Saturday, March 29, 2014

Jesus & reality, part three

Jesus seems to have been real, but the diagnosis would be .. more than a little bonkers. More from Bart Ehrman's "Did Jesus exist?"

In part 1, I considered the theory that Jesus as a historical figure did not exist at all and was made up out of whole cloth, drawing on the rich archetypes, mistold tales, and inflated belief that characterize religion generally. Then in part 2, the opposing view, based on Bart Ehrman's book "Did Jesus exist" was presented, concluding that Jesus really did exist historically, though that is far from implying that all that was later written about him was true. The truth is somewhere in the middle, between complete fabrication and a kernel of truth surrounded by many-colored and textured swaths of fabrication.

The later parts of Ehrman's book touch on the next logical question- if we can use critical historical methods to conclude that Jesus really existed, what else do they allow us to conclude with confidence about him?

The central point of this analysis is that Jesus was a apocalyptic preacher, in the template of John the Baptist. This is a very significant conclusion, since this was a relatively small group in the community of his time. The Jewish community of Palestine had about five noticeable social-theological groupings, as Ehrman and others present it.

First were the Saducees. This was the establishment, ran the temple, and was the economic elite. They collaborated with Rome, and were thus thought traitors by more orthodox Jews, not to mention theologically impure, permissive, corrupt, etc.

Second were the Pharisees. These get plenty of airtime in the gospels, as they were more orthodox than the Saducees, sticklers for Jewish law, kosher, etc.. One might think of them as the hat-and-locks wearing set of the time. Jesus makes lots of points off them, but who killed him? The Saducees, as discussed further below.

Next was the Essenes, the ascetics whose Dead Sea scrolls have provided such trove of knowledge about their time. They were an even more extreme off-shoot of the Pharisees, and might be thought the mystics of the society, segregating themselves in the desert, (for the most dedicated), seeking purity, celibacy, poverty, silence, and community (men only!). They thought the temple, as run by the Saducees, hopelessly corrupt and impure. They certainly didn't have any role in running things, and seem to have strongly messianic hopes.

The last substantial set mentioned by Ehrman are the revolutionaries, (the Zealots), sort of the heirs to the Maccabee tradition. This was a more political outlook, that chafed strongly under the boot of Rome, and thought that the Jewish land was defiled not so much from lack of fidelity to the Levitical and Mosaic laws, as from lack of their own laws, and own government. This class would eventually lead the revolt of the later first century, which prompted the final destruction of the second temple by Rome.

Last is the apocalypticists. Ehrman paints them (as exampled by John the Baptist and Jesus) as quite different from the Essenes, let alone the other groups. But I have to say that the more I read about the Essenes, the closer these two groups appear. While the Essenes were very secretive about their teachings and mostly kept to themselves, the teachings were largely the same- a messianic assumption that someday, each would get what was coming, and that some kind of resurrection would occur. Each were strongly moral and focused on service to others. Each was anti-family, almost pathologically so, preferring to live in like-minded community. So it looks to me as though John the Baptist and Jesus could be thought of as Essenes who took the teaching outwards, to the people at large, and even challenged the Temple and its sponsors directly.

A side-note of interest was their attitude towards morality. The Essenes and apocalypticists were intense moralists and demanders of repentence. But the point was not to make a more pleasant or successful society for us all to live in. No, it was to get right with god before the judgement day, lest you be sent off to everlasting torment in hell. Family values it was not.. the exact opposite, actually. But somehow, subsequent generations have so bowlderized and cherry-picked it that, naturally, it now means that open carry is a Christian commandment, plus whatever else one favors.

This all was kooky enough. But Jesus took it up a notch by predicting that the Kingdom would come soon. In his lifetime, or in that of this hearers. And that his apostles would be the 12 kings, sitting on 12 thrones of the 12 tribes of Israel. This implied that he himself would be the top King.. the new David.

Ehrman makes a highly significant surmise that this plays right into the Judas story. What was his notorious "betrayal"? Jesus couldn't have been hard to find, with an entourage and all, staying in a city he didn't know very well, speaking in the public square to crowds. No, the betrayal had nothing to do with location, but everything to do with theology and politics, since if Jesus gave his disciples a secret teaching that they would inherit the kingdoms and he was to be the messiah and future super-king, then this was something both the Saducees and the Romans might want to hear about.
"Jesus, of course, did not understand his kingship [cause of his conviction and execution] in this way. He was an apocalypticist who believed that God would soon interfere in the course of human affairs and destroy the Romans, and everyone else who opposed him, before setting up his kingdom on earth. And the Jesus would be awarded the throne."
Needless to say, the kingdom never came, Jesus never returned, and never became king (except in our hearts!). Jesus himself was evidently somewhat surprised by the turn of events which left him hanging, so to speak, without god's intervention. His followers never expected him to resurrect, as shown by their complete lack of vigilence over his body, but came up with that story later on to rationalize a commitment and ministry whose rationale had otherwise been buried.

Which gets us to the theme of this post, which is that the historical record, as far as we can make it out with any reliability, indicates that Jesus was real, and was clinically insane. He believed not only in all the normal crack-pot things that were prevalent in his time, and were concentrated within the Essene sect. But on top of that he believed he was the ONE, the future king, and judge of all, etc.. etc.. When we see people in our day calling themselves Jesus Christ, or the postapocalyptic king, who will separate the sheep from the goats after the resurrection, etc.. etc.. we typically call them insane.

"But perhaps even more interesting are the implications for the secular stagnation hypothesis, which holds that we are in a long-run stagnating economy because of inadequate demand. Is it a coincidence that the secular stagnation hypothesis is being revived exactly when income inequality is accelerating? If a higher share of income goes to the wealthiest households who spend very little of it, then perhaps these two trends are closely related."

Saturday, March 22, 2014

Memory on the knife's edge

Amyloid-type proteins may be essential for long-term memory, even as they risk destroying it.

As we learn about the genetic aspects of many diseases, one is prompted to ask.. how could susceptibility to such a conditions ever have evolved? Susceptibility to Alzheimers and other degenerative dementias is a case in point. If they are caused by amyloid, or prion-like proteins that aggregate excessively, thereby destroying their cells and tissues, then the obvious question is: what do they normally do, and why hasn't this tendency towards aggregation been more stringently policed by evolution?

A recent paper on memory in flies (reviewed) offers the theory that in the case of memory, proteins that aggregate are central to the ability to form long-term memories. Aggregation is a feature, not a bug, and the only problem would then arise when this system works too well, or with abnormal partners.

Following the general trend in brain science, memory is being studied as, and found to be, a physical phenomenon. As far as we know, it consists of the persistence of physical and functioning synaptic connections among neurons that are re-inforced by use. The vast mesh of synapses connecting neurons in the brain form engrams that can be read back out upon partial stimulation of the encoded pattern. And memories are quite resistant to brain degradation- when symptoms of Alzheimer's appear, vast amounts of brain tissue are already gone. On the other hand, a specific injury to a key area can instantly destroy a lifetime of memory, the ability to form new ones, or other functions.

How do synapses work? Neurons have to grow if we are to learn, and they have to selectively connect with their downstream partners, the dendrites, cell bodies, and axons of other neurons, via synapses. All these are molecular processes, and one can imagine that if we are to have durable memories of anything, that molecular process has to have the contradictory features of durability as well as reversibility. We forget most of what we have ever experienced, and our sleep seems to be some kind of clearance and consolidation process, keeping some, and throwing out the rest. However that works, the synapse is well-known to be the focal point of memory, and protein synthesis has long been known to be required for new synapses to be made.

The fruit fly, despite its lowly intellect, has been an excellent organism to study neuronal activities, and even cognition and learning. In this case, prior work has identified one protein, CEPB, as one that is essential to memory durability. Without it, synapses still form, but then die off within a day of a training regimen, corresponding to the fly's inability to remember what it was trained for.
"Interestingly, ApCPEB [name of this gene/ protein in the sea snail] and Orb2 [the gene name in the fly] form self-sustaining amyloidogenic oligomers (prion-like) in response to the neurotransmitters serotonin in Aplysia and octopamine or tyramine in Drosophila. More importantly, the oligomeric CPEB is required for the persistence of synaptic facilitation in Aplysia and for the stabilization of memory in Drosophila. These observations led us to propose that the persistent form of memory recruits an amyloidogenic oligomeric form of neuronal CPEB to the activated synapse, which in turn maintains memory through the sustained, regulated synthesis of a specific set of synaptic proteins."
A second protein/gene was also found in this process, called Erb2. Mutations in either Orb2 or Erb2 do not affect initial learning, but destroy the fly's ability to remember a day afterwards what it would otherwise have remembered, as shown by unmutated control flies. The two proteins bind to each other, and Erb2 promotes the oligomerization of Orb2, which it to say, it helps it form long strings or globs, as one sees in magnified, extreme form in amyloid plaques, tau tangles, and the other hallmarks of the Alzheimers and related diseases.

The present researchers add a little to our knowledge by finding that Erb2 performs this feat of altering the behavior of Orb2 by getting a third protein, Lim kinase, to phosphorylate Orb2. Phosphorylation is a very common way to modify and regulate the activity of proteins, so this is not shocking. It is also quite reversible, in this case by yet another protein, protein phosphatase 2A. Erb2 apprears to be regulated itself by the state of the synapse, so it is a leading candidate to transmit the establishment / maintenance signals from neighboring cells or firing rates to the activities of Orb2.

But what is the point of this interaction, phosphorylation, and oligomerization? Orb2 interacts with a variety of other proteins active in protein translation, and seems to promote the various translation events needed for building a synapse. "The Cytoplasmic Polyadenylation Element Binding (CPEB) proteins are a family of RNA binding proteins that regulate the translation and subcellular distribution of a specific set of cellular mRNAs in various cell types including neurons." This is the hypothesized mechanism by which the signals transmitted by Erb2 to alter the behavior of Orb2 end up growing and stabilizing the synapse.

What is their data? First, they do a general assay for proteins that stick to Orb2. This nets over 50 proteins, many of which are involved in translation, like eIF4E, EIF3-S4, etc. Others are specific to the synaptic location, like Snap25 an Vap33. And one was Erb2, which they also saw stablized one form of Orb2, a tip-off to an important function. Then they show that Erb2 promotes oligomerization of Orb2 in vitro as well as promoting its collection in tiny physical globs in fly neurons.

This is typical data, and not very user-friendly. But it shows that Erb2 (here called Tob) and Orb2 interact, and that this interaction is promoted by neuronal activity, and that the resulting Orb2 protein complexes are amyloid-like. They used an antibody to Erb2 to collect anything sticking to it in a soup made from ground-up fly heads. They had used the chemical tyramine (top) to put the flies into neuronal overdrive before killing them. The matrix is full of controls: with tyramine, without, and with the anti-Erb2(Tob) antibody, or without (using "pre"-immune serum lacking the antibody). Then they ran all the proteins out on an electrophoretic gel that separated them by size (biggest at top), and stained the result with a separate antibody that binds to the Orb2 protein (in fact two of them: versions against only one of its forms (Orb2b) or against both (Orb2a, b)). This way, they can see only the Orb2 that was "brought down" by the Erb2 protein.

You can see that the Orb2 protein comes in two forms- a small monomer, and the larger dimer and higher oligomers, as indicated at the 107 kDa (aka molecular weight) and higher levels. Part B shows the whole experiment redone while treating the collected proteins with 2M urea, which is denaturant that blows up any conventional protein complexes. But it does not dissociate these Orb2 oligomers; evidence that they are very strongly associated as is typical for amyloid-type proteins.

Similar work explores the phosphorylation of Orb2 by Erb2, and its regulation by the protein phosphatase 2A and Lim kinase. This phosphorylation dramatically alters the lifespan of Orb2, from 1 hour to 24 hours or more, which is again a sign that its amyloid-like character can be specifically regulated.
"PP2A, an autocatalytic phosphatase, is known to act as a bidirectional switch in activity-dependent changes in synaptic activity. PP2A activity is down-regulated upon induction of long-term potentiation of hippocampal CA1 synapses (LTP) and up-regulated during long-term depression (LTD). Similarly, Lim Kinase, which is synthesized locally at the synapse in response to synaptic activation, is also critical for long-term changes in synaptic activity and synaptic growth."

Finally, they show data for the theory that Erb2 (Tob) is specifically needed in vivo to support long-term memory, not short-term memory. The test is a little sad. They place male flies with unreceptive females. Normal males get the hint in a hurry, and quit courtship attempts within 5 minutes. And normal males remember that female and her brushoff for several days, as shown in the controls in the two graphs at left. Red is the trained males, with suppressed (learned lack of) courtship. The "UAS-TobRNAi" and "201:Gal4" are partial versions of the transgenic construct, which is fully present in the far-right graph, and which expresses a sort of anti-Erb2, (by way of RNAi), when engineered into these flies. When the genetic alteration is fully present (right), the males have totally forgotten their training at 24 and 48 hours.

So, while the steps are small, these researchers have dug up some evidence for the idea that a central molecular component of memory in fly neurons, which has relatives in all animals including humans, has a regulated interaction with signalling molecules upstream that induce it to form aggregates that resemble those formed far more extravagantly by the culprits in degenerative brain diseases like Alzheimers. These aggregates have the virtue of longevity, though how they act on their downstream targets remains rather vague. Which may explain why those proteins susceptible to aggregation have been kept around in evolution, despite their dire risk when aggregation gets out of hand.

One might well ask a follow up question whether this Orb2 protein resembles in its sequence any of those known to go pathogenic in brain disease. I think the answer is no, but it is known to interact with an actual amyloid protein APLP1 in the mouse system, which provides a logical connection to a role in creating the kind of goop / plaque that can run amok in our heads. What those amyloid proteins are originally there for remains unsolved, but probably relates pretty closely to this synaptic establishment and maintenance system.

Saturday, March 15, 2014

Jesus & reality, part two

The opposite view, supporting the historical reality of Jesus, from Bart Ehrman.

In a recent blog post on the Jesus as myth theory, I reviewed a book by Robert Price who tentatively holds the myth position (i.e. that there was no historical person with the name or characteristics of Jesus), and puts the best case he can for it. But it is far from the mainstream, and Bart Ehrman, an equally if not better-versed(!) scholar recently wrote the opposite position in "Did Jesus exist?", kindly linked by a commenter on that previous post. Ehrman's is the better organized and better argued book, and makes the more pursuasive case. Indeed he brings up some very interesting topics, like the traces of other languages in the Greek of the gospels, and the Jewish understanding of a messiah. But there are some interesting themes that come up from the synthesis of both positions.

Ehrman offers numerous strands of evidence that Jesus was a real, historical person. They include the fact that the mythicists mis-represent the evidence of Paul. Paul did indeed quote Jesus's sayings, about three times. It is not much, but more than the "none" claimed by the mythicist position. And more importantly, Paul clearly says and knows of Jesus as having been a true person, killed by crucifixion. Paul says he met with two of the apostles, even though he only met Jesus in a vision. So at least Paul is clearly convinced of Jesus's reality, which was incidentally as true prior to his conversion as it was after, since his earlier opposition to the Christians was (Ehrman speculates) due to the traditional Jewish position that the messiah would be a powerful king, not someone nailed to a cross by the Romans. In either case, a real person was the object of scorn or adoration.

Secondly, everyone else who reports anything about the Jesus movement likewise regards Jesus as a real person, whatever they think about it. Ehrman cites Pappias, Ignatius, Josephus, as well as the gospel writers, Paul, the non-Pauline letters / acts, and all the later church leaders. Even the gnostics, however way-out their theology, didn't say he didn't exist, only at worst that he seemed like a real person, while actually being a god. So that is broad agreement, among those we know anything about, that the core of the Jesus tradition was of one mind on this matter.

Thirdly, Ehrman puts quite a bit of credence in the gospels as historical sources, at least to the extent of, firstly, agreeing on the historicity of Jesus, and secondly, of integrating and drawing on what appear to be numerous oral and written sources in the movement (Q, sayings, M, L, and Luke's claimed numerous other sources, etc.) that were by that time, of about 40 to 60 years after the putative death of Jesus, rather separate, even conflicting, traditions, each, however, agreeing on this central point. Some even carry traces of their source in the Aramaic language, which is significant in dating their origin well before the transition to the Greek of the gospels, back to the Palestinian Jesus movement.

There is a great deal more, of course, but that is a brief capsule that indicates that, in any normal historical sense, one has to accept that the bulk of evidence, despite its scanty & distant nature, supports the historicity of Jesus.

Where I would bring back Price's work is in his critique of the gospels as anything like historical documents. While Price's contention is that the midrash-ic and mythic nature of the gospels point to the entirely mythic nature of their protaganist, one can easily take a less extreme position. Which is that the failure of Paul to mention much of this material, (which Ehrman subjects to extensive defense, not entirely successfully in my view), its so-often unbelievable nature, and its heavily templated nature, based on passage after passage of the old testament, indicate that most of it was made up by the later Greek authors (and their various oral sources) who followed the time-honored practice of classic historians of putting words in people's mouths, presenting likely scenarios, and generally creating what they thought was the case, rather than documenting what was actually the case. In this case also heavily larded with their own theological agendas, which are so clearly different among Mark, Luke, and John. After all, no one had tape recorders. The problems of accurate history are truly enormous in this kind of setting.

Stories about Jesus multiply and expand in fabulousness over time. When traced back, do they hit the Y-intercept at zero, or at some point of positive factuality?

Price also makes a point that Ehrman expounds on at some length, which is the rapidly inflating nature of Jesus over time. At first, he had a brother, taught in the Jewish tradition, was thought a wise person, maybe a healer and philosophical deviant, and was finally killed by the Romans. Then he became the Jewish messiah, then rose from the dead, then the redeemer of sins, then the redeemer for all people, then the son of god, then literally born of a virgin by the direct seed of god, and eventually co-substantial with god, etc. Paul didn't give a fig for any birth stories. That mythology, among so much else, was clearly added later on. There is no question that the vast majority of the later understandings, creeds, and traditions- as is usual in any social movement, let alone a religion- had nothing to do with the originating facts of the matter, in any historical sense, versus in an archetypal sense.

So we are left with a more narrow debate, if one is interested, on the nature of the original Jesus movement, and, if one wants to engage in science fiction arguments, whether the various miracles attributed to Jesus happened. The Jesus Seminar is, to me, looking a bit better on that front, throwing out the mythical bathwater, while retaining something of the oral traditions that may or may not have flowed from the person or at least immediate time period of Jesus. Yet it should still be said that they are groping in the historical dark. Making the case for the bare historicity of Jesus is a far different matter than judging every jot of the gospels and other traditions. Ehrman writes extensively of the novelistic (historical novel, in this case) nature of the gospels, partaking both of invention and oral transmission, little of which itself originated in fact. But what was the proportion?
"Once we move from the fact of Jesus's existence to the question of who he really was, we move from the remarkably firm ground of virtual historical certainty to greater depths of uncertainty." -Ehrman

What is the significance of all this? The mythicist position is a bracing and useful one, in the spirit of offering a counter-hypothesis to the conventional wisdom. But it does not withstand sustained scrutiny. I might add that Robert Price has another skeleton in his closet, which is flagrant denial of climate heating. It makes one wonder about his critical judgment in general, despite his great knowledge and humor.

Saturday, March 8, 2014

What is the oldest cell?

Some comparisons of the most ancient lineages of life- Archaea, Bacteria, and Eukaryotes.

Take your mind back.. way back.. four billion years back. Now fast-forward over chemical evolution, or whatever happened to cause the origin of life, a few hundred million years, on to the first cellular life. Now stop- what was that? A recent paper argues from a novel analysis of protein domain lineages that, of the major domains of life, the Archaea (also called archaebacteria) are in some respects closest to that original form, and that the other domains- Bacteria (also called eubacteria) and Eukaryotes- are more distant. (Apologies that biologists use the term "domain" in these two very different senses.) This is an interesting hypothesis, since up till now, it has been indeterminate which of the two bacterial lineages came first, or at least, most resembles the ur-life form, also called the progenote.

Tree of life, deep edition. Note that while eukaryotes arose from Archaea, (with plenty of later additions from Bacteria by engulfment / symbiosis, but that is another story), the root between Archaea and Bacteria as shown here is indeterminate. Which was really first, or is that even a reasonable question to ask? The current paper also disputes that Eukaryotes derived from Archaea as diagrammed, and puts Archaea at the root of the tree.

Non-biologists may not get excited about the distinction between Archaea and Bacteria, but molecular biologists regard it as the most fundamental division of life, far more consequential than vertebrates / invertebrates, plants / animals, etc. All of the latter you can see in the little brown stubs far to the right of the diagram above. In molecular and deep phylogenetic terms, they don't contribute much to the diversity of life.

The Archaea / Bacteria division was only recognized relatively recently, however, since the nature of Archaea was not appreciated until the 1970's when ribosomal RNA began to be sequenced. It provided the first primitive molecular sequence that was common to every single form of life and thus provided a metric of diversity and geneology. The great American microbiologist Carl Woese labored to gather these sequences from obscure organisms and bacteria of all sorts. He made the shocking discovery that there were "bacteria" out there that were very, very different from the usual run of laboratory bacteria- the E. coli and various other disease-causing and easily-cultured bacteria that were the staff of biology since Pasteur. When he plotted out the sequences, these "bacteria" had ribosomal RNA that was a little more like animal sequences than bacterial, but not terribly similar to either. They weren't from another planet, but they were different enough that he took the very bold step of claiming an entirely new domain of life, co-equal with the heretofore only domains of life, Bacteria and Eukaryotes.

He named them Archaebacteria, on a hunch that they had something important to say about the origin of life. This name has subsequently been shorted to Archaea, so that the traditional bacteria can just be called Bacteria. These Archaea look like Bacteria, however- they are the same tiny cells whose wonders are not apparent from their looks. They are super-diverse, living in all sorts of environments from the coldest to the hottest known. They have phenomenal metabolic diversity, creating the methane in our guts and living off rocks, sulfur, and other obscure chemicals. Some have a primitive form of photosynthesis. They are typically sensitive to oxygen, a sign of their preference for a world predating the oxygenation of the atmosphere about 2 billion years ago (and making them very difficult to culture).

They also share most of their informational machinery (transcription, translation) with Eukaryotes, indicating strongly that Eukaryotes derived from Archaea that later engulfed bacteria (which eventually turned into mitochondria and chloroplasts) that provided some of the remarkable resources, both genetic and metabolic, for the eukaryotic triumph over the macroscopic world.

But ribosomal RNA, as convenient and informative as it is, has some problems. It is only a single, if large, molecule, among the thousands of other genes an organism has, and its sequence is somewhat inaccurate as a "clock" for molecular evolution. Few other sequences, such as those encoding proteins, are as completely universal among all life forms, however. The authors of a recent paper take a broader approach to the question of sharpening the universal geneology (or, tree of life) by treating whole complements of proteins and their domain, or "fold" sub-sections as geneological markers, testing which protein domains arose when, and which were lost in various lineages.

This gets around the issue of aligning individual sequences, to some extent, taking a wider lens view of the evolutionary process. A view that is well-suited to this question of the ultimate priority of the most ancient life forms. Protein domains / folds have been generated and lost quite frequently on this time scale, though there are core domains that are universal over all life forms. Eukaryotes are particularly prolific in generating new protein domains. About 3% of protein domains are unique to primates, for instance, though this may have as much to do with sampling & investigation bias as with reality.
"In fact, recruitment of ancient domains to perform new functions is a recurrent phenomenon in metabolism."

A protein with two domains. This one binds to DNA. The domains fold independently, have structure that is distinct from other domains, and can be easily linked, making them easy to re-shuffle in evolution, hooking functions together, leggo-like.

The authors assembled a compendium of about 2400 protein domain, or fold "families" from 420 sequenced organisms of all kinds, and used well-known methods to arrange them into trees based on their occurrence in the individual organisms (though sometimes a fold might be missed even if present, if its sequence diverged from its family consensus pattern too far). The gain and loss of such folds is a particularly powerful method of lineage analysis, giving more information than the comparison of sequences can, if those sequences are distant, with all the problems of alignment, assumed modes of mutational change, etc. Thirteen of their folds were present in every single organism, and 62 more were recognizably present in 95% or more.

A Venn diagram showing the distribution of fold families among the three domains of life, whether shared or not. Note than a large core is shared by all life forms, while Eukaryotes take the prize for the development of new protein domains, despite originating after the divergence of Bacteria and Archaea.

"To determine the relative age of FF [fold family] domains in our dataset, we reconstructed trees of domains (ToDs) from the abundance and occurrence matrices used in the reconstruction of ToLs [trees of life]. The matrices were transposed, treating FFs as taxa and proteomes as characters. The reconstructed ToDs described the evolution of domains grouped into FFs and identified the most ancient and derived FFs. ... Specifically, it considers that abundance and diversity of individual FFs increases progressively in nature by gene duplication (and associated processes of subfunctionalization and neofunctionalization) and de novo gene creation, even in the presence of loss, lateral transfer or evolutionary constraints in individual lineages. Consequently, ancient domains have more time to accumulate and increase their abundance in proteomes. In comparison, domains originating recently are less popular and are specific to fewer lineages."

The next diagram shows the phylogenetic tree they deduce from all this data, with time along the horizontal axis, and species ordered up the side. The two trees were created from the same data by slightly different methods. Note how in both of these trees, the Eukaryotes (green) split from the Bacteria (blue) only a short time after the Bacteria split from the Archaea (red). The lavender arrows are mine. Both trees also show (the numbers, which are percentage of time their simulations came out the same way) that this split is relatively less clearly supported than some of the other major divergences.

Author's phylogenetic trees.

Returning to the Venn diagram, the Archaea-only group of folds is tiny, and does not seem particularly ancient, even though their trees put Archaea first. The hypothesis is that the other groups (The BE and AB (or AE) groups) generated far more protein diversity later on, whereas the Archaea did not, indeed losing quite a bit of the original complement of protein domains. In this way, Archaea end up resembling the progenote somewhat more than the Bacteria that diverged from the progenote simultaneously, but were more active in later evolution, in molecular terms.

Both the Bacteria and Archaea took the streamlining route in evolution, casting off quite a bit of machinery, focusing on small-ness of size and specialization of metabolism. The Eukaryotes, in contrast, branched off from the Archaea after the Bacteria did, and retained a good deal of the transcriptional, replicational, and translational machinery that the bacteria particularly lost or reduced (at least, by the conventional theory). And Eukaryotes in general took the opposite route with respect to streamlining, retaining molecular diversity & sloppiness, metabolic generalization, great physical size, gaining sex as a means to more effective evolution, and gaining the final upper hand with the endosymbiosis of two different Bacteria- the proto-mitochondrion, and the proto-chloroplast. These properties led eventually to multicellularity and the invasion of land. It was (depending on what one values!) a triumph of complexity and cooperation over brutal, cost-cutting competition.

The authors plot their organisms in an "economic" space. This is based on two scores- the number of protein folds occurring that are unique (economy), and the redundancy of protein folds occurring in each organism (flexibility), with the ratio between them serving as the last measure (robustness), which is, frankly, sort of an amplification of the flexibility score. Obviously, Eukaryotes will do very well in these measures.

Since in the author's scheme the AE goup of domains appeared very late, and the BE group was the first to branch off from the universal ancestors, they hypothesize that Eukaryotes branched off from Bacteria, and their informational-class resemblance to Archaea is due either to later lateral transfer, or to comprehensive loss in many Bacterial lineages (though the latter is very unlikely). To me this seems hard to swallow, as this class of functions is particularly unlikely to be transferred wholesale between organisms.
"Informational FFs were significantly over-represented in the AE taxonomic group and appeared during the late evolutionary epoch. This suggested that both Archaea and Eukarya work with a very similar apparatus for decoding their genetic information, which is different from Bacteria. However, as we explained above, all these innovations occurred in the late epoch (nd>0.55), highlighting ongoing secondary adaptations in the superkingdoms. In comparison, the BE taxonomic group was enriched in metabolic FFs (Figure 2A). This toolkit was probably acquired via HGT [horizontal gene transfer] during endosymbiosis of primordial microbes rich in diverse metabolic functions."

This idea would significantly alter / extend the well-known endosymbiotic hypothesis, in that the Eukaryotic precursor would presumably have to acquire not only the proto-mitochondrial cell, but also the proto-nuclear cell that provided these informational functions, from Archaea. It is hard to know what would characterize this original precursor at all ... why not just take the crucial Archaeal additions as the benchmark of the whole lineage? Wouldn't the large protein repertoire commonality between Bacteria and Eukaryotes be better accounted by the known endosymbiosis than by this proposed lineage derivation? The authors have very little to say about what this early Eukaryotic stem organism might be, other than that it was quite advanced and had escaped the brutal streamlining that characterizes both the Archaeal and Bacterial lineages. Thus it, whatever it was, might represent the closest thing to the progenote, in some respects, before the vast elaborations that have been added in that line since, and the massive losses that took place in the other two domains.
"Thus, the primordial stem line, which was already structurally and functionally quite complex, generated organismal biodiversity first by streamlining the structural make up in Archaea (at nd = 0.15), then by generating novelty in Bacteria (nd = 0.26), and finally by generating novelty and co-opting bacterial lineages as organelles in Eukarya (nd less than 0.55)". [nd is their measure of time, from beginning (0) to now (1).]

In the end, the progenote is heavily veiled from our view. The common repertoire of sequences common to all cells is small, (484 fold families in this analysis), and not enough to model what it may have been like, other than to say it had a membrane, functioning metabolism, and informational / genetic system likely similar to what archaebacteria have today. It may have been a good deal more complex, depending on how one interprets the intervening events- as ones primarily of loss, or ones of gain.

Saturday, March 1, 2014

Jesus: miracle, midrash, or myth?

Did Jesus really exist? A review of Robert Price's "The Christ myth theory and its problems".

What?! Doesn't everyone agree on this most central historical fact? The fact from which our very historical time is measured? Indeed, wasn't Jesus blond-haired and blue-eyed? Well, no, and the reason is that the evidence for the existence of Jesus in any historical sense is extremely thin to non-existent. Biblical scholar and professor Robert Price weighs the evidence, and comes down very tentatively on the myth side of the equation. I will be following his analysis, more or less, below. But the fact of the matter is that we have so little to go on that either position is equally valid, and equally tenuous- Jesus might have existed, might not ... no one really knows. Indeed it would be accurate to say that we know that the Jesus we know is mostly myth. The only question is where in the low figures the percentage of reality is: 20%, 10%, or 0%?

The Jesus as myth hypothesis posits that the gospel writers were furiously filling an entirely blank biography with an amalgam of Old Testament rewrites, (similar to the Jewish practice of midrash), Homeric themes, and new archetypal and theological material. Whether the subject was historically real or not was, as frequently in the ancient world, (and today!), not of the highest concern, once the community had fastened onto its inverted Jewish Messiah story. Even today, the insistence of the political right wing in the US on its "facts" is an object lesson in real-time myth-making. And the Messiah itself was such a common theme in this tumultuous time, both in the Jewish world, and in the Roman world generally, that a miracle-working, dying and rising superman was easy to conjure, whatever the historical seed may or may not have been. Many others have raked over this territory far better than I, so take this as an appetizer of sorts for the critical analysis of others.

But let's get to the main points of the case- the evidence, and lack thereof.

  • The historical traces.
Aside from the New Testament, we have virtually no mention of Jesus, and those mentions are decades after his time, in some cases inserted by unnamed later authors, and in any case merely mention the Jesus story as was current among Christians of the time, with no detailed or independent information:
Josephus, writing ~93 CE
"Festus was now dead, and Albinus was but upon the road; so he assembled the sanhedrin of judges, and brought before them the brother of Jesus, who was called Christ, whose name was James, and some others; and when he had formed an accusation against them as breakers of the law, he delivered them to be stoned."
Tacitus, writing ~116 CE
"Consequently, to get rid of the report, Nero fastened the guilt and inflicted the most exquisite tortures on a class hated for their abominations, called Christians by the populace. Christus, from whom the name had its origin, suffered the extreme penalty during the reign of Tiberius at the hands of one of our procurators, Pontius Pilatus, and a most mischievous superstition, thus checked for the moment, again broke out not only in Jud├Ža, the first source of the evil, but even in Rome, where all things hideous and shameful from every part of the world find their centre and become popular."

Pilate was a true historical figure, attested by archeology as well as historical writings. But Tacitus is evidently referring to the story as told by the Christian followers, so the connection to Jesus is here one of hearsay, as is the passage by Josephus. Now, the absence of evidence is in no way conclusive. Even though the miracles attributed to him, the quasi-revolution fostered by him, and the brutal judgement by his community and execution by Rome might well have excited some kind of contemporary commentary, none has come to light. Nor is likely to ever come to light, considering how fervently such material has already been sought.

  • The name. 
Jesus is a form of the Hebrew Joshua, meaning Yahweh saves ... a savior. While this was a reasonably common name, "The works of Josephus refer to at least twenty different people with the name Jesus... ", it is awfully convenient for the presumptive Messiah to have this name. One hypothesis might be that Mary received her vision of why she happened to be miraculously pregnant, and had Joseph choose this propitious name. Or it might have been a coincidence, or a miracle. Or there may have been many valid messiahs in Palestine at this time, of whom only those named Jesus rose above the noise or took the mission onto themselves. A bit like someone in Mexico named "Jesus" becoming the next religious founder. Or, it might have been applied after the fact to a mythical savior, along with the equally honorific "Christus", meaning messiah. Critical historical analysis, in which Price gives a few lessons, tends to favor the easier hypotheses over the outlandish, convoluted, or coincidental.

The hometown of "Nazareth" is hardly more helpful, since it is not clear that such town existed at the time. It is quite possibly yet another power-name to go with "Christ" and "Jesus", this one meaning "branch", another reference to the messiah. "Jeremiah 23:5: 'Behold, the days are coming,' declares the Lord, 'When I will raise up for David a righteous Branch. And He will reign as King and act wisely and do justice and righteousness in the Land.'"

  • The Epistles.
The earliest writing within Christianity is regarded as whatever of the Pauline Epistles are genuine, from about the 50's CE. These have a far different picture of Jesus than the storybook Gospels. Paul never claims to have met Jesus, other than by a vision, and refers to him always in a sort of Homeric formula, as Christ crucified, or our Lord, etc. Price mentions that if Paul had the various sayings from Jesus that are thought to have been current in the community via the Q source or gospel of Thomas material, he would surely have used them in his various arguments recorded in the epistles. But no quotes at all, indeed no biographical Jesus at all, other than indirectly in references to Jesus's brother James, which we will get to below. (For a contrary view..) Perhaps this was just Paul's style, and a mark of his "outsider" status vs the Jerusalem church, but it is hard to square with a personality cult, like the one developed from Muhammed, for instance. The vast Hadith collection, all of it thought to be false, grew up in Muhammed's wake, and it hardly made a difference whether he was real or not. But Paul's ignorance of such a tradition indicates that it may have arisen later, just in time for the gospel writers, or been distrusted as a source by Paul.

  • The Gospels.
The four gospels are great artistic achievements, certainly when transmitted through the language of the  King James committee. But where did they come from, and what were they really saying? Firstly, the authors are unknown, as the canonical names were applied by others. They were written in the 70's-80's CE, except for John, which comes later by a couple of decades. I won't even deal with the contradictions among them, which are legion despite being partly derived from some common sources.

Price notes that each of the gospels tells a very archetypal story. Each anecdote has a lesson, each epsiode a moral. It is not history in the conventional or modern sense, since the story is there to push the theology rather than say simply what happened. Jesus becomes the archetypal hero, with plenty of precedent, both ancient and modern. Born of a virgin, precocious, foretold in countless ways from the old testament, possessing special powers and insights, disbelieved, becoming a king (if in an inverted way), then brought down, only to rise again as the scapegoat for all sins. The Jews had long been on the lookout for a messiah, and the wider Roman world indulged in many similar hero-mystery religions.

Price spends most of the book going literally chapter and verse through the New Testament to dredge up the models that inform each passage. Most come from the Old Testament, though some also come from Homer or Euripedes. Many of the comparisons seem rather strained to me, but there are also quite convincing sections. For instance, a long section of Luke is passage for passage pretty much a re-casting of Deuteronomy. A few examples of Price's comments:

Deuteronomy 8:1-3 / Luke 10:38-42
"Luke has created the story of Mary and Martha as a commentary on Deuteronomy 8:3, 'Man does live by bread alone, but... man lives by every word that proceeds from the mouth of the lord.' Luke has opposed the contemplative Mary who hungers for Jesus' ('the lord's') 'words' with the harried Martha ('Lady of the house', hence an ideal, fictive character), whose preoccupation with domestic chores, especially cooking and serving, threatens to crowd out spiritual sustenance (cf. Deuteronomy 8:11-14). It is not unlikely that the passage is intended to comment in somne way on the issue of celibate women and their various roles in the church of Luke's day (cf. 1 Timothy 5:3-16)."

Deuteronomy 8:4-20 / Luke 11:1-13
"Deuteronomy compares the discipline meted out to Israel by God with the training a father gives his son, then remind the reader of the fatherly provision of God for his children in the wilderness and promises of security, prosperity, and sufficient food in their new land. Luke matches this with his version of he Q Lord's Prayer, sharing the same general themes of fatherly provision and asking God to spare his children 'the test', recalling the 'tests' sent upon the people by God in the wilderness. Luke adds the Q material about God giving good gifts to his children (Luke 11:9-13/Matthew 7:7-11), certainly the point of the Deuteronomy text, together with his own parable of the Importunate Friend, which (like its twin, the parable of the Unjust Judge, 18:1-8, also uniquely Lukan) urges the seeker not to give up praying 'How long, O Lord?'"

Deuteronomy 13:12-18 / Luke 12:54-13:5
"Whole judgement of his people.. Whole cities lapsing into pagan apostasy are to be eliminated, destroyed, Deuteronomy mandates, with nothing ever to be rebuilt on their desolation, so seriously does Israel's God take spiritual infidelity. No less gravely does the Lukan Jesus take the lack of repentance on the part of the Galileans and Jews. Past tragedies and atrocities will be seen as the mere beginning of the judgments to fall like the headsman's axe on an unrepentant people. Of course, the Lukan Jesus prophesies long after the fact, referring to the bloody triumph of Rome in Galilee and Judea culminating in 73 CE."

The idea is that the New Testament is a sort of midrash, a common form of Jewish literature, where homilies are given on scripture themes, sometimes with only glancing or metaphorical reference to the source. Old wine into new bottles, so to speak. While one might argue that Jesus himself may have delivered all these homilies in structured form, commenting on Torah passages and stories, in sequence, as he preached through the land, with scribal listeners taking careful note. But the much likelier hypothesis is that the structure as well as the content came much later, in the quiet of the authorial chamber, with the relevant scrolls at hand.

Hindu traditions are full of this kind of thing, (though generally oral, not scribal), as gods make multiple re-appearances, (avatars), each one provided with related, but different, stories. No one wonders whether any of these characters were "really real" or not. The human need for transcendent, not to say magical, heroic drama seems universal and insatiable. Harry Potter comes to mind also, including the vast fan literature it has generated. The Jewish community in its many sects and off-shoots was very active in this respect, to the point that one can imagine a fresh hero derived from the messaianic and prophetic strains of the old testament, who spend his (fictive) time fulfilling OT prophecies and updating lesson after lesson out of the OT. And the Hellenized proto-Christians took off with it, in perhaps unexpected and unintended directions.

The Jesus Seminar was a conclave of biblical scholars who attempted a sort of Jeffersonian re-write / re-daction of the bible, casting stones on all the less believable material (miscellaneous miracles, infancy stories), while keeping the moral sayings and teachings, as presumptively "genuine". But Price (who was a member of this august body!) points out that this hardly addresses the basic question of believability, let alone historicity. It is like taking the Superman story and deleting the flying-through-the-air parts, and thinking that what you have left is more truthful. No, the whole story was of a piece. An archtypal piece that has a purpose for its time, taking the form of history, but not necessarily being history.

Two other examples that come to mind are Islam and Mormonism. Islam would be amenable to the Jesus Seminar approach, since Muhammed is certainly a historical figure. Here it makes sense to separate, say, his night flight to Jerusalem from his marriage to nine-year old Aisha bint Abu Bakr. The latter, quite believable. The former, not so much. Mormonism, on the other hand, is fabricated from top to bottom. Not that Joseph Smith was not a historical person, but that the book of Mormon is a work of utter fantasy, concocted from Bible bits, completely made-up history, and portentious language. This type of thing seems endemic to the human condition, cropping up again in Scientology even more recently. The ancient world had even more porous relations between factual and fantasy history, and even sci-fi dystopia / analogy / futurology, as the book of Revelation makes clear. Heroes can be made to order.

A small further example is the birthday of Jesus, i.e. Christmas. This is a total fabrication, merely the co-optation of the existing Saturnalia by the new religion, with no knowledge whatsoever of the true birth date. Yet this too is taken as "gospel" by plenty of people.

  • James, brother of Jesus.
Then there is the reputed brother of Jesus, James, who is substantially better-attested historically, leading the early Jerusalem church, with plenty of tangles with Paul, among others. Price has some fun with the Catholic summersaults on the nature of James, since by its interpretation, Mary was a perpetual virgin, and thus Jesus having a brother was a no-no. But he is called by Paul and others the brother of Jesus. This is perhaps the biggest single problem with the myth hypothesis- the one thread that best testifies to the reality of Jesus himself. But "brother" is a notoriously flexible term. The medieval monestaries were rife with them, and Price offers that James was perhaps a follower of higher grade than the rest in some other respect, as was later reflected by his temporal leadership, and was thus inducted, whether contemporaneously or latterly, into the inner-most circle of the heroic mystery. One has to admit this interpretation is quite strained, given how Paul (and then Josephus, as above) refers to James as the lord's brother very casually in passing.

  • Analogous to climate heating denial?
Lastly, one has to ask whether this myth hypothesis is just headstrong denialism- the last gasp of the dedicated atheist. Price points out, however, that the Jesus myth theory is largely unrelated to atheism per se. Jesus could easily have been real, and done all the Seminar-approved things, and there still not be a god. Conversely, god could exist, yet Jesus not be his messaih, as the Jews have long maintained, or have not existed at all. There are plenty of other gods to choose from, after all.

It is certainly cantakerous, even in this skeptical age, to point out that the reality of Jesus is far from secure. And as everyone points out, the vast majority, even of Biblical scholars, take the opposing postion. But the vast majority of Biblical scholars are both believing Christians and have a vested interest in their subject. So a majority here does not count for as much as one might think.

A comparison with climate denialism is instructive. On that front, the majority is led by scholars working with far more data, much of which is contemporary, public, and reproducible. Their interaction with the historical record is far more dynamic, as new forms of evidence, like tree rings, stalagtite rings, fossil coral, isotope analyses, etc., allow us all to peer ever farther and more accurately into the instructive past. What a difference from the Biblical scholars (or ourselves) ruminating over their feelings about this or that passage!

Importantly, in contrast to the case of Christianity, it is the climate denialists who bear the metaphorical cross of motive in this case, since they are often paid by the very industries whose economic interest (indeed existance) lies in denying what has been patently obvious for over a century- that CO2 is a greenhouse gas, that our atmosphere acts as a greenhouse, and that the biosphere is currently being decimated by (geologically) rapid heating.

While climate scientists have a coherent theory of their topic, (and their deniers really do not), the Jesus myth theorists have yet to come up with a detailed theory of which community among the first century Jews had the motivations and materials to generate the tradition that was taken up by the apostles and Paul, as described more or less in Acts, before it was so nicely and systematically elaborated in the gospels. Robert Price takes a few stabs at this issue, invoking Marcion as a key generator and organizer of eary gospel material, with certain theological visions and axes to grind. Nevertheless, key data is missing from the story's origin period, perhaps necessarily so, since any heresies have been well and truly expunged from the record by this point. What we have is heavily sanitized and twice-told tales from many decades after, and little else.

At any rate, one should appreciate that, whether entirely mythical or not quite entirely mythical, there is precious little to nothing known about Jesus, once all the encrustations are pared away and one takes a careful and skeptical look at what is left. Our contemporary knowledge of the rapidity with which myths can grow, from seeds either fictional or factual, and the enthusiasm people show in augmenting them and expressing their own views through them, should be a big piece of the historical & critical approach we bring to bear on this question. The Jewish messianism & escatology that constructed early Christianity could have arisen either from a community of writers consulting their many sources for appropriate passages and prophesies, or, quite a bit less plausibly, a remarkably inspired (and scholarly) single person simultaneously embodying and preaching a precise set of midrashes based on Torah themes, brought up to date for the Hellenized, post Roman-conquest Middle East.