths, major study design limitations may explain this result, temper interpretations, and inform further clinical implementation of screening for distress programs.

And if anyone tries to access Hollingworth’s  article through Google Scholar or the Journal of Clinical Oncology website, they run smack into a paywall. Yet they can get through to Carlson’s commentary without obstruction and download a PDF for free.  So, easier to access the trashing of the article than the article itself. Doubly unfair!

Why we need open access, reason #21035.

I also found it interesting that the critical opinion piece had references…but most were to the author, or lab groups that had published with the author. Signs of a circle-jerk in the citations are always a warning sign.

The opinion piece also talks at length about problems with the Hollingworth paper’s protocols. I think it’s important to point out such failings, but shouldn’t they be done by editors and reviewers before publication? And why nitpick at studies that disagree with you, while ignoring major methodological flaws in your own approach?

Try this experiment: Ignore what is said in abstracts of screening studies and instead check the results section carefully. You will see that there are actually lots of negative studies out there, but they have been spun into positive studies. This can easily be accomplished by authors ignoring results obtained for primary outcomes at pre-specified follow-up periods. They can hedge their bets and assess outcome with a full battery of measures at multiple timepoints and then choose the findings that make screening looked best. Or they can just ignore their actual results when writing abstracts and discussion sections.

Especially in their abstracts, articles report only the strongest results at the particular time point that make the study looked best. They emphasize unplanned subgroup analyses. Thus, they report that breast cancer patients did particularly well at 6 months, and ignore that was not true for 3 or 12 month follow up. Clever authors interested in getting published ignore other groups of cancer patients who did not benefit, even when their actual hypothesis had been that all patients would show an improvement and breast cancer patients had not been singled out ahead of time. With lots of opportunities to lump, split, and selectively report the data, such results can be obtained by chance, not fraud, but won’t replicate.

Oh, boy, another of my peeves: fishing with statistics, gaming with your data.

Jul 22 2014

Behold the wrath of god

Remember, everything has a purpose.

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