March for Science…in Morris!

morrismarchforscience

There will be a Morris Area March for Science, and I’m planning to be there. Especially given the announced savage cuts to science funding, it’s important that we stand up and testify to the importance of science.

The Union of Concerned Scientists interviewed a number of scientists about whether they’ll participate in the march, and the answers were overwhelmingly in the affirmative. However, there was also one naysayer, and it’s a good idea to consider the opinions of those who disagree in an intelligent way. Here’s Troy Livingstone’s opinion:

I believe strongly in the values inspiring the march. But I also believe it will be a mostly white, mostly privileged and elitist group who will not be or appear inclusive of all people.

Unintentionally, marchers may reinforce the negative stereotype that science isn’t for everyone.

Finally, I believe that the millions of dollars marchers will spend would have had more tangible benefit advocating for science if they went into the accounts of AAAS or the Union of Concerned Scientists or similar organizations.

I’m all for political activism, but I worry, just like with the women’s march, that many people will call this march their contribution to this cause and leave it at that.

What will matter most is not what happens on the day of the march but everything all of us have done and will do every other day of the year.

Those are very good points. I think he’s right that institutional science, by it’s nature, is privileged, and the people who participate will not be representative of the broader group that benefit from, and will contribute to, science (this problem was also not helped by the dudebro scientists who immediately started whining about identity politics as soon as the organizers tried to emphasize diversity). I think we need to reach out to our public schools and school teachers in addition to lab scientists to make it clear that these are issues that affect everyone. It has to be a march for all, not just working scientists, in support of science.

The concern that motivated individuals will spend “millions of dollars” on a demonstration is silly. Don’t try to police how individuals spend their personal efforts. We should be encouraging everyone to go public with their concerns.

But he’s exactly right that this can’t just be a one-shot, one-day show. This has to be the start of the work. It doesn’t immediately solve anything, but it can be a chance to get a greater commitment to working to tear down the ignoramuses in office.

Mutual harm at Middlebury

Tristero strikes exactly the right note in this letter to the professor who was injured in the protests against Charles Murray at Middlebury. There is no excusing the harm done to Professor Stanger, but there is also no excusing the harm done by Murray.

I have, in fact, read The Bell Curve, the book Charles Murray co-authored with Richard Herrnstein (who died before publication).As I recall, the book appeared to me to be little more than a spectacularly pathetic attempt to boost the low self-esteem of the authors by claiming that blacks in general had inherently lower IQs than their own ethnic groups. My heart went out to Murray and I hoped he would find a good therapist that would instill some some self-confidence in him.

But even more so, my heart went out to the people who would be surely harmed by his terrible book. I knew that The Bell Curve would be mistaken as being super-serious intellectual research (it’s got charts and things!) when it was nothing of the sort.

Here’s where you come in.

Murray is a hero to racists with pretensions to intellectuality, like college-age right-wingers. But having regular access to the Wall Street Journal’s Op-Ed pages (I’ve also read many of Murray’s op-eds and they’re as unserious as The Bell Curve) makes it difficult for Murray to complain that someone’s trying to suppress his freedom of speech. For that, he needs useful idiots who are prepared to invite him not to fawning right wing think tanks or Klan meetings, but to places where the people who his writings actually harm can confront him.

Make no mistake about it: the racism that Murray empowers is as inexcusable and irresponsible as the injuries you suffered. I’m extremely sorry that you were hurt, but I’m also extremely sorry that Murray was provided an excuse to claim the high road. Both are utterly disgraceful outcomes of this unfortunate set of circumstances.

I too read The Bell Curve way back when it first came out, although, thankfully, the details of that pile of shit have faded from my memory, leaving only the recollection of a sensation of disgust. Murray relies on baffling his audiences with the arcana of statistical analysis which neither he nor most of his readers understand, but which earns him the love and appreciation of racists who don’t really care how he gets to his conclusions, as long as those conclusions support their prejudices.

I’m only competent enough in those arcana to see the flaws in his arguments, but not to explain them well. For that, I recommend the invaluable Cosma Shalizi, who made the case against g:

To summarize what follows below (“shorter sloth”, as it were), the case for g rests on a statistical technique, factor analysis, which works solely on correlations between tests. Factor analysis is handy for summarizing data, but can’t tell us where the correlations came from; it always says that there is a general factor whenever there are only positive correlations. The appearance of g is a trivial reflection of that correlation structure. A clear example, known since 1916, shows that factor analysis can give the appearance of a general factor when there are actually many thousands of completely independent and equally strong causes at work. Heritability doesn’t distinguish these alternatives either. Exploratory factor analysis being no good at discovering causal structure, it provides no support for the reality of g.

And also argued against misinterpretations of heritability:

To summarize: Heritability is a technical measure of how much of the variance in a quantitative trait (such as IQ) is associated with genetic differences, in a population with a certain distribution of genotypes and environments. Under some very strong simplifying assumptions, quantitative geneticists use it to calculate the changes to be expected from artificial or natural selection in a statistically steady environment. It says nothing about how much the over-all level of the trait is under genetic control, and it says nothing about how much the trait can change under environmental interventions. If, despite this, one does want to find out the heritability of IQ for some human population, the fact that the simplifying assumptions I mentioned are clearly false in this case means that existing estimates are unreliable, and probably too high, maybe much too high.

Once you knock those two props out from under Murray’s claims, he flops down into a disreputable heap.

But he keeps getting invited to speak at universities. I don’t know why. Stanger claims that the protest was a result of people not reading Murray’s book, but I think the real problem is people who read Murray’s book and don’t understand what a pile of garbage it is.

Australia reassures me that it isn’t just my country full of idiots

Senator Malcolm Roberts must be Australia’s version of Louie Gohmert.

He does make a good case that he is a waste of carbon, but you know, atmospheric CO2 is the problem, not carbon bound up in proteins and carbohydrates.

Born 150 million years too late

I’m reading a few papers on cephalopod evolution, and one helped me pinpoint my happy time.

Coleoid cephalopod molluscs comprise squid, cuttlefish and octopuses, and represent nearly the entire diversity of modern cephalopods. Sophisticated adaptations such as the use of colour for camouflage and communication, jet propulsion and the ink sac highlight the unique nature of the group. Despite these striking adaptations, there are clear parallels in ecology between coleoids and bony fishes. The coleoid fossil record is limited, however, hindering confident analysis of the tempo and pattern of their evolution. Here we use a molecular dataset (180 genes, approx. 36 000 amino acids) of 26 cephalopod species to explore the phylogeny and timing of cephalopod evolution. We show that crown cephalopods diverged in the Silurian–Devonian, while crown coleoids had origins in the latest Palaeozoic. While the deep-sea vampire squid and dumbo octopuses have ancient origins extending to the Early Mesozoic Era, 242 ± 38 Ma, incirrate octopuses and the decabrachian coleoids (10-armed squid) diversified in the Jurassic Period. These divergence estimates highlight the modern diversity of coleoid cephalopods emerging in the Mesozoic Marine Revolution, a period that also witnessed the radiation of most ray-finned fish groups in addition to several other marine vertebrates. This suggests that that the origin of modern cephalopod biodiversity was contingent on ecological competition with marine vertebrates.

There are lots of details, but the summary is this: they’ve used the molecular data to calibrate a tree of cephalopod phylogeny to place the major diversifications of the group in context, and they’ve also looked at degrees of diversity over time. And the answer is summarized in this one diagram:

Chronogram of cephalopods, plus 26 bivalve and gastropod molluscs, one scaphopod and four annelids as outgroups and calibration nodes; 36 156 amino acid positions analysed under CAT-GTR substitution model, CIR clock model, Yule birth–death process, soft bound of 0.05, and a root prior of 565 Ma with a standard deviation of ±10 Ma. Bars at nodes represent 95% confidence intervals (recent nodes not labelled with bars to aid clarity). Red dots indicated calibrated nodes; red dotted lines represent extent of calibration minima. Environmental conditions and sea-level curve simplified from Miller et al. Curves for belemnite, actinopterygian, chondrichthyan and Palaeozoic fish diversity are based on fossil observations on diversity, data from Palaeobiology Database (pbdb.org), electronic supplementary material, table S5. Red vertical lines represent major extinction events. Aqua-blue vertical bar signifies the extent of the Mesozoic Marine Revolution.

Chronogram of cephalopods, plus 26 bivalve and gastropod molluscs, one scaphopod and four annelids as outgroups and calibration nodes; 36 156 amino acid positions analysed under CAT-GTR substitution model, CIR clock model, Yule birth–death process, soft bound of 0.05, and a root prior of 565 Ma with a standard deviation of ±10 Ma. Bars at nodes represent 95% confidence intervals (recent nodes not labelled with bars to aid clarity). Red dots indicated calibrated nodes; red dotted lines represent extent of calibration minima. Environmental conditions and sea-level curve simplified from Miller et al. Curves for belemnite, actinopterygian, chondrichthyan and Palaeozoic fish diversity are based on fossil observations on diversity, data from Palaeobiology Database (pbdb.org), electronic supplementary material, table S5. Red vertical lines represent major extinction events. Aqua-blue vertical bar signifies the extent of the Mesozoic Marine Revolution.

They’ve got a good story behind it, too. What drove the concurrent evolution of both cephalopods and bony fish was a competition to occupy the nektonic space. That is, before the Devonian, animals were primarily benthic — the lowest level of the aquatic environment than includes the floor of the body of water — and that the hot new space to occupy was the nekton, the upper levels of the water. This required new strategies, fish evolved jaws, cephalopods evolved beaks, that opened up new predator/prey relationships. Further, as these groups evolved in the nekton, there was a switch in defensive strategies from making heavy armor to stripping down and becoming more agile. Those trends are conspicuous in both groups.

Taken together, molecular divergence times and the cephalopod fossil record are consistent with a scenario in which predator–prey arms races shaped the coleoid body plan, biodiversity and ecology. The coincidence with the evolution of jawed vertebrates and teleost fishes during the Devonian Nekton Revolution and the Mesozoic Marine Revolution, suggests that nektonic marine vertebrates have been key antagonists towards cephalopods throughout most of their evolution.

So it all started with the Devonian Nekton Revolution, and reached completion in the Mesozoic Marine Revolution, which they call “the final stage in the shift from Palaeozoic ecologies into the modern structure of marine ecosystems”. What you can also see in the diagram is that there has been a shift in the diversity of the phyla occupying that nektonic niche, with cephalopods owning the Mesozoic seas, and teleosts taking over in the Cenezoic.

Which tells me that when I retire, I need to set the dials on my time machine to the late Jurassic/early Cretaceous, and settle down to start fishing/squidding. I was just checking my maps and I see that there was a big inland sea stretching from British Columbia and Calgary, down to most of North Dakota and the western part of South Dakota, so I would only have to move a few hundred miles west.

And 150 million years back.


Tanner AR, Fuchs D, Winkelmann IE, Gilbert MT, Pankey MS, Ribeiro ÂM, Kocot KM, Halanych KM, Oakley TH, da Fonseca RR, Pisani D, Vinther J. (2017) Molecular clocks indicate turnover and diversification of modern coleoid cephalopods during the Mesozoic Marine Revolution. Proc Biol Sci. 284(1850). pii: 20162818. doi: 10.1098/rspb.2016.2818.

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.