Maki Naro and Matthew Francis nail it.
Also, I now have my sign for the Science March in April.
That is perfection. Or it would be, if there were a zebrafish embryo somewhere in there, but close enough.
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.
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.
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.
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:
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.
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”.
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”.
That’s a tempting summary map of what is on chromosome 2, but ignore it for now. Look at top left menu.
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.
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 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.
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.
I’m reading Cordelia Fine’s Testosterone Rex: Myths of Sex, Science, and Society –it’s my airplane reading for today, as I travel east — and am getting increasingly enlightened. It addresses these terrible myths about men and manliness and sex that afflict us all, and most importantly, knocking down a lot of scientific fables that seem to be readily disseminated and accepted. Here’s an example from chapter two. She quotes a psychologist who describes a common hypothetical scenario, it’s even one that I think I’ve used in the past, the idea that the reproductive capacity of men is vastly greater than that of women, because we produce lots of cheap sperm, while they are limited by all that pregnancy and child-rearing stuff. Beat your chests in pride at your immense potential virility, men! She quotes a psychologist who makes this kind of facile quantitative argument.
Consider that a man can produces as many as 100 offspring by indiscriminately mating with 100 women in a given year, whereas a man who is monogamous will tend to have only one child with his partner during that same time period. In evolutionary currencies, this represents a strong selective pressure—and a potent adaptive problem—for men’t mating strategies to favor at least some desire for sexual variety.
Then — and this is what I love about this book — she takes it seriously and introduces all the factors involved in conception and does a simple calculation, assuming a man seriously goes on a crusade to impregnate 100 random women.
So what’s the likely return on this exhausting investment? For healthy couples, the probability of a woman becoming pregnant from a single randomly timed act of intercourse is about 3 percent, ranging (depending on the time of the month) from a low of 0 to a high of nearly 9 percent. On average, then, a year of competitive courtship would result in only about three of the one hundred women becoming pregnant. (Although a man could increase his chances of conception by having sex with the same woman repeatedly, this would of course disrupt his very tight schedule.) This estimate, by the way, assumes that the man, in contradiction with the principle of “indiscriminately mating,” excludes women under twenty and over forty, who have a greater number of cycles in which no egg is released. It also doesn’t take into account that some women will be chronically infertile (Einon estimates about 8 percent), or that women who are mostly sexually abstinent have long menstrual cycles and ovulate less frequently, making it less likely that a single coital act will result in pregnancy. We’re also kindly overlooking sperm depletion, and discreetly turning a blind eye to the possibility that another man’s sperm might reach the egg first. In these unrealistically ideal condition, a man who sets himself the annual project of producing one hundred children from one hundred one-night stands has a chance of success of about 0.000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000363.
(Number of zeroes only approximate — I just estimated from the layout on the page, which is hard to do. If only she’d used exponential notation!)
Let’s make the math even simpler and more stark.
Indeed, a promiscuous man would need to have sex with more than 130 women just to have 90 percent odds of outdoing the one baby a monogamous man might expect to father in a year.
Suddenly, my preferred reproductive strategy, monogamy and paternal investment in offspring, seems to be the best evolutionary strategy. It’s much less exhausting, too, and has given me time to do other things in my life.
Anyway, this is a delightful book that has made me question ‘facts’ I’ve long taken for granted multiple times so far, and I haven’t yet finished it. It really pays to think about one’s assumptions now and then, and it’s making me aware of how badly a lot of gender essentialism has poisoned our culture with lies.
She also takes a lot of swift, sharp pokes at evolutionary psychology, if you find that entertaining. I certainly do!
Tomkins is at it again. He’s a creationist who, for some reason, detests the idea that human chromosome 2 is the production of a fusion of a pair of ancestral ape chromosomes. I don’t understand why; all he’s got to do is invoke The Fall and claim it’s an error of Biblical origin, it’s not as if the Bible has anything at all to say about chromosomes. But he does like to go on and on about searching for evidence of a fusion at the fusion site, like he’s expecting an intact centromere and telomere to be right there, fossilized in the sequence. He’s written another article for Answers in Genesis that is an amazing welter of obfuscation.
In 2013, it was shown that the alleged interstitial telomeric repeat site of the human chromosome 2 fusion corresponding to chimpanzee chromosomes 2A and 2B of a hypothetical common ancestor was actually a second promoter in the DDX11L2 long noncoding RNA gene. Additional ENCODE related data are provided in this report that not only debunk evolutionary criticism and obfuscation in response to this discovery, but solidify the original finding. New data come from epigenetic-modifications, transcription factor binding, and transcription start site information. It is also shown that the alleged cryptic centromere site, which is very short in length compared to a normal centromere, is completely situated inside the actively expressed protein coding gene ANKRD30BL—encoding both exon and intron regions. Other factors refuting this region as a cryptic centromere are also discussed. Taken together, genomic data for both the alleged fusion and cryptic centromere sites refute the concept of fusion in a human-chimpanzee common ancestor.
This is remarkable. His entire ‘evidence’ consists of looking in a region of poorly conserved, non-functional DNA, and failing to find a conserved sequence, as if that’s what is expected. It’s the wrong approach. He has to ignore all the other cytological and sequence data that show that chromosome 2 is similar in structure to two chimpanzee chromosomes. This makes no sense. I explained all this before.
…what they do is focus on just the region of the fusion, and complain that it is a tangled mess and hard to interpret — that it is a degenerate telomeric region, rather than a complete and intact telomere, which is what they demand be present. This is an unrealistic expectation, given that every paper on the structure of the fusion region makes the point that it is degenerate.
An analogy: imagine a red Ford Mustang and a blue BMW X6 are in a head-on collision, and both have totally wrecked front ends, with bumpers and radiators and headlights interlocked and everything about their grilles in tangled confusion, and with bits and pieces torn loose and flung about. You’d be able to look at the crash and still tell by everything in and behind the engine compartment that Car #1 was a Mustang and Car #2 was an X6.
Bergman and Tomkins are the bewildered and incompetent investigators who ignore every other factor in the crash, look at a few particularly mangled bits of the wreckage, and declare that they can’t identify it, therefore…the two vehicles were assembled at the factory in this particular configuration, and no crash occurred. But they use lots of sciencey language to explain this at tendentious length, which is sufficient to convince non-scientists that the interpretation of an obvious historical event has been refuted. And that’s all they need to do to accomplish their goals: fling about unfounded fear, uncertainty, and doubt to win over the ignorant.
Tomkins has done it again. He stares fixedly at the debris and fails to pay any attention at all to the intact, functional regions of the human chromosome and ape chromosomes, which are all you need to tell the tale.
I’m watching this video of Ben Carson’s recent speech, and I can’t believe what I’m hearing. I know everyone is aghast at his trivializing of the slave trade, and that’s the more important example of negligent ignorance to focus on, but good grief, I was trained as a neuroscientist, and his remarks about the brain are appalling.
It remembers everything you’ve ever seen. Everything you’ve ever heard. I could take the oldest person here, make a hole right here on the side of the head, and put some depth electrodes into their hippocampus and stimulate, and they would be able to recite back to you verbatim a book they read 60 years ago. It’s all there; it doesn’t go away. You just have to learn how to recall it. But that’s what your brain is capable of. It can process more than 2 million bits of information per second. You can’t overload it. Have you ever heard people say, “Don’t do all that, you’ll overload your brain.” You can’t overload the human brain. If you learned one new fact every second, it would take you more than 3 million years to challenge the capacity of your brain.
None of that is true! Not one bit of it! I can’t imagine anyone who learned the slightest bit of neurobiology in the 20th century believing any of that. The brain throws away most of its sensory input. We don’t know what the “storage capacity” (and it’s fundamentally wrong to think of it that way, as if it’s a flash drive) of the brain is, and we don’t know the storage requirement of a “fact”, so that’s just a bullshit estimation.
Do you even need to know anything to be a brain surgeon? Somebody wack him upside the head with a copy of Kandel and tell him to start reading this stuff he pretends to know.
Apparently, he’s been reciting this pseudoscientific claptrap for years, in his books and speeches before religious groups, but we all know that anybody who read or listened to that stuff wasn’t competent to criticize his bad science.
