Thursday, December 5, 2019

Trees with moss, fungus, and severed limbs



Hybrid genomes in eukaryotes

Runemark A, Vallejo-Marin M, Meier JI (2019) Eukaryote hybrid genomes. PLoS Genet 15(11): e1008404. https://doi.org/10.1371/journal.pgen.1008404
Abstract

Interspecific hybridization is the process where closely related species mate and produce offspring with admixed genomes. The genomic revolution has shown that hybridization is common, and that it may represent an important source of novel variation. Although most interspecific hybrids are sterile or less fit than their parents, some may survive and reproduce, enabling the transfer of adaptive variants across the species boundary, and even result in the formation of novel evolutionary lineages. There are two main variants of hybrid species genomes: allopolyploid, which have one full chromosome set from each parent species, and homoploid, which are a mosaic of the parent species genomes with no increase in chromosome number. The establishment of hybrid species requires the development of reproductive isolation against parental species. Allopolyploid species often have strong intrinsic reproductive barriers due to differences in chromosome number, and homoploid hybrids can become reproductively isolated from the parent species through assortment of genetic incompatibilities. However, both types of hybrids can become further reproductively isolated, gaining extrinsic isolation barriers, by exploiting novel ecological niches, relative to their parents. Hybrids represent the merging of divergent genomes and thus face problems arising from incompatible combinations of genes. Thus hybrid genomes are highly dynamic and undergo rapid evolutionary change, including genome stabilization in which selection against incompatible combinations results in fixation of compatible ancestry block combinations within the hybrid species. The potential for rapid adaptation or speciation makes hybrid genomes a particularly exciting subject of in evolutionary biology. Here we summarize how introgressed alleles or hybrid species can establish and how the resulting hybrid genomes evolve.

Background

Genetic exchange between species can impede the evolution of biodiversity because gene flow between diverging species counteracts their differentiation and hybridization between recently diverged species can lead to loss of genetic adaptations or species fusion[1]. Traditionally, zoologists have viewed interspecific hybridization as maladaptive behaviour[2] which can result in breaking up co-adapted gene complexes[3]. In contrast, plant biologists recognized early on that hybridization can sometimes be an important evolutionary force, contributing to increasing biodiversity[4][5]. Recently, evidence has been accumulating showing that hybridization is also an important evolutionary process in animals[1][6][7]. Interspecific hybridization can enrich the genetic diversity of introgressed taxa, lead to introgression of beneficial genetic variation or even generate new hybrid species[1]. Hybridization is now also known to contribute to the evolutionary potential in several textbook examples of adaptive radiation, including the Geospiza Galapagos finches[8], African cichlid fishes[9], Heliconius butterflies[10][11][12] and Hawaiian Madiinae tarweeds and silverswords[13]. Here we review the evolutionary outcomes of interspecific hybridization and the properties of genomes of hybrid genomes. Many of the discussed topics also apply to hybridization between different subspecies or populations of the same species, but here we focus on interspecific hybridization (referred to as hybridization in this review).

Wednesday, December 4, 2019

Description via diagram

Nuts and bolts, monochrome

Those pesky memes: Theoretical imagery as a block to progress in thinking about cultural evolution [Image schemas in the annals of conceptual confusion]

What to I mean by “theoretical imagery”? I mean image schemas as the notion is used in, e.g., the cognitive metaphor notions of George Lakoff and Mark Johnson. While I think cognitive metaphor theory is badly overextended (thus I was unable to finish reading Philosophy in the Flesh because the nonsense was piling up so fast I couldn’t breathe) that’s no reason to toss out the useful stuff. And one of the useful ideas is that many of our ideas are grounded in simple visual images, called image schemas.

In the case of cultural evolution I’m thinking of orthodox memetics of the Dan Dennett kind, where memes are little packets of “information” in people’s brains that flit about from brain to brain. This nonsense reached its high point with the 2002 publication Brian Auger’s The Electric Meme: A New Theory of How We Think. I retaliated – the martial metaphor is apt since the book was an assault against reason and evidence – with a review entitled “Colorless Green Homunculi” (Human Nature Review 2 (2002) 454-462). But that’s a digression.

Container schema
Back on track, theoretical imagery. In this case the imagery is that of a container. Think about biology. Considered as physical entities, phenotypes are relatively large while genes are relatively small. Further, genes are physically contained within phenotypes, not vice versa. When we transfer this implicit imagery into the cultural realm we are led to think of memes as relatively little things that must be enclosed in some relatively large thing, such as the human brain. Hence, we have the common notion of memes as quasi-autonomous agents hopping around from brain to brain, taking over mental real estate, and often driving their “hosts” to irrational acts, like belief in God, psychoanalysis, Marxism, or, for that matter, homuncular memetics.

Back to biology, phenotypes play a certain role in the little story of biological evolution. They are the things that are exposed to an environment where they either thrive or die. If they thrive, then the genes they contain within themselves will be passed onto another generation; if they die, well, that’s not so good for their genes, is it? In this story the environment is the container and the phenotypes are the little things within it.

When we transmute this story into one about culture, where’s the environment? What determines whether songs, stories, works of art, and so forth have a living presence in a group? Surely it’s the human mind, and the human mind is in the brain which is in the head. Now we’ve got a problem.

If memes are the cultural analog to biological genes, then they are little things inside a bigger thing, like the head. Now biology: genes are inside phenotypes, and phenotypes, in turn, are in the larger environment. So, in culture, memes are in the head and cultural phenotypes...They’re in the head as well because that’s where the cultural environment is as well. Whoops!

Does not compute. Does not compute. Does not compute.

What do we do? One strategy memeticists have taken is to trivialize the idea of a cultural phenotype so that, for example, a book becomes the phenotype for the word memes written on its pages, or a record or CD becomes the phenotype for sound waves, and so forth, and its really the memes that are the targets of election. Since they’re inside the head where the selective environment is as well, that’s fine.

Another strategy is simply to drop the notion that there is a cultural analog to the phenotype. In this version, memes are like biological viruses, not genes, and so no phenotype analog is needed. This is what Dan Dennett has done. Brian Auger took it to an extreme form in The Electric Meme, where he speculated – I kid you not – that memes raced one another along axons and only the winners got to make the Big Leap to another brain.

In Beethoven’s Anvil I took a different route altogether. But that required some fairly sophisticated conceptual construction of the sort that’s difficult to make convincing in a short note. Basically, I put the cultural analog to genes out there in the physical environment, where they need to be to mix and mingle and be available to people and stuck the cultural analogy to the phenotype in something like a collective brain. That’s where the tricky construction comes into play.

In the specific case of people making music together, I argued that they movements are so closely coordinated that we may consider their brains as being linked together into a single physical system. Some signals in the system are internal to individual brains while others pass between brains through sound waves in the external world; but it all functions as a single system. When the music making stops, the system decouples into autonomous individuals each with their own brain. But, here’s the point, if it was sufficiently pleasurable, they’ll get together again on a different occasion, re-couple, and do it again, thus re-creating the musical phenotype that had given them pleasure the first time.

I’ll stop here. You can get a richer story in Beethoven’s Anvil (2001). I’ve placed some of the story online here, where you’ll find final drafts of the 2nd and 3rd chapters, which is where I provide some of the conceptualization needed to think about linked brains as a single physical system. There is a now a fairly large literature about coordinated activity in brains of humans interacting with one another. While I'd like to be able to claim my book helped that work along, the fact of the matter is that the idea was in the air at the time. I link to some of that work in posts labeled "synchrony" and/or "coupling".

Tuesday, December 3, 2019

They went (only) so far : The Crown, S3 E7 Moondust [Media Notes 24]

The episode is framed by Apollo 11’s lunar landing. Was it profound?

Not in any message one might distill from it, such messages would be as empty as those that Apollo 11 astronauts Armstrong, Aldrin, and Collins offered Prince Philip in a private audience in Buckingham Palace. But perhaps in the flow of it.

Philip is feeling dissatisfied in his middle age. He’d wanted a life of adventure. Instead, he got a life of protocol. The new Rector establishes a retreat house for priests seeking to revivify their faith. He’s asked to speak with the first cohort and, as they tell him why they’ve come to this retreat, he gets restless and ridicules them. “Action, that’s what you need, action” – not an exact quote, but the spirit of the thing is there.

And then he watches the moon landing in the palace surrounded by family – and (liveried) servants, of course. When he learns that the astronauts are being toured about the world and that they’ve been offered to the British royals he’s eager to see them, even requests a private audience. Just him and the astronauts, pilot to pilot(s).

It doesn’t meet his expectations. At all. As they tell banal anecdotes and give pedestrian answers to his questions, and Philip realizes that they not going to give him whatever it is he doesn’t even know how to ask, we’re thinking of those disaffected priests Philip had ridiculed. One wonders whether or not their spiritual seeking is what Philip wanted from these engineer/pilots, but not so much the seeking as the having found it now overflowing with it. But it’s not there.

He shares his disappointment with his wife, the Queen. She understands. They didn’t ask for this. Now they’ll be on public display the rest of her life. She knows what THAT’s about. In an earlier episode she’d revealed that she’d have been much happier breeding and riding horses.

And so the episode closes on Philip once again talking with the priests, this time apologizing for having ridiculed them. And asking for their help.

Very nicely turned.

* * * * *

This episode bares comparing with a post from last year, First Man and our capacity for experience.

Variations, A couple of drops of ink diffusing through water

It's very simple. You fill a tumbler, or some other suitable container, with water. Then drop a little ink into it and watch the ink diffuse, taking photos every so often. Here we have variations on just one such photo. I've posted the original photo at the bottom. I cropped it to eliminate the tumbler and then played around with the resulting ink pattern.







I was a politically incorrect seven-year old: Kowabunga, dude, and “How”

So let me tell you about the Halloween costume I wore when I was seven. I was an Indian chief. My parents made the costume (they made all the Halloween costumes for me and my sister.) My mother sewed the leggings, breech cloth, and shirt out of burlap, with red felt fringe. My father made the war bonnet. I helped him. Twenty-four (I think it was) turkey feathers died to look like eagle feathers, because eagle feathers were illegal, national bird and all. Horse-hair extensions. Hand-beaded headband; I chose the design motifs and did some of the beading myself. Side ornaments of abalone shell with ermine tails hanging from them. It was beautiful and I loved it.

Of course, it was also an act of cultural appropriation. It would be hard to get away with such a costume these days. But how the hell would you explain cultural appropriation to a seven year old boy who wants to grow up to be an Indian? I’m not even sure you could explain the concept to my parents, who were quite intelligent, and were certainly aware of and sensitive to injustice visited on the Indians.

But it was more than a costume, you see. When I played at ‘cowboys and Indians’ I made sure that the Indians won some of the battles. Fair is fair, right? I remember at summer camp in 4th grade when we were watching some Western. The Indians were slaughtered. I complained that it wasn’t a fair fight. The white people had Gatling guns ferchrisake while the Indians only had bows and arrows.

A couple years after that I’d adopted Rafael Mendez, a Mexican American, as my first music hero. And you know what I specifically like about his repertoire? all that Spanish/Mexican stuff he played, all that Latin tinge duende. A couple of years later and I was buying records of jazz trumpeters, some white, some black.

And then I bought a collection of transcription of Louis Armstrong trumpet solos. I spent a lot of time working on those solos; my teacher, Dave Dysert, incorporated them into my regular trumpet lessons. However you may think about it, playing a person's music is necessarily a profound identification with them. And, looking at the copyright dates on those solos, they must have been transcribed and on the market within weeks or at most months after they were recorded in the mid 1920s. That's an awful lot of identification going on through the years by an awful lot of trumpeters.

I figure my identification with Indians, aided and abetted by my parents, was a secure foundation for that, and a lot else besides.

* * * * *

Psssst.... Don’t tell anyone, but I have some very nice Navajo silver that my father bought me over the years, four bolo ties (two with turquoise stones), and two belt buckles.

Monday, December 2, 2019

This whole thread about German pulps before WWII is a hoot and a half

You should read the whole thing, 35 tweets.

Today's liberated woman, a dialectical exchange across eons and boundaries



Toward a Computational Historicism. Part 2: From History to Abstraction

I'm bumping this to the top of the queue because it's about the direction of time in literary history, something I'm thinking about quite intensely these days. Note that this post is included as the first section in my working paper, Toward a Computational Historicism: From Literary Networks to the Autonomous Aesthetic.
I examined three different uses of network vizualizations, topic models, Moretti’s plot diagrams, and cognitive networks in first part of this essay, Discourse and Conceptual Topology. When I posted that I imagined only a second part. In the writing, though, that second part grew and grew, so I cut it in two.

In this part I pose the problem of time and discuss two essays by Stephen Greenblatt, “The Cultivation of Anxiety: King Lear and His Heirs” and “Psychoanalysis and Renaissance Culture” and then compare Amleth (Saxo-Grammaticus) with Hamlet (Shakespeare). I then move back to cognitive networks and talk about Hays’s concept of metalingual defintion and conclude with more Shakespeare, Sonnet 129. I’ll get to Heuser and Le-Khac in Part 3: Prophesy.

Time and History

For physics, I understand, time presents a problem. It seems to have a direction, as some processes are irreversible. Why? If you drop a small quantity of ink into a tumbler of water – as I did in A Primer on Self-Organization: With some tabletop physics you can do at home – it diffuses, irreversibly so. The ink particles never collect together into the compact volume they had when first dropped into the water. Why?

IMGP6658rd

IMGP6661rd

IMGP6672rd

For biologists the problem of temporal direction becomes the question of whether or not evolution tends towards complexity. For some it would seem that more complex species turn up in the biological record at later times than less complex. Others stop with the very notion of complexity: What do you mean, MORE complex?

For literary theorists, well, that depends on the theorist and the theory, no? But I’m not interested in the issue in its most general form. I’m interested in a particular thinker, Stephen Greenblatt.

In “The Cultivation of Anxiety: King Lear and His Heirs” (Learning to Curse, Routledge, 1990, pp. 80—98) Greenblatt opens with a long passage from an early 19th century magazine article on the how the Reverend Francis Wayland broke the will of his 15-month old child. Greenblatt notes that “Wayland’s struggle is a strategy of intense familial love, and it is the sophisticated product of a long historical process whose roots lie at least partly in early modern England, in the England of Shakespeare’s King Lear.” To be sure, one need not read that as any more than a statement of historical contingency, that Shakespeare’s play just happened to have been written before Wayland’s article. But when one considers the larger institutional changes Greenblatt considers – from the public space of the king’s court (and Elizabethan stage) to the privacy of the bourgeois home – one may suspect that Greenblatt is tracking the directionality of literary time, that one text must necessarily have been earlier in the historical process in which both texts exist. Later in that same collection, in a chapter entitled “Psychoanalysis and Renaissance Culture” contrasts the conception of the self implicit in the story of Martin Guerre in 16th Century France with the conception of the self implicit in Freud’s psychoanalytic theorizing. Those conceptions are very different.

In both of those cases there is a difference between two historical situations such that not only is one later than the other, but that order is not merely contingent. It seems that somehow one set of events MUST have been before the other set.

Preserving Democracy: The Crown, S3 E5 Coup [Media Notes 23]

I’ve been watching The Crown, which I think is excellent. In episode five of season three Harold Wilson, the Prime Minister, decided to devalue the pound. And bunch of aristocrats and plutocrats decided the sky’s falling and think it’s time for a coup. To this end they contact Lord Mountbatten, who has just been fired from his post as head of the British armed services, and ask him to lead (serve as a figurehead for) the coup. He decides it can succeed only if the Queen agrees to go along with it. Wilson gets wind of the plot and alerts the Queen. She summons Mountbatten.

This is their conversation, starting at roughly 43:05 into the episode:
LORD MOUNTBATTEN: Your Majesty.
You asked to see me.
QUEEN ELIZABETH: I did.
MOUNTBATTEN: Well, great minds think alike.
As it happens, I was planning to drop by myself,
on a matter of great importance.
I'm getting a feeling that I've not had since Dieppe,
that I'm walking into a trap.
ELIZABETH: I'd like to think you had that sinking feeling on another occasion recently,
when going to see your friends at the Bank of England.
Is it even true?
MOUNTBATTEN: Yes, I did go to lunch at the Bank of England to meet and listen to people who are horrified by what's happening to the country.
A horror I hope you share.
ELIZABETH: Perhaps.
But conspiring with them is not the solution.
MOUNTBATTEN: It is the beginning of a solution.
Why are you doing this?
Why would you protect a man like Wilson?
ELIZABETH: I am protecting the Prime Minister.
I am protecting the constitution.
I am protecting democracy.
MOUNTBATTEN: But if the man at the heart of that democracy threatens to destroy it, are we supposed to just stand by and do nothing?
ELIZABETH: Yes.
Doing nothing is exactly what we do,
and bide our time,
and wait for the people that voted him in to vote him out again, if indeed that is what they decide to do.
MOUNTBATTEN: Mm-hmm. [CLEARS THROAT.]
ELIZABETH: I'm sure you find it near impossible to do nothing and to not have the role and responsibilities you've always had.
You were born to be busy and to lead.
But you still have a huge role to play in this family.
A father figure to my husband.
An uncle and a guide to me.
A king to make in Charles,
not to mention a brother to your sister.
When was the last time you even visited her?
Cheered her up?
That would be a greater service to the Crown than leading unconstitutional coups.
Notice this bit:
ELIZABETH: Perhaps.
But conspiring with them is not the solution.
MOUNTBATTEN: It is the beginning of a solution.
Why are you doing this?
Why would you protect a man like Wilson?
ELIZABETH: I am protecting the Prime Minister.
I am protecting the constitution.
I am protecting democracy.
Mountbatten refers to Wilson specifically, but Elizabeth replies in terms, not of the man, but of his position in the government; and she refers to the constitution and to democracy.

That’s a small matter, but it quite explicitly makes the distinction between an individual human and the post that individual happens to occupy within the state. That’s a distinction that, in America, Donald Trump has trampled to the ground.

* * * * *

See my earlier post, Trump, Gibbs & NCIS, and the Queen @3QD.

I obtained a transcription of this episode from Springfield! Springfield!, https://www.springfieldspringfield.co.uk/view_episode_scripts.php?tv-show=the-crown-2016&episode=s03e05.

Hanging in the breeze

Adaptation and exaptation in escaping optimisation traps in cultural evolution


Fell abstract of the article:
ABSTRACT: Explaining the origins of cumulative culture, and how it is maintained over long timescales, constitutes a challenge for theories of cultural evolution. Previous theoretical work has emphasized two fundamental causal processes: cultural adaptation (where technologies are refined towards a functional objective) and cultural exaptation (the repurposing of existing technologies towards a new functional goal). Yet, despite the prominence of cultural exaptation in theoretical explanations, this process is often absent from models and experiments of cumulative culture. Using an agent-based model, where agents attempt to solve problems in a high-dimensional problem space, the current paper investigates the relationship between cultural adaptation and cultural exaptation and produces three major findings. First, cultural dynamics often end up in optimization traps: here, the process of optimization causes the dynamics of change to cease, with populations entering a state of equilibrium. Second, escaping these optimization traps requires cultural dynamics to explore the problem space rapidly enough to create a moving target for optimization. This results in a positive feedback loop of open-ended growth in both the diversity and complexity of cultural solutions. Finally, the results helped delineate the roles played by social and asocial mechanisms: asocial mechanisms of innovation drive the emergence of cumulative culture and social mechanisms of within-group transmission help maintain these dynamics over long timescales.

Sunday, December 1, 2019

Is a reworked social media the new jetpack of the future?

That is to say, we're living in the Singularity and social media is its most visible and pervasive manifestation. But it's not working all that well, not for we the people anyhow, but it seems to be just fine for those running it according the industrial strength business values of the previous era. What to do? Annalee Newitz addresses that in, A Better Social Media World Is Waiting for Us, NYTimes 30 Nov 2019. Here's a taste:
[John Scalzi] imagines a new wave of digital media companies that will serve the generations of people who have grown up online (soon, that will be most people) and already know that digital information can’t be trusted. They will care about who is giving them the news, where it comes from, and why it’s believable. “They will not be internet optimists in the way that the current generation of tech billionaires wants,” he said with a laugh. They will not, he explained, believe the hype about how every new app makes the world a better place: “They’ll be internet pessimists and realists.”

What would “internet realists” want from their media streams? The opposite of what we have now. Today, platforms like Facebook and Twitter are designed to make users easy to contact. That was the novelty of social media — we could get in touch with people in new and previously unimaginable ways.

It also meant, by default, that any government or advertiser could do the same. Mr. Scalzi thinks we should turn the whole system on its head with “an intense emphasis on the value of curation.” It would be up to you to curate what you want to see. Your online profiles would begin with everything and everyone blocked by default.

Think of it as a more robust, comprehensive version of privacy settings, where news and entertainment would reach you only after you opted into them. This would be the first line of defense against viral falsehoods, as well as mobs of strangers or bots attacking someone they disagree with.

The problem is that you can’t make advertising money from a system where everyone is blocked by default — companies wouldn’t be able to gather and sell your data, and you could avoid seeing ads. New business models would have to replace current ones after the demise of social media.
Not feeling it. A different take:
When she thinks about the future, Ms. Noble imagines a counterintuitive and elegantly simple solution to the algorithm problem. She calls it “slow media.” As Ms. Noble said: “Right now, we know billions of items per day are uploaded into Facebook. With that volume of content, it’s impossible for the platform to look at all of it and determine whether it should be there or not.”

Trying to keep up with this torrent, media companies have used algorithms to stop the spread of abusive or misleading information. But so far, they haven’t helped much. Instead of deploying algorithms to curate content at superhuman speeds, what if future public platforms simply set limits on how quickly content circulates?
To rebuild the public sphere, we’ll need to use what we’ve learned from billion-dollar social experiments like Facebook, and marginalized communities like Black Twitter.
It would be a much different media experience. “Maybe you’ll submit something and it won’t show up the next minute,” Ms. Noble said. “That might be positive. Maybe we’ll upload things and come back in a week and see if it’s there.”

That slowness would give human moderators or curators time to review content. They could quash dangerous conspiracy theories before they lead to harassment or worse.
Not feeling that either. Don't thing Annalee is either.
Twitter and Facebook executives often say that their services are modeled on a “public square.” But the public square is more like 1970s network television, where one person at a time addresses the masses. On social media, the “square” is more like millions of karaoke boxes running in parallel, where groups of people are singing lyrics that none of the other boxes can hear. And many members of the “public” are actually artificial beings controlled by hidden individuals or organizations.

There isn’t a decent real-world analogue for social media, and that makes it difficult for users to understand where public information is coming from, and where their personal information is going.
We need to stop handing off responsibility for maintaining public space to corporations and algorithms — and give it back to human beings.
It doesn’t have to be that way. As Erika Hall pointed out, we have centuries of experience designing real-life spaces where people gather safely. After the social media age is over, we’ll have the opportunity to rebuild our damaged public sphere by creating digital public places that imitate actual town halls, concert venues and pedestrian-friendly sidewalks. These are places where people can socialize or debate with a large community, but they can do it anonymously. If they want to, they can just be faces in the crowd, not data streams loaded with personal information.

That’s because in real life, we have more control over who will come into our private lives, and who will learn intimate details about us.
OK. I like that. Let it be over. Let's put the Singularity behind us and get on with it.

What about a reality check?
“We’re going to have really intricately fake people,” [Mikki Kendall] said. But there will also be ways to get at the truth behind the airbrushing and cat-ear filters. It will hinge on that low-tech practice known as meeting face to face. “You’re going to see people saying, ‘I met so-and-so,’ and that becomes your street cred,” she explained.

People who aren’t willing to meet up in person, no matter how persuasive their online personas, simply won’t be trusted.
Too baroque.

And whoever wrote that title,  "A Better Social Media World Is Waiting for Us", missed the boat, didn't they? That's no way to take responsibility.

Rings and support structures