It just goes round and round and round

I joined the Great Debate Community last night to talk about this chromosome 2 fusion thing again. One of the topics was about why we have to keep hammering away at the obvious beyond the point where any rational human being would have to accept the facts. Another question was why Jeffrey Tomkins is so committed to promoting a counterfactual that is neither supported by the evidence nor is required by the doctrines of his religion.

If you have an explanation, tell me. Or just watch the video.

Racism is a state of mind

A woman — this woman — pestered poor Sean Spicer with a volley of criticisms while he was out shopping. He mostly ignored her, as is his right, but he opened his mouth once to reply to her. And this is what he chose to say.

We live in a great country that allows you to be here, Spicer said.

Wow. What makes Spicer think that her right to be here might be in question? That he gets to make what sounds an awful lot like a threat? Read Shree’s own response to that comment.

If the price of homogeneity is that we all have to look like Steve King, I’m not paying

Steve King, who is definitely one of the dumbest politicians in America, put his foot in his mouth once again. He is endorsing openly racist ideas, making David Duke happy, and confirming once again that the Republican party has become the shit-hole where we dump our very worst people.

King in a tweet praised Geert Wilders, including a cartoon depicting Wilders plugging a hole in a wall that reads Western civilization.

Wilders understands that culture and demographics are our destiny. We can’t restore our civilization with somebody else’s babies, the congressman wrote.

Actually, yes you can. In fact, you must. Our country alone contains over 300 million people, is Steve King planning to fill the nation with the fruit of his loins? Obviously not. When he says our civilization, he has a broader group of people in mind than just his immediate family. When he says somebody else’s babies, he’s explicitly making a division among the people living here to exclude a group. The question is, where is he drawing the line within our people?

I think we can all guess. And it’s understood that somebody else’s babies are quite simply the brown people who don’t look like him.

There’s a word I like: ecumene. It recognizes that there is a broader community of people living in a land, bound together by the ties of our culture, but still allowing for diversity. I don’t like people who want to shatter our ecumene.

It’s a clear message, King said on Monday. We need to get our birth rates up or Europe will be entirely transformed within a half century or a little more. And Geert Wilders knows that and that’s part of his campaign and part of his agenda.

Guess what, Steve King? Our countries are going to be transformed whether you like it or not, and whether one ethnic group or another has greater birth rates. People gripe about different generations within a population, and always have. Cultures change, always. It’s human nature. The concern is to shape those changes in positive directions. One example of that is public education, which Steve King’s party wants to destroy.

Also, our birth rates? Whose? Is Steve King a resident of the Netherlands? Perhaps he thinks he’s being inclusive. I warn you, though: allow Iowans to find commonality with the Nederlanders, and next thing you know, you’re going to have to let Belgians into the club. And if you let Belgians in, you’re going to have to recognize your affinity to the French. From there it’s a slippery slope to Iowans becoming cosmopolitan people of the world, and there goes your dream of redneck insularity.

King went on to criticize illegal immigration to the United States and immigrants who don’t assimilate into the American culture.

I’m in a state where you can buy lefse and lutefisk any day of the year, where communities celebrate Syttende Mai, where individuals proudly fly blue and yellow flags, where we tell Ole and Lena jokes. Is that OK, Steve King? I notice that you have a motley assortment of flags on your desk, including a Traitor’s Flag.

Steve-King-Confederate-Flag

I think that it is fine to be proud of your heritage, and people should celebrate the customs of their Latin American or African or European or Asian ancestors. It’s when it becomes exclusionary, and you try to shame people for their history, or you use your history to justify oppression, that it becomes a problem.

Living in enclaves, refusing to assimilate into the American culture and civilization. Some embrace it, yes. But many are two and three generations living in enclaves that are pushing back now and resisting against the assimilation, he said.

Like, say, Minnesota? My family came over from Sweden and Norway in the early 19th century, it’s been like five generations, and they haven’t forgotten old customs. My grandparents even moved again from Minnesota to Washington state and found communities of like-minded Scandinavians to live among! Yet somehow second-generation citizens who speak English at school and still speak Spanish to their abuelita are a problem?

How much assimilation do you want?

King also emphasized his view that western civilization is a superior civilization.

I like Western civilization, too, but I think its strengths are openness and willingness to share the benefits of society with all (which, come to think of it, was also true once upon a time of Islamic civilization and Roman civilization and Chinese civilizations, or at least, those civilizations that thrived and grew).

So why does Steve King want to make changes that turn us into an inferior civilization?

I’d like to see an America that’s just so homogenous that we look a lot the same, from that perspective, he said.

Oh, jebus. I just imagined an America populated exclusively by balding, potato-nosed, pop-eyed, pale-skinned, thin-lipped stupid people, and it was horrific.

There’s a reason the Tower is made of Ivory

I saw the problems emerging from the day the March for Science was announced — only it wasn’t weird outsiders who were dissenting, it was a small group of prominent white male scientists who immediately started griping about “identity politics”. There was also a tendency for people who had embraced certain myths about science to try to find shelter behind the idea that science, and the science march, would be “apolitical”. How naive can you be? You’re organizing a march on Washington, DC, in the long tradition of other marches for civil rights, and it was motived by the need to protest the destructive policies of a recently-elected politician? Give me a break. This is a political action, and what muddles it isn’t the multiplicity of causes that drive it, but the foolish people who try to pretend they can organize such an event without it being political.

Zuleyka Zevallos carries out a thorough analysis of the politics of the March for Science. It’s a mess.

Since the march was announced in January 2017, the organisers in the central committee of Washington DC have struggled to respond to issues of diversity. From inadequately addressing inclusion and accessibility, to reproducing discourses of inequality, March for Science has problematically promoted the idea that the march is not a political protest. (It has only been in recent days that the organisers have attempted to address this; but it had not happened at the time of the events with the Los Angeles march.)

The discourse that a march is “not political” is, in fact, very much the outcome of political dynamics. Only people from dominant groups, especially White people, can claim that science is free from politics. It isn’t – as I show with research, further below.

This narrative that science is not political has impacted dialogue about the march: what it stands for (interests of White, heterosexual, cisgender, able-bodied people); who it doesn’t stand for (everyone else, especially people of colour and disabled scientists); and who is erased from the conversation altogether (lesbian, gay, bisexual, transgender, queer, intersex and asexual LGBTQIA people).

This should not have been allowed to build to this level of chaos and concern. There should have been a forthright declaration from the very beginning that this was a march by scientists to protest the anti-scientific bullshit coming out of the current administration, to show that scientists have a strong commitment to the truth. It should be about a great many causes driving us to speak out: the destruction of the environment, the need for better support to combat emerging diseases, the maintenance of safety standards for food and drugs, changes in energy to reduce CO2 emissions, keeping our oceans healthy, etc., etc., etc., a thousand factors that our government wants to ignore or oppose. But it must also include improving diversity in science, providing good education to all people, not just the wealthy ones, and breaking down barriers to women and minorities entering science…all those things that certain people call “identity politics” because it makes them uncomfortable.

The “alt-right” have had a presence in the American science establishment for a long, long time. Remember, the Nazis were inspired by American eugenics, which was not just grassroots racism, but endorsed at the highest levels of academe.

Eugenics was the racist pseudoscience determined to wipe away all human beings deemed “unfit,” preserving only those who conformed to a Nordic stereotype. Elements of the philosophy were enshrined as national policy by forced sterilization and segregation laws, as well as marriage restrictions, enacted in twenty-seven states. In 1909, California became the third state to adopt such laws. Ultimately, eugenics practitioners coercively sterilized some 60,000 Americans, barred the marriage of thousands, forcibly segregated thousands in “colonies,” and persecuted untold numbers in ways we are just learning. Before World War II, nearly half of coercive sterilizations were done in California, and even after the war, the state accounted for a third of all such surgeries.

California was considered an epicenter of the American eugenics movement. During the Twentieth Century’s first decades, California’s eugenicists included potent but little known race scientists, such as Army venereal disease specialist Dr. Paul Popenoe, citrus magnate and Polytechnic benefactor Paul Gosney, Sacramento banker Charles M. Goethe, as well as members of the California State Board of Charities and Corrections and the University of California Board of Regents.

Eugenics would have been so much bizarre parlor talk had it not been for extensive financing by corporate philanthropies, specifically the Carnegie Institution, the Rockefeller Foundation and the Harriman railroad fortune. They were all in league with some of America’s most respected scientists hailing from such prestigious universities as Stanford, Yale, Harvard, and Princeton. These academicians espoused race theory and race science, and then faked and twisted data to serve eugenics’ racist aims.

Yet now some want to declare science “apolitical”, and it’s because they dislike the idea that the values of non-white people might taint the purity of their theories about race.

I’m planning to join in the march, but it sure as hell isn’t because I have deluded myself into thinking science is non-political.

Would you like to play a game?

Later today, I’m going to chat with some folks about the creationist claim that human chromosome 2 is not the product of a fusion of chromosomes 2A and 2B in a primate ancestor. I’ve mentioned this guy before, Jeffrey Tomkins, and I’ve criticized the silliness of his approach, which involves staring fixedly at the putative fusion site and ignoring everything else and pompously declaring that he doesn’t see what he expects to see. My response is always “LOOK AT THE SYNTENY OF THE WHOLE CHROMOSOME, YOU ADDLED DOOFUS!”

Synteny is the conservation of blocks of order within two sets of chromosomes that are being compared with each other. That is, stop looking at one tiny little spot and look at the whole chromosome, and ask if there are similar genes in a similar order between human chromosome 2 and chimpanzee chromosomes 2A and 2B. That’s the evidence.

And then I realized that most people don’t know how to look at the genomic data and do these kinds of comparisons. So in this post I’m going to tell you how to do that. It’s fun! It’s easy! It’s like a little game!

First step: go to ensembl.org. Here’s what you’ll see:

browse

We’re going to select “human”. GRCh38.p7 is just the latest, most up-to-date, complete assembly. You can come back later if you want to play with all that data from other species.

viewkaryo

Oh, look. You could suck in the whole human genome sequence to your computer, but then you’d be wondering how to read it and what you can do with it, and might turn into a bioinformatician. Play it safe and easy for now and click on “view karyotype”.

karyotype

There you are, all 23 human chromosomes and the mitochondrial genome! For now, just click on chromosome 2. From the popup menu, choose “view summary”.

chromsummary

That’s a tempting summary map of what is on chromosome 2, but ignore it for now. Look at top left menu.

summarymenu

Select “Synteny” from the “Comparative Genomics” section.

It’s going to default to showing you how regions with similar sequences line up with human chromosome 2. That’s interesting — you can see that human chromosome 2 is made up of chunks of DNA from mouse chromosomes 12, 17, 6, 1, 19, 16, 5, 11, 2, 10, and 18, but use “Change Species” to switch to “Chimpanzee”. It’s simpler, because we are more closely related to chimps than to mice. Shocking, I know.

chimphumansynteny

Are we done now?

Now if you’d like, you can play with looking at other chromosomes. Or if you’re really clever, you’ll just browse the zebrafish genome.

A sweet kid

I find birthdays rather depressing — you just get older and older until you die. My sister always reminds me that there is something worse, though. She and I approximated the same birthday, I was born on 9 March, she was born on 11 March, 11 years after me. I always knew her birthday, and I always knew exactly how old she was, and I got to watch my baby sister grow up. Here she is, with my father:

Lisa Marie Myers Clendening, 1968-2001

Lisa Marie Myers Clendening, 1968-2001

I think of her every 11th of March.

She died when she was only 33.

See? The thing that’s worse than birthdays is not having any any more, and she’s always reminding me of that.

Gender essentialism is not scientific

A reader let me know that I was mentioned on the March for Science Seattle page.

An excellent example of the perils of ideology trumping science.... from the left. Yes, we love talking about how the Right is so anti-science and ideologically based and praise the Left for being so much better. But they aren't. They just have different ideologies and therefore reject different science. We laugh at those dumb Republicans for denying climate science while our own "tribe" screams about the (false) perils of nuclear power, the (false) dangers of GMOs, and now, with the Regressive Left (of which PZ Myers is as deeply dogmatic as the worst Evangelical) the idea that there are no biological differences between men and women, that there are no evolutionary differences in male and female psychology, and that everyone is a clean slate (tabula rasa hypothesis - false) with gender being 100% socially determined without biological basis.Men and women ARE different. We have evolved over hundreds of thousands of years to be different. Yes there is a lot of variation and there is more in group heterogeneity than between group heterogeneity (meaning that there will be a lot of overlap where on just about any characteristic there will be men that are less "manly" than some women and so on), but that doesn't mean that there aren't legitimate differences based purely in our biology and contingent evolutionary history.But as Steven Pinker points out, it is ALWAYS a mistake to tie your *ethics* to your *science*. Different =/= better or worse. It CAN be, but usually isn't. Acknowledging that men and women are biologically different is not the same as as saying one is "better" than the other. But in a bizarre and ironic twist the Left (particularly the regressives) have fetishized science to the point where they can't make an argument that they see as valid without referencing science, and so they twist and deny scientific facts to fit into their ideology, bastardizing it just as much as their counterparts on the right.

An excellent example of the perils of ideology trumping science…. from the left. Yes, we love talking about how the Right is so anti-science and ideologically based and praise the Left for being so much better. But they aren’t. They just have different ideologies and therefore reject different science. We laugh at those dumb Republicans for denying climate science while our own “tribe” screams about the (false) perils of nuclear power, the (false) dangers of GMOs, and now, with the Regressive Left (of which PZ Myers is as deeply dogmatic as the worst Evangelical) the idea that there are no biological differences between men and women, that there are no evolutionary differences in male and female psychology, and that everyone is a clean slate (tabula rasa hypothesis – false) with gender being 100% socially determined without biological basis.

Men and women ARE different. We have evolved over hundreds of thousands of years to be different. Yes there is a lot of variation and there is more in group heterogeneity than between group heterogeneity (meaning that there will be a lot of overlap where on just about any characteristic there will be men that are less “manly” than some women and so on), but that doesn’t mean that there aren’t legitimate differences based purely in our biology and contingent evolutionary history.

But as Steven Pinker points out, it is ALWAYS a mistake to tie your *ethics* to your *science*. Different =/= better or worse. It CAN be, but usually isn’t. Acknowledging that men and women are biologically different is not the same as as saying one is “better” than the other. But in a bizarre and ironic twist the Left (particularly the regressives) have fetishized science to the point where they can’t make an argument that they see as valid without referencing science, and so they twist and deny scientific facts to fit into their ideology, bastardizing it just as much as their counterparts on the right.

Wow. Let me repeat that amazing accusation.

…the idea that there are no biological differences between men and women, that there are no evolutionary differences in male and female psychology, and that everyone is a clean slate (tabula rasa hypothesis – false) with gender being 100% socially determined without biological basis.

I am a fairly conventional cis-het man, steeped in Western culture, married to a conventional cis-het woman. I have seen porn. I have had heterosexual intercourse. I’m entirely conscious of the biological differences between men and women.

I’m also a biologist. I know the difference between a testis and an ovary, between a Mullerian duct and a Wolffian duct, between testosterone and estrogen (which, in the latter case, isn’t much). I’m also fairly well acquainted with the literature in evolutionary biology, and even know a bit about neuroscience.

To say that I claim there are no biological differences between men and women is so patently absurd and totally divorced from reality that Mr Pavlov ought to be embarrassed about saying something so stupid while accusing me of saying something so stupid. He won’t be.

What he’s doing is a common rhetorical trick. It’s obvious that most men have a penis and most women have a vagina, therefore, with a bit of clumsy sleight of hand, he wants to claim that every bit of cultural bias about the relative abilities of men and women is equally valid. He wants to pretend that because ovaries exist, all his notions about femininity must be equally rooted in biological reality.

Similarly, he reveals his hand with that odious Pinkerism about blank slates — that’s exactly the same game! Argue that some element of human psychology is not fixed by genetics and that it arises in a social context, and you are castigated by Pinker fans who like to bring the discourse to a dead stop with the ludicrous accusation that you must believe everything is 100% socially determined without biological basis. It’s idiotic and dishonest, but right now it’s Pinker’s main claim to fame.

Some things are complex and culturally determined. Biological sex is strongly canalized to produce a bimodal distribution of physical properties, but intersexes do exist. The brain is a plastic organ that responds to its environment in sophisticated ways, and carries both predispositions and the potential to develop in new ways, and gender is less strongly specified by genes than is the reproductive tract. If anyone is anti-science, it’s these people who want to argue for a less responsive, less adaptive, less diverse pattern of possible behaviors from the human brain.

You don’t get to claim that you have a solid biological footing in arguing that women are more nurturing, are less capable of doing math, and prefer the color pink because estrogen unless you’ve done actual work to demonstrate that those differences are real. Breasts aren’t your shortcut for imposing a mass of narrow Victorian cultural prejudices on how people should be, and you don’t get to hide behind science on this one.

Also…hiding behind trivially exposed lies isn’t science, even if some of your scientific heroes who try to defend a regressive conventionality think so.

On turning 60

Way back when I was a kid, there were a couple of things I looked forward to on Sunday morning: 1) Sunday school, 2) my grandmother’s French toast, and 3) Walter Cronkite’s television series, The 21st Century, which was all about the wonders to come in that magical rolling over of the calendrical chronometer to a grand round number. None of this lasted. Sunday school, obviously, did not stick. Grandma died. And Cronkite was basically wrong about everything — the vision of science in the late 1960s was all about engineering, and the space program, and you may have noticed a dearth of jet packs and moon colonies.

One aspect that was somewhat successful was that at least once a week I was thinking about my future, which, as it turned out was another example of a colossal failure of imagination. I tried to picture what my life would be like in the year 2000. I could do arithmetic, so I calculated that I’d be 43 then — really old. Unimaginably old. Older than my parents then, even. I guessed that I’d be bald, because everyone told me to look at your mother’s father to see what would happen to you…and yeah, he was really bald. I knew that I’d be old enough to qualify to run for president (not that I had the slightest interest in the job). Beyond that, nothing, except for the bit about living on the moon with a jet pack.

Now I’m well into the 21st century, and I’ve just turned 60 — impossibly ancient, an age my 10 year old self would have found inconceivable, incomprehensible, and totally discombobulating. So I tried flipping my perspective. Instead of imagining the future, imagine trying to explain the last half century to myself.

First, the important stuff: not bald yet. Also, not president, and given the string of crooks and incompetents you’re going to witness in the coming decades, You should be happy that your resume is going to be untainted by the title.

Next, the bad news.

People you love are going to die. You’ll never get used to it, you’ll never get over it, and by the time you’re 60 you’re going to be carrying around a lot of scar tissue deep down inside. This is inescapable, sorry.

The space program as Cronkite knew it is a dead end that will sputter out and become tediously mundane. There will be really cool robots, though.

You’ll become a tiny bit famous, which isn’t a good thing, because you’ll get nothing out of it but a hell of a lot of hate mail. You’ll get to wake up every day to a chorus singing about how much they despise you. Don’t worry too much though, because the scar tissue will actually help.

Most people mostly suck. The world is an unjust place. Fight against it, you’ll only regret those moments when you let injustice pass by.

Hey, think about this: you’re going to have a longer life than your father will. Try processing that when you’re 10 years old.

I guess I also suck to say that to a kid.

It’s OK. There is some good news.

Science turns out to be cool. Think about the questions more than the answers, and you’ll be perpetually surprised when the answers do emerge.

You find someone you can trust and rely upon. Stick with her, and be reliable and trustworthy, too. It makes all the difference. You won’t be able to imagine life without her, and she’ll help you get through the rotten bits.

You’ll grow up. That’s bittersweet, as you’ll find out when you have kids of your own — they’ll become the most important people in your life, you’ll like them, and then they’ll just keep changing and growing up and becoming people who don’t need you anymore. It’ll feel strange — both deeply proud and regretful at the same time. It’s uncomfortable and confusing, like most of life, but worth it.

Other stuff will happen. Most of it isn’t important. Not even Walter Cronkite’s imaginary future, and especially not Sunday School.