Saturday, May 27, 2017

Cromwell, Superman

A brief review of Wolf Hall.

The press of business prevents a longer post, so just a few words on a novel I have been laboring over, Wolf Hall, by Hillary Mantel. First, the style- it is offensively eliptical and unclear, not indicating dialog or who is speaking or thinking. How it could have been the rage of the prize committees and reviewers a few years ago is simply beyond me. Edgy, yes. But respectful of the reader, no. Comparing it to another bit of current reading, Thomas Hardy's Far From the Maddening Crowd, couldn't make the contrast starker. Hardy treats his reader as well as his subjects with great respect. Humor, yes, and deep insight, but first of all clarity, and rich context and exposition. 

Ann Boleyn, secondary subject of Wolf Hall.

Mantel, in contrast, plays games with the reader, telling the story through a straw of cynical mannerism, hiding far more than she tells. Thomas Cromwell, the main character, is made out to be a 100% pargon of competence and compassion, and all other characters are given temperatures directly in proportion to how close they are to him. Those he hates are vile, those he likes are good and virtuous. Yet the story is not really told from his perspective, but from Mantel's snarky omnicient voice, making all this characterization absurd as well as historically unbelievable. I assume that the BBC production was able to, thankfully, jettison virtually all the novelistic apparatus and return to whatever of the history was presentable, using only the broadest outlines of Matel's selection of scenes and personalities.

Sunday, May 21, 2017

Sponges Are Animals Too

A brief look at some innovations at the bottom of the animal evolutionary tree.

Of the many great innovations in evolution, the development of multicellular animals ranks pretty high. It was based on the many innovations that had previously generated eukaryotes and their ramifications into protists and other complex single cells. It was a big step to realize (unconsciously!) that, however big and complex one could make a lone cell, (think of a paramecium), possibilities of greater scale and specialized organization were being left on the table. Sponges are the most primitive animal that currently exists. To us, sponges are small and simple. But to their protist brethren, they are giants- vacuum cleaners of the sea that suck up protists and other detritus like so many dust mites.

Sponges have several distinct cell types, like outer epidermal cells, pore cells, and interior collar cells that have the flagella that keep water moving through the pores. Sponges also contain wandering cells that secrete collagen in the intersitial areas- the same protein that keeps our bodies together as well. And they have primitive muscle cells / myocytes, which can cause contractions to close pores when needed, and also the larger openings of some species. These myocytes necessarily have some electrical communication, to coordinate their activities around the osculum. So, not exactly Brad Pitt, but they have quite a bit of anatomical complexity

A sponge.

Key innovations of this (relatively) massive and complex organism were not just the novel molecules, such as collagen, and skeletal "spicule" molecules, but the regulatory apparatus that generates different cell types and keeps them at their work, diligently pumping, or waving, or opening/closing, etc. A recent paper looked at this regulatory system and found that sponges already have most of the special mechanisms that other animals use to specify cell fates and body organization.

Those mechanisms revolve around gene control. In the human genome, about 1% of the DNA codes for proteins- the actual stuff of our bodies. Roughly about 7 to 10% of the genome functions in other ways, principally as regulatory regions, RNA-encoding genes, etc. The rest seems to be junk, more or less. The sponge that has been sequenced to date has a genome with roughly the same number of genes as ours (20,000), in 1/20 the genome size. So there is quite a bit less junk and complexity, but still a very large tool chest.

Particularly, it has plenty of regulatory control, and the researchers explore its use of one hallmark of metazoan gene control- histone modification. While the basic role of histones is very simple- to act like tiny wheels around which the DNA wraps, keeping it both secure and compact- its position also allows it to regulate the access to that DNA by other proteins, especially regulators of expression. Higher metazoans have a dizzyingly complex "histone code", composed of chemical modifications to the positively charged tails. These modifications include methylation, di- and tri-methylation, and acetylation, on lysines at positions 4, 5, 9, 14, 20, 27, 79, and 122 of one of three different histones. Each modification and position means something different, and combinations can mean other things again, all affecting the degree and type of gene activity.

A small part of the Amphimedon queenslandica genome, with DNA positions on the X-axis, and annotation tracks in separate rows. Description and codes below.

One example of their data is show above. They tested the locations of five different histone modifications, (H3K4me3 and similar rows), as well as the RNA polymerase (RNAPII) that is the ultimate target of all the regulation. Also laid along the small segment of the genome (X-axis) are rows (tracks) that describe the predicted locations of genes (bottom rows, purple) and the expression of each location of the genome into RNA (dark and light orange, next rows up). At the very top, under the genomic coordinates, are predictions about chromatin states, based on the histone modification analysis, using knowledge from other (higher) animals. The code for this analysis is shown below
Codes for the top annotation tracks above.

The color codes for inferred chromatin states. "Active TSS" means an active transcription start site, or gene being expressed. "Transcr. at gene 5' and 3'" indicates signatures for boundaries of transcription units, though this is clearly not very precise. "Genic activated enhancers" mark upstream regulatory elements that regulate a local transcription start site, sometimes from far away. "Weak enahancers" mark the same, but less active. The "Bivalent/poised" notations indicate non-active transcription units or enhancers, which may have RNA polymerase parked, but not active. Lastly, the gray annotations indicate states of chromative repression of gene activity which are very important, and regulated by histone modification, but not relevant in this genomic location at the (adult) stage sampled.

A few sponge genes with differential expression in larval vs adult stages. Expression in orange and blue,  and the histone marks (H3K4me3) in purple at top. Genes are in purple at the bottom, complete with their complex exon-intron structure.

Another example of their data shows the developmental difference in a small genomic region between larva and adult stages. The triple methylation of Histone H3 at lysine 4 (H3K4me3) turns out to be the most clearly informative chromatin marker, and comes up reliably at active gene start sites/promoters, where it plays a role in activating transcription.

All this goes to show that the tools and knowledge that have been accumulated over the last couple of decades for the study of model animals like mice, fruit flies, and humans, are also totally relevant for the study of sponges at the base of the animal tree. And in turn, that sponges already had and have complex molecular mechanisms that drive their developmental and morphological complexity, such as it is.

If this study revolved around the histone code alone, it would not have been very novel, since yeast cells share much of this apparatus, and are tenaciously unicellular. But the researchers also delve into several other properties that are more diagnostic of animals, such as the the locations of enhancer elements. This sponge genome can have enhancers over 10,000 basepairs away from the sites they regulate, which allows multiple enhancer cassettes can operate on the same gene to provide complex combinatorial and developmentally variable control. Additionally, the large set of gene regulatory proteins is more reminiscent of the set available in animals, many of which themselves have complex enhancer-influenced control.

The large number of introns (interruptions in the blue coding areas in the diagrams above) is another sign of animal-like organization, and in the sponge turn out to be where many of the enhancers live that regulate genes at a distance. Lastly, the researchers mention that about 60 pairs of sponge genes are similarly paired in other animal species, (i.e., they are micro-syntenic), indicating another level of unexpected conservation over about 700 million years. These are some of the ingredients that molecular biologists are learning are important to climb the organizational ladder to multicellularity.

Saturday, May 13, 2017

Hanging On For Dear Life

DNA synthesis on both the leading and lagging strands is done by an integrated, quasi-stable complex.

At the very heart of our hereditary and developmental lives is DNA synthesis- replication that copies one duplex into two. But each beautiful, classic DNA duplex has two strands, each of which needs to be copied. Not only that, but those two strands go in opposite directions. The one is the complement, or anti-sense, of the other one, and in chemical terms heads the other way. This creates a significant problem, since the overall direction of replication can only go one way- the direction of the fork where the parental duplex splits into two.

Complementarity of DNA. When one strand is synthesized in one direction, the other strand has to be synthesized in the opposite direction.

Replication of one of the resulting strands is easy- the "leading strand" is synthesized continuously from 5' starting phosphate onwards as the replication fork progresses. But the other strand, likewise synthesizing from 5' to 3', must head in the opposite direction, away from the replication fork. It is thus called the "lagging strand". Not only must it go in the wrong direction, but it has to work in pieces, synthesizing a short piece away from the replication fork, and then start over again once more single stranded template has been uncovered as the replication fork progresses. These units of newly synthesized DNA on the lagging strand, which are short and separated before they are later repaired and ligated together, are called Okazaki fragments, for the first person to observe and understand them, Reiji Okazaki.

Lagging strand being made in fragments. A helicase unwinding the fork is shown in gold, and the polymerases are show as beige doughnuts. The lagging strand polymerase has to go backwards, away from the direction of fork progression.

Naturally, DNA synthesis happens best when done on a smooth continuous basis, with as few interruptions and errors as possible. So the complexes assembled at the replication fork are quite stable, and held on by special protein clamps which surround the DNA like little doughnuts. An interesting finding was that in addition to the leading strand DNA polymerase, the replication complex also contains the polymerase used for lagging strand DNA synthesis, even while they are heading in opposite directions! This obviously helps keep the whole process orderly, but is a little hard to envision, since in DNA terms, the two polymerases can be hundreds of base pairs apart as they chug along their separate tracks.

More detail on the replication complex. The two polymerases (yellow) doing leading and lagging strand synthesis are actually tethered into one master complex (green), and the lagging strand polymerase, once done with one Okazaki fragment, is yanked back to start the next from near the replication fork. The clamps (red) are loaded by the green central complex in advance of each lagging strand re-initiation.

A recent paper investigated the notorious stability of these complexes. If you dilute an operating replication complex to homeopathic concentrations, the proteins will still stay on track, and continue synthesizing DNA. That indicates that the proteins do not spontaneously fall off by diffusion during their work, or even during the intricate switch between initiation points that is required in lagging strand synthesis. On the other hand, if you add inactive enzyme to ongoing replication complexes, they will grind to a halt, indicating that some kind of polymerase enzyme exchange is going on. What gives?

These authors used a microscopic method and fluorescently labeled polymerases to look at this question in detail. They were able to use a flow cell to stage replication as a visual process, watching a single molecule of DNA extend over time downstream as it was synthesized. With fluorescent polymerase, the progression is even clearer, and a hangup was observed at the first and second Okazaki fragment boundaries (C, the middle lines), since they had not added the ligases that could resolve those boundaries and free up the polymerase to return to the replication fork for another round.

A single DNA molecule being replicated, over time, to longer lengths from a tethered end. When the polymerase is fluorescently labeled, (bottom, purple), it shows the edge of the fork (top) and also the Okazaki fragment boundaries (lower lines).

When a mixture of two different fluorescent polymerases is used, (green and purple), they seem to exchange on the replicating complex, as it goes forth.

But when they used a mixture of two polymerases with different fluorescent colors, the interesting thing was that the colors changed while underway. A fork that started with purple polymerase changed suddenly to green, and then later back to purple. This is very odd for a stable complex. And if they fired a laser at the complex, bleaching its fluorophore permanently, the fluorescence eventually returned, indicating that a new polymerase molecule had hopped on and replaced the original one.

Lastly, if the progressing polymerase is zapped with permanently bleaching light, other fluorescent molecules take its place relatively quickly as the replication proceeds. Bottom is just a graph of the fluorescence intensity from the upper single molecule image.

The replication fork is thus a little like a basketball team. Substitutions can be made while the action is going on, but there can never be less than a full complement of players on the floor. The complexes are stable, but only if there is no other polymerase around. If there are, a new polymerase can jump into the existing fork / complex. It is a clever design that allows resolution of stalled complexes and defunct enzymes, while insuring that the process of replication goes forth as relentlessly and stably as possible.

  • GOP vs not just medicaid, and exchanges, but medicare too.
  • And then, naturally, lies about it.
  • Please stand up for net neutrality.
  • Facts, Schmacts.
  • Puerto Rico in the hands of a very few.
  • Timeline of the fraudulent firing.
  • Our president: "James Comey better hope that there are no "tapes" of our conversations before he starts leaking to the press!"
  • Krugman on our new, great, GOP.
  • Inequality diminishes our society.

Saturday, May 6, 2017

Thinking in Symbols, Speaking in Tongues

Theology, schmeology. Jimmy Swaggart's musical, tribal, shamanistic approach to religion.

What is church without music? Probably not much fun. Even Islam has smuggled in a musical tradition in the form of the call to prayer, which is often a virtuoso vocal performance. The important role music has in most religions is a sign that their gatherings are social bonding events, not scientific conferences. One of the clearest instances is the televangelism of Jimmy Swaggart, still going strong after 45 years. At its core are his amazing piano and vocal abilities, combined with a very tight band and other featured singers. A cousin of Jerry Lee Lewis, his talent was recognized early on, but instead of joining the recording industry, he built his own evangelical empire, whose broadcasts are heavy on the music, and light on the theology. The music is an extremely comforting, a sort of bluesy, (this is from Louisiana, after all), cross between Lawrence Welk and African American Church gospel. The focus is on praise and succor from god ("Take my hand, precious lord", "Jesus, use me", "I'll never be lonely again", "Sheltered in the arms of God", "What a friend we have in Jesus").

It is a little reminiscent of the gatherings of DeadHeads, finding a comforting sacrament of friendship and love in an endless bluesy/country jam, heavy on the sentiment. Yes, the Pentecostal / Swaggart version is a lot more conservative, and its love doesn't come from a puff of smoke, but the equally vaporous triumvarate of holy spirit, Jesus, and god. What theology there is is virtually stripped of any sense, however, consisting of archetypal references to give the whole jam more emotional power. It is, essentially, the power of shamanism.

For example, the creed of the ministry is:
“Dear Lord Jesus, I now realize that I am a sinner. I accept the fact that You died for me on the rugged Cross of Calvary. I now open my heart’s door and receive You as Saviour and Lord of my life. Please take full control of me and help me to be the kind of Christian You want me to be. Amen.”

Why "rugged"? How can Jesus take control when he no longer exists, and we do not know where he is or what he wants? OK, call me skeptical! Anyhow, the answer is always prayer, and the Swaggarts claim "Without a daily communication with our heavenly Father, we will only go so far in this Christian life, which won’t be very far, spiritually speaking." Prayer is the cell phone call to god, keeping Him up to date with what we want, and telling us what He wants. What does this really mean? It means one's conscience is going to do the talking, (at best), and its quality is going to be the tenor of our supposed talk with god. This might expain the problems that Swaggart himself has had in the sin department. It also means that anyone who can infiltrate our conscience and purport to tell us what god wants may end up with a great deal of control over our actions. For example, the ministry offers a wide range of "The truth about..." videos, telling the flock why Mormons, Catholics, Muslims, even Seventh-Day Adventists, are wrong and bad. The "full control of me" formulation could be taken as a little sinister, not just to keep the tribal boundaries clear, but to milk the flock for money, and drive a highly conservative political message that is in many respects rather uncharitable.

And control is surely what is going on here. The bonding is very strong and social, starting with the music and the TV shows, but extending to more intense "Camp Meetings" and other events around the country. Advertisements for youth events gush about how attendees feel the presence of the lord during the event. Theoretically, god is supposed to be everywhere, not anywhwere in particular, so these charismatic settings and climaxes are a clear sign of shamanism, not of any coherent theology, let alone philosophy.

The magazine, aside from advertisements for a rich assortment of ministry products, is full of word-salad theology, with submission urged to the will of Christ, or other spirits, so that the "Blood of the Lamb" can wash over the sinners in the pews, cleansing them of their sins. Sermons and blessings are "anointed", messages are "Spirit-baptized", and the "Powers of Darkness" are fought. This church is the "Bride of Christ", and good believers have "eyes of the spirit" to see "the things that lurk in darkness". The whole thing is a work of art, really- a poetry of metaphor which is highly meaningful without actually meaning anything concrete or real in this world. But when it comes to the prices, things are naturally far more explicit "Your price just $10 each".

Televangelism remains a remarkable phenomenon, drawing on the implicit cultural assumptions in favor of Christianity, on blues and gospel music, and on the power of personal magnetism and group bonding to comfort the lonely and lost. If the message were stripped down to the hymns alone, it would be a positive social force.
"If God Is Dead Who's This Living In My Soul?"

  • Our government, regular people not invited.
  • Even the National Review wonders about inequality. And then concludes that it should be made worse.
  • GOP busy making things worse.. Things which clearly could be better.
  • Making Afghanistan great again.