Easy Does it

The eukaryotic ribosome is significantly slower than, and more accurate than, the bacterial ribosome.

Despite the focus, in molecular biology, on interesting molecules like genes and regulators, the most striking thing facing anyone who breaks open cells is the prevalence of ribosomes. Run the cellular proteins or RNAs out on a gel, and bulk of the material is always ribosomal proteins and ribosomal RNAs, along with tRNAs. That is because ribosomes are critically important, immense in size, and quite slow. They are sort of the beating heart of the cell- not the brains, not the energy source, but the big lumpy, ancient, shape-shifting object that pumps out another essential form of life-blood- all the proteins the cell needs to keep going.

With the revolution in structural biology, we have gotten an increasingly clear view of the ribosome, and a recent paper took it up another notch with a structural analysis of how tRNA handling works and how / why it is that the eukaryotic ribosome is about ten times slower than its bacterial progenitor. One of their figures provides a beautiful (if partial) view of each kind of ribosome, showing how well-conserved this structure is, despite the roughly three billion or more years that have elapsed since their divergence into the bacterial and archaeal lineages, from which the eukaryotic ribosome comes. 

Above, the human ribosome, and below, the ribosome of E. coli, a bacterium, in partial views. The perspective is from the back, relative to conventional views, and only a small amount of the large subunit (LSU) appears at the top of each structure, with more of the small subunit (SSU) shown below. Between them is the cleft where tRNAs bind, in a dynamic sequence of incoming rRNA at the A (acceptor) site, then catalysis of peptide bond addition at the P (peptidyl transfer) site, and ejection of the last tRNA at the E (ejection) site. In concert with the conveyor belt of tRNAs going through, the nascent protein is being synthesized in the large subunit and the mRNA is going by, codon by codon, in the small subunit. Note the overall conservation of structure, despite quite a bit of difference in detail.

The ribosome is an RNA machine at its core, with a lot of accessory proteins that were added later on. And it comes in two parts, the large and small subunits. These subunits do different things, do a lot of rolling about relative to each other, and bind a conveyor belt of tRNAs between them. The tRNAs are pre-loaded with an amino acid on one end (top) and an anticodon on the other end (bottom). They also come with a helper protein (EF-Tu in bacterial, eEF1A in eukaryotes), which plays a role later on. The anticodon is a set of three nucleotides that constitute the genetic code, whereby this tRNA is always going to match one codon to a particular amino acid. 

The ribosome doesn't care what the code is or which tRNA comes in. It only cares that the tRNA matches the mRNA held by the small subunit, as transcribed from the DNA. This process is called decoding, and the researchers show some of the differences that make it slower, but also more accurate, in eukaryotes. In bacteria, ribosomes can work at up to 20 amino acids per second, while human ribosomes top out at about 2 amino acids per second. That is pretty slow, for an enzyme! Its accuracy is about one error per thousand to ten thousand codons.

See text for description of this diagram of the ribosomal process. 50 S is the large ribosomal subunit in bacteria (60S in eukaryotes). 30S is the small subunit in bacteria (40S in eukaryotes). S stands for Svedberg units, a unit of sedimentation in high-speed centrifugation, which was used to study proteins at the dawn of molecular biology.

Above is diagrammed the stepwise logic of protein synthesis. The first step is that a tRNA comes in and lands on the empty A site, and tests whether its anticodon sequence fits the codon on the mRNA being threaded through the bottom. This fitting and testing is the key quality control process, and the slower and more selective it is, the more accurate the resulting translation. The EF-Tu/eEF1A+GTP protein holds on to the tRNA at the acceptor (A) position, and only when the fit is good does that fit communicate back up from the small subunit to the large subunit and cause hydrolysis of GTP to GDP, and release of the top of the tRNA, which allows it to swing into position (accommodation) to the catalytic site of the ribosome. This is where the tRNA contributes its amino acid to the growing protein chain. That chain, previously attached to the tRNA in the P site, now is attached to the tRNA in the A site. Now another GTP-binding protein comes in, EF-G (EEF2 in eukaryotes), which bumps the tRNA from the A site to the P site, and simultaneously the mRNA one codon ahead. This also releases whatever was in the E site of the ribosome and frees up the A site to accept another new tRNA.

See text for description. IC = initiation complex, CR = codon recognition complex, GA = GTPase activation complex, AC = accommodated complex. FRET = fluorescence resonance energy transfer. Head and shoulder refer to structural features of the small ribosomal subunit.

These researchers did both detailed structural studies of ribosomes stuck in various positions, and also mounted fluorescent labels at key sites in the P and A sites. These double labels allowed one to be flashed with light, (at its absorbance peak), and the energy to be transferred between them, resulting in fluorescence of light back out from the second fluorophore. The emitted energy from the second fluorophore provides an exquisitely sensitive measure of the distance between the two fluorophores, since its ability to capture light from the first fluorophore is sensitive to distance (cubed). The graph above (right) provides a trace of the fluorescence seen in one ribosomal cycle, as the distance between the two tRNAs changes slightly as the reaction proceeds and the two tRNAs come closer together. This technical method allows real-time analysis of the reaction as it is going along, especially one as slow as this one.

Structures of the ribosome accentuating the tRNA positions in the A, P, and E sites. Note how the green tRNA in the A site starts bent over towards the eEF1A GTPase (blue), as the decoding and quality control are going on, after which it is released and swings over next to the P site tRNA, ready for peptide bond formation. Note also how the structure of the anticodon-codon pairing (pink, bottom) evolves from loose and disordered to tight after the tRNA straightens up.

Above is shown a gross level view in stop-motion of ribosomal progress, achieved with various inhibitors and altered substrates. The mRNA is in pink (insets), and shows how the codon-anticodon match evolves from loose to tight. Note how at first only two bases of the mRNA are well-paired, while all three are paired later on. This reflects in a dim way the genetic code, which has redundancies in the third position for many amino acids, and is thought to have first had only two letters, before transitioning to three letters.

Higher detail on the structures of the tRNAs in the P site and the A site as they progress through the proof-reading phase of protein synthesis. The fluorescence probes are pictured, (Red and green dots), as is more the mRNA strand (pink).

These researchers have a great deal to say about the details of these structures- what differentiates the human from the E. coli ribosome, why the human one is slower and allows more time and more hindrance during the proof-reading step, thereby helping badly matched tRNAs to escape and increasing overall fidelity. For example, how does the GTPase eEF1A, docked to the large subunit, know when a match down at the codon-anticodon pair has been successful down in the small ribosomal subunit?

"Base pairing between the mRNA codon and the aa-tRNA anticodon stem loop (ASL) is verified through a network of ribosomal RNA (rRNA) and protein interactions within the SSU A site known as the decoding centre. Recognition of cognate aa-tRNA closes the SSU shoulder domain towards the SSU body and head domains. Consequent ternary complex engagement of the LSU GTPase-activating centre (GAC), including the catalytic sarcin-ricin loop12 (SRL), induces rearrangements in the GTPase, including switch-I and switch-II remodeling, that trigger GTP hydrolysis"

They note that there seem to be at least two proofreading steps, both in activating the eEF1A and also afterwards, during the large swing of the tRNA towards the P site. And they note novel rolling motions of the human ribosome compared with the bacterial ribosome, to help explain some of its distinctive proofreading abilities, which may be adjustable in humans by regulatory processes. Thus we are gaining ever more detailed window on the heart of this process, which is foundational to the origin of life, central to all cells, and not without medical implications, since many poisons that bacteria have devised attack the ribosome, and several of our current antibiotics do likewise.

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• Endgame Ukraine.
• How now, IBM?
• Death by gun.
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• Immigration is the key.

The Way We Were: Origins of Meiosis and Sex

Sex is as foundational for eukaryotes as are mitochondria and internal membranes. Why and how did it happen?

Sexual reproduction is a rather expensive proposition. The anxiety, the dating, the weddings- ugh! But biologically as well, having to find mates is no picnic for any species. Why do we bother, when bacteria get along just fine just dividing in two? This is a deep question in biology, with a lot of issues in play. And it turns out that bacteria do have quite a bit of something-like-sex: they exchange DNA with each other in small pieces, for similar reasons we do. But the eukaryotic form of sex is uniquely powerful and has supported the rapid evolution of eukaryotes to be by far the dominant domain of life on earth.

A major enemy of DNA-encoded life is mutation. Despite the many DNA replication accuracy and repair mechanisms, some rate of mutation still occurs, and is indeed essential for evolution. But for larger genomes, the mutation rate always exceeds the replication rate, (and the purifying natural selection rate), so that damaging mutations build up and the lineage will inevitably die out without some help. This process is called Muller's ratchet, and is why all organisms appear to exchange DNA with others in their environment, either sporadically like bacteria, or systematically, like eukaryotes.

An even worse enemy of the genome is unrepaired damage like complete (double strand) breaks in the DNA. These stop replication entirely, and are fatal. These also need to be repaired, and again, having extra copies of a genome is the way to allow these to be fixed, by processes like homologous recombination and gene conversion. So having access to other genomes has two crucial roles for organisms- allowing immediate repair, and allowing some way to sweep out deleterious mutations over the longer term.

Our ancestors, the archaea, which are distinct from bacteria, typically have circular, single molecule genomes, in multiple copies per cell, with frequent gene conversions among the copies and frequent exchange with other cells. They routinely have five to twenty copies of their genome, and can easily repair any immediate damage using those other copies. They do not hide mutant copies like we do in a recessive allele, but rather by gene conversion (which means, replicating parts of a chromosome into other ones, piecemeal) make each genome identical over time so that it (and the cell) is visible to selection, despite their polyploid condition. Similarly, taking in DNA from other, similar cells uses the target cells' status as live cells (also visible to selection) to insure that the recipients are getting high quality DNA that can repair their own defects or correct minor mutations. All this ensures that their progeny are all set up with viable genomes, instead of genomes riddled with defects. But it comes at various costs as well, such as a constant race between getting lethal mutation and finding the DNA that might repair it. 

Both mitosis and meiosis were eukaryotic innovations. In both, the chromosomes all line up for orderly segregation to descendants. But meiosis engages in two divisions, and features homolog synapsis and recombination before the first division of the parental homologs.

This is evidently a precursor to the process that led, very roughly 2.5 billion years ago, to eukaryotes, but is all done in a piecemeal basis, nothing like what we do now as eukaryotes. To get to that point, the following innovations needed to happen:

• Linearized genomes, with centromeres and telomeres, and >1 number of chromosomes.
• Mitosis to organize normal cellular division, where multiple chromosomes are systematically lined up and distributed 1:1 to daughter cells, using extensive cytoskeletal rearrangements and regulation.
• Mating with cell fusion, where entire genomes are combined, recombined, and then reduced back to a single complement, and packaged into progeny cells.
• Synapsis, as part of meiosis, where all sister homologs are lined up, damaged to initiate DNA repair and crossing-over.
• Meiosis division one, where the now-recombined parental homologs are separated.
• Meiosis division two, which largely follows the same mechanisms as mitosis, separating the reshuffled and recombined sister chromosomes.

This is a lot of novelty on the path to eukaryogenesis, and is just a portion of the many other innovations that happened in this lineage. What drove all this, and what were some plausible steps in the process? The advent of true sex generated several powerful effects:

1. A definitive solution to Muller's ratchet, by exposing every locus in a systematic way to partial selection and sweeping out deleterious mutations, while protecting most members of the population from those same mutations. Continual recombination of the parental genomes allows beneficial mutations to separate from deleterious ones and be differentially preserved.
2. Mutated alleles are partially, yet systematically, hidden as recessive alleles, allowing selection when they come into homozygous status, but also allowing them to exist for limited time to buffer the mutation rate and to generate new variation. This vastly increases accessible genetic variation.
3. Full genome-length alignment and repair by crossing over is part of the process, correcting various kinds of damage and allowing accurate recombination across arbitrarily large genomes.
4. Crossing over during meiotic synapsis mixes up the parental chromosomes, allowing true recombination among the parental genomes, beyond just the shuffling of the full-length chromosomes. This vastly increases the power of mating to sample genetic variation across the population, and generates what we think of as "species", which represent more or less closed interbreeding pools of genetic variants that are not clones but diverse individuals.

The time point of 2.5 billion years ago is significant because this is the general time of the great oxidation event, when cyanobacteria were finally producing enough oxygen by photosynthesis to alter the geology of earth. (However our current level of atmospheric oxygen did not come about until almost two billion years later, with rise of land plants.) While this mainly prompted the logic of acquiring mitochondria, either to detoxify oxygen or use it metabolically, some believe that it is relevant to the development of meiosis as well. 

There was a window of time when oxygen was present, but the ozone layer had not yet formed, possibly generating a particularly mutagenic environment of UV irradiation and reactive oxygen species. Such higher mutagenesis may have pressured the archaea mentioned above to get their act together- to not distribute their chromosomes so sporadically to offspring, to mate fully across their chromosomes, not just pieces of them, and to recombine / repair across those entire mated chromosomes. In this proposal, synapsis, as seen in meiosis I, had its origin in a repair process that solved the problem of large genomes under mutational load by aligning them more securely than previously. 

It is notable that one of the special enzymes of meiosis is Spo11, which induces the double-strand breaks that lead to crossing-over, recombination, and the chiasmata that hold the homologs together during the first division. This DNA damage happens at quite high rates all over the genome, and is programmed, via the structures of the synaptonemal complex, to favor crossing-over between (parental) homologs vs duplicate sister chromosomes. Such intensive repair, while now aimed at ensuring recombination, may have originally had other purposes.

Alternately, others suggest that it is larger genome size that motivated this innovation. This origin event involves many gene duplication events that ramified the capabilities of the symbiotic assemblage. Such gene dupilcations would naturally lead to recombinational errors in traditional gene conversion models of bacterial / archaeal genetic exchange, so there was pressure to generate a more accurate whole-genome alignment system that confined recombination to the precise homologs of genes, rather than to any similar relative that happened to be present. This led to the synapsis that currently is part of meiosis I, but it is also part of "parameiosis" systems on some eukaryotes, which, while clearly derived, might resemble primitive steps to full-blown meiosis.

It has long been apparent that the mechanisms of meiosis division one are largely derived from (or related to) the mechanisms used for mitosis, via gene duplications and regulatory tinkering. So these processes (mitosis and the two divisions of meiosis) are highly related and may have arisen as a package deal (along with linear chromosomes) during the long and murky road from the last archaeal ancestor and the last common eukaryotic ancestor, which possessed a much larger suite of additional innovations, from mitochondria to nuclei, mitosis, meiosis, cytoskeleton, introns / mRNA splicing, peroxisomes, other organelles, etc.  

Modeling of different mitotic/meiotic features. All cells modeled have 18 copies of a polypoid genome, with a newly evolved process of mitosis. Green = addition of crossing over / recombination of parental chromosomes, but no chromosome exchange. Red = chromosome exchange, but no crossing over. Blue = both crossing over and chromosome exchange, as occurs now in eukaryotes. The Y axis is fitness / survival and the X axis is time in generations after start of modeling.

A modeling paper points to the quantitative benefits of the mitosis when combined with the meiotic suite of innovations. They suggest that in a polyploid archaean lineage, the establishment of mitosis alone would have had revolutionary effects, ensuring accurate segregation of all the chromosomes, and that this would have enabled differentiation among those polyploid chromosome copies, since they would be each be faithfully transmitted individually to offspring (assuming all, instead of one, were replicated and transmitted). Thus they could develop into different chromosomes, rather than remain copies. This would, as above, encourage meiosis-like synapsis over the whole genome to align all the (highly similar) genes properly.

"Modeling suggests that mitosis (accurate segregation of sister chromosomes) immediately removes all long-term disadvantages of polyploidy."

Additional modeling of the meiotic features of chromosome shuffling, and recombination between parental chromosomes, indicates (shown above) that these are highly beneficial to long-term fitness, which can rise instead of decaying with time, per the various benefits of true sex as described above. 

The field has definitely not settled on one story of how meiosis (and mitosis) evolved, and these ideas and hypotheses are tentative at this point. But the accumulating findings that the archaea that most closely resemble the root of the eukaryotic (nuclear) tree have many of the needed ingredients, such as active cytoskeletons, a variety of molecular antecedents of ramified eukaryotic features, and now extensive polyploidy to go with gene conversion and DNA exchange with other cells, makes the momentous gap from archaea to eukaryotes somewhat narrower.

• SNL says goodbye to George Santos.
• Surveillance vs spying.
• The South China Sea.

Are Archaea Archaic?

It remains controversial whether the archaeal domain of life is 1 or 4.5 billion years old. That is a big difference!

Back in the 1970's, the nascent technologies of molecular analysis and DNA sequencing produced a big surprise- that hidden in the bogs and hot springs of the world are micro-organisms so extremely different from known bacteria and protists that they were given their own domain on the tree of life. These are now called the archaea, and in addition to being deeply different from bacteria, they were eventually found to be the progenitors of eukaryotic cell- the third (and greatest!) domain of life that arose later in the history of the biosphere. The archaeal cell contributed most of the nuclear, informational, membrane management, and cytoskeletal functions, while one or more assimilated bacteria (most prominently the future mitochondrion and chloroplast) contributed most of the metabolic functions, as well as membrane lipid synthesis and peroxisomal functions.

Carl Woese, who discovered and named archaea, put his thumb heavily on the scale with that name, (originally archaebacteria), suggesting that these new cells were not just an independent domain of life, totally distinct from bacteria, but were perhaps the original cell- that is, the LUCA, or last universal common ancestor. All this was based on the sequences of rRNA genes, which form the structural and catalytic core of the ribosome, and are conserved in all known life. But it has since become apparent that sequences of this kind, which were originally touted as "molecular clocks", or even "chronometers" are nothing of the kind. They bear the traces of mutations that happen along the way, and, being highly important and conserved, do not track the raw mutation rate, (which itself is not so uniform either), but rather the rate at which change is tolerated by natural selection. And this rate can be wildly different at different times, as lineages go through crises, bottlenecks, adaptive radiations, and whatever else happened in the far, far distant past.

Carl Woese, looking over filmed spots of 32P labeled ribosomal RNA from different species, after size separation by electrophoresis. This is how RNAs were analyzed, back in 1976, and such rough analysis already suggested that archaea were something very different from bacteria.

There since has been a tremendous amount of speculation, re-analysis, gathering of more data, and vitriol in the overall debate about the deep divergences in evolution, such as where eukaryotes come from, and where the archaea fit into the overall scheme. Compared with the rest of molecular biology, where experiments routinely address questions productively and efficiently due to a rich tool chest and immediate access to the subject at hand, deep phylogeny is far more speculative and prone to subjective interpretation, sketchy data, personal hobbyhorses, and abusive writing. A recent symposium in honor of one of its more argumentative practitioners made that clear, as his ideas were being discarded virtually at the graveside.

Over the last decade, estimates of the branching date of archaea from the rest of the tree of life have varied from 0.8 to 4.5 Gya (billion years ago). That is a tremendous range, and is a sign of the difficulty of this field. The frustrations of doing molecular phylogeny are legion, just as the temptations are alluring. Firstly, there are very few landmarks in the fossil record to pin all this down. There are stromatolites from roughly 3.5 Gya, which pin down the first documented life of any kind. Second are eukaryotic fossils, which start, at the earliest, about 1.5 Gya. Other microbial fossils pin down occasional sub-groups of bacteria, but archaea are not represented in the fossil record at all, being hardly distinguishable from bacteria in their remains. Then we get the Cambrian explosion of multicellular life, roughly 0.5 Gya. That is pretty much it for the fossil record, aside from the age of the moon, which is about 4.5 Gya and gives us the baseline of when the earth became geologically capable of supporting life of any kind.

The molecules of living organisms, however, form a digital record of history. Following evolutionary theory, each organism descends from others, and carries, in mutated and altered form, traces of that history. We have parts of our genomes that vary with each generation, (useful for forensics and personal identification), we have other parts that show how we changed and evolved from other apes, and we have yet other areas that vary hardly at all- that carry recognizable sequences shared with all other forms of life, and presumably with LUCA. This is a real treasure trove, if only we can make sense of it.

But therein lies the rub. As mentioned above, these deeply conserved sequences are hardly chronometers. So for all the data collection and computer wizardry, the data itself tells a mangled story. Rapid evolution in one lineage can make it look much older than it really is, confounding the whole tree. Over the years, practitioners have learned to be as judicious as possible in selecting target sequences, while getting as many as possible into the mix. For example, adding up the sequences of 50-odd ribosomal proteins can give more and better data than assembling the 2 long-ish ribosomal RNAs. They provide more and more diverse data. But they have their problems as well, since some are much less conserved than others, and some were lost or gained along the way. 

A partisan of the later birth of archaea provides a phylogenetic tree with countless microbial species, and one bold claim: "inflated" distances to the archaeal and eukaryotic stems. This is given as the reason that archaea (lower part of the diagram, including eukaryotes, termed "archaebacteria"), looks very ancient, but really just sped away from its originating bacterial parent, (the red bacteria), estimated at about 1 Gya. This tree is based on an aligned concatentation of 26 universally conserved ribosomal protein sequences, (51 from eukaryotes), with custom adjustments.

So there has been a camp that claims that the huge apparent / molecular distance between the archaea and other cells is just such a chimera of fast evolution. Just as the revolution that led to the eukaryotic cell involved alot of molecular change including the co-habitation of countless proteins that had never seen each other before, duplications / specializations, and many novel inventions, whatever process led to the archaeal cell (from a pre-existing bacterial cell) might also have caused the key molecules we use to look into this deep time to mutate much more rapidly than is true elsewhere in the vast tree of life. What are the reasons? There is the general disbelief / unwillingness to accept someone else's work, and evidence like possible horizontal transfers of genes from chloroplasts to basal archaea, some large sequence deletion features that can be tracked through these lineages and interpreted to support late origination, some papering over of substantial differences in membrane and metabolic systems, and there are plausible (via some tortured logic) candidates for an originating, and late-evolving, bacterial parent. 

This thread of argument puts the origin of eukaryotes roughly at 0.8 Gya, which is, frankly, uncomfortably close to the origination of multicellular life, and gives precious little time for the bulk of eukaryotic diversity to develop, which exists largely, as shown above, at the microbial level. (Note that "Animalia" in the tree above is a tiny red blip among the eukaryotes.) All this is quite implausible, even to a casual reader, and makes this project hard to take seriously, despite its insistent and voluminous documentation.

Parenthetically, there was a fascinating paper that used the evolution of the genetic code itself to make a related point, though without absolute time attributions. The code bears hallmarks of some amino acids being added relatively late (tryptophan, histidine), while others were foundational from the start (glycine, alanine), when it may have consisted of two RNA bases (or even one) rather than three. All of this took place long before LUCA, naturally. This broad analysis of genetic code usage argued that bacteria tend to use a more ancient subset of the code, which may reflect their significantly more ancient position on the tree of life. While the full code was certainly in place by the time of LUCA, there may still at this time have been, in the inherited genome / pool of proteins, a bias against the relatively novel amino acids. This finding implies that the time of archaeal origination was later than the origination of bacteria, by some unspecified but significant amount.

So, attractive as it would be to demote the archaea from their perch as super-ancient organisms, given their small sizes, small genomes, specialization in extreme environments, and peripheral ecological position relative to bacteria, that turns out to be difficult to do. I will turn, then, to a very recent paper that gives what I think is much more reasoned and plausible picture of the deeper levels of the tree of life, and the best general picture to date. This paper is based on the protein sequences of the rotary ATPases that are universal, and were present in LUCA, despite their significant complexity. Indeed, the more we learn about LUCA, the more complete and complex this ancestor turns out to be. Our mitochondrion uses a (bacterial) F-type ATPase to synthesize ATP from the food-derived proton gradient. Our lysosomes use a (archaeal) V-type ATPase to drive protons into / acidify the lysosome in exchange for ATP. These are related, derived from one distant ancestor, and apparently each was likely to have been present in LUCA. Additionally, each ATPase is composed of two types of subunits, one catalytic, and one non-catalytic, which originated from an ancient protein duplication, also prior to LUCA. The availability of these molecular cousins / duplications provides helpful points of comparison throughout, particularly for locating the root of the evolutionary tree.

Phylogenetic trees based on ATP synthase enzymes that are present in all forms of life. On left is shown the general tree, with branch points of key events / lineages. On right are shown sub-trees for the major types of the ATP synthase, whether catalytic subunit (c), non-catalytic (n), F-type, common in bacteria, or V type, common in archaea. Note how congruent these trees are. At bottom right in the tiny print is a guide to absolute time, and the various last common ancestors.

This paper also works quite hard to pin the molecular data to the fossil and absolute time record, which is not always provided The bottom line is that archaea by this tree arise quite early, (see above), co-incident with or within about 0.5 Gy of LUCA, which was bacterial, at roughly 4.4 Gya. The bacterial and archaeal last common ancestors are dated to 4.3 and 3.7 Gya, respectively. The (fused) eukaryotic last common ancestor dates to about 1.9 Gya, with the proto-mitochondrion's individual last common ancestor among the bacteria some time before that, at roughly 2.4 Gya. 

This time line makes sense on many fronts. First, it provides a realistic time frame for the formation and diversification of eukaryotes. It puts their origin right around the great oxidation event, which is when oxygen became dominant in earth's atmosphere, (about 2 to 2.4 Gya), which was a precondition for the usefulness of mitochondria to what are otherwise anaerobic archaeal cells. It places the origin of archaea (LACA) a substantial stretch after the origin of bacteria, which agrees with the critic's points above that bacteria are the truly basal lineage of all life, and archaea, while highly different and pretty archaic, also share a lot of characteristics with bacteria, and perhaps more so with certain early lineages than with others that came later. The distinction between LUCA and the last common bacterial ancestor (LBCA) is a technical one given the trees they were working from, and are not, given the ranges of age presented, (see figure above), significantly different.

I believe this field is settling down, and though this paper, working from only a subset of the most ancient sequences plus fossil set-points, is hardly the last word, it appears to represent a consensus view and is the best picture to date of the deepest and most significant waypoints in the deep history of life. This is what comes from looking through microscopes, and finding entire invisible worlds that we had no idea existed. Genetic sequencing is another level over that of microscopy, looking right at life's code, and at its history, if darkly. What we see in the macroscopic world around us is only the latest act in a drama of tremendous scale and antiquity.

• Platitude.
• There are a lot of single-celled eukaryotes.
• Hitting bottom.

Missing Links in Eukaryotic Evolution

The things you find in Slovenian mud! Like an archaeal cell that is the closest thing to the eukaryotic root organism.

Creationists and "intelligent" design advocates tirelessly point to the fossil record. Not how orderly it is and revealing of the astonishingly sequenced, slow, and relentless elaboration of life. No, they decry its gaps- places where fossils do not account for major evolutionary (er, designed) transitions to more modern forms. It is a sad kind of argument, lacking in imagination and dishonest in its unfairness and hypocrisy. Does the life of Jesus have gaps in the historical record? Sure enough! And are those historical records anywhere near as concrete and informative as fossils? No way. What we have as a record of Christianity's history is riven with fantasy, forgery, and uncertainty.

But enough trash talk. One thing that science has going for it is a relentlessly accumulating process by which new fossils appear, and new data from other sources, like newly found organisms and newly sequenced genomes, arise to clarify what were only imaginative (if reasonable) hypotheses previously. Darwin's theory of evolution, convincing and elegantly argued as it was originally, has gained such evidence without fail over the subsequent century and a half, from discoveries of the age of the earth (and thus the solar system) to the mechanics of genetic inheritance.

A recent paper describes the occurence of cytoskeletal proteins and structures in an organism that is neither a bacterium nor a eukaryote, but appears to be within the family of Archaea that is the closest thing we have to the eukaryotic progenitor. These are the Asgard Archaea, a family that was discovered only in the last decade, as massive environmental sequencing projects have sampled the vast genetic diversity hidden in the muds, sediments, soils, rocks, and waters of the world. 

Sampling stray DNA is one thing, but studying these organisms in depth requires growing them in the lab. After trolling through the same muds in Slovenia where promising DNA sequences were fond, this group fished out, and then carefully cultured, a novel archaeal cell. But growing these cells is notoriously difficult. They are anaerobic, never having made the transition to the oxygenated atmosphere of the later earth. They have finicky nutritional requirements. They grow very slowly. And they generally have to live with other organisms (bacteria) with which they have reciprocal metabolic relationships. In the ur-eukaryote, this was a relationship with the proto-mitochondrion, which was later internalized. For the species cultured by this research group, it is a pair of other free-living bacteria. One is related to sulfur-reducing Desulfovibrio, and the other one is related to a simpler archaeal Methanogenium that uses hydrogen and CO2 or related simple carbon compounds to make methane. Anaerobic Asgard archaea generally have relatively simple metabolisms and make hydrogen from small organic compounds, through a kind of fermentation.

A phylogenetic tree showing relations between the newly found organisms (bottom) and eukaryotes (orange), other archaea, and the entirely separate domain of bacteria (red). This is based on a set of sequences of universally used / conserved ribosomal proteins. While the eukaryotes have strayed far from the root, that root is extremely close to some archaeal groups.

Micrographs of cultured lokiarchaeal cells, with a scale bar of 500 nanometers. These are rather amoeboid cells with extensive cytoskeletal and membrane regulation.

Another micrograph of part of a lokiarchaeal cell, showing not just its whacky shape, but a good bit of internal structure as well. The main scale bar is 100 nanometers. There are internal actin filaments (yellow arrowheads), lined up ribosomes (gray arrowhead) and cell surface proteins of some kind (blue arrowheads).

What they found after all this was pretty astonishing. They found cells that are quite unlike typical bacterial or even archaeal cells, which are compact round or rod shapes. These (termed lokiarchaeal) cells have luxurious processes extending all over the place, and a profusion of internal structural elements reminiscent of eukaryotic cells, though without membrane-bound internal organelles. But they have membrane-bound protrusions and what look like vesicles budding off. At only six million base pairs (compared to our three billion) and under five thousand genes, these cells have a small and streamlined genome. Yet there are a large number (i.e. 258) of eukaryotic-related (signature) proteins (outlined below), particularly concerning cytoskeletal and membrane trafficking. The researchers delved into the subcellular structures, labeling actin and obtaining structural data for both actin and ribosomes, confirming their archaeal affinity with added features. 

A schematic of eukaryotic-like proteins in the newly cultured lokiarchaeal Asgard genome. Comparison (blue) is to a closely related organism isolated recently in Japan.

This work is the first time that the cytoskeleton of Asgard cells has been visualized, along with its role in their amoeboid capabilities. What is it used for? That remains unknown. The lush protrusions may collaborate with this organism's metabolic partners, or be used for sensing and locomoting to find new food within its sediment habitat, or for interacting with fellow lokiarchaeal cells, as shown above. Or all of these roles. Evolutionarily, this organism, while modern, appears to be a descendent of the closest thing we have to the missing link at the origin of eukaryotes, (that is, the archaeal dominant partner of the founding symbiosis), and in that sense seems both ancient in its characteristics, and possibly little changed from that time. Who would have expected such a thing? Well, molecular biologists and evolutionary biologists have been expecting it for a long time.

• Fossil fuel consumption is still going up, not down.

Melting Proteins Through a Wall

Peroxisomes use a trendy way to import their proteins.

As has been discussed many times in this space, membranes are formidable barriers ... at the molecular level. Having a plasma membrane, and organelles enclosed within membranes, means needing to get all sorts of things across them, from the tiniest proton to truly enormous mega-complexes like ribosomes. Almost eight percent of the proteins encoded by the human genome are transporters, that concern themselves with getting molecules from one place to another, typically across membranes. A critical type of molecule to get into organelles is the proteins that belong there, to do their day-in, day-out jobs. 

But proteins are large molecules. There are two ways to go about transporting them across membranes. One is to thread them across linearly, unfolding them in process, and letting them refold once they are across. This is how proteins get into the endoplasmic reticulum, where the long road to secretion generally starts. Ribosomes dock right up to the endoplasmic reticulum membrane and pump their nascent proteins across as they are being synthesized. Easy peasy.

However other organelles don't get this direct (i.e. cotranslational) method of protein import. They have to get already-made full-length proteins lugged across their membranes somehow. Mitochondria, for instance, are replete with hard-working proteins, virtually all of which are encoded in the nucleus and have to be brought in whole, usually through two separate membranes to get into the mitochondrial matrix. There are dedicated transporters, nicknamed the TOM/TIM complexes, that thread incoming proteins (which are detected by short "signal" sequences these proteins carry) through each membrane in turn, and sometimes use additional helpers to get the proteins plugged into the matrix membrane or other final destination. Still, this remains a protein threading process, (of the first transport type), and due to its need to unfold and the later refold every incoming protein, it involves chaperones which specialize in helping those proteins fold correctly afterwards.

Schematic of the nuclear pore. The wavy bits are protein tails that are F-G rich (phenylalanine-glycine) that are unstructured and form a gel throughout the pore, allowing like-minded F-G proteins through, which are the nuclear transport receptors. These receptors carry various cargo proteins in an out of the nucleus, without having to unfold them. "Nup" is short for nuclear pore protein; GLFG is short for glycine, leucine (another hydrophobic amino acid), phenylalanine, glycine.

But there is another way to do it, which was discovered much more recently and is used principally by the nucleus. The nuclear pore had fascinated biologists for decades, but it was only in the early 2000's that this mechanism was revealed. And a recent paper found that peroxisomes also use this second method, which side-steps the need to thread incoming proteins through a pore, and risk all the problems of refolding. This method is to use a curiously constructed gel phase of (protein) matter that shares some properties with membranes, but has the additional property that specifically compatible proteins can melt right through it. 

The secret lies in repetitive regions of protein sequence that carry, in the case of the nuclear pore, lots of F-G sequences. That is, phenylalanine-glycine repeated regions of proteins that form these transit gel structures, or pores. The phenylalanine is hydrophobic, the glycine is flexible, and the protein backbone is polar, though not charged. This adds up to a region that is a totally disordered mess and forms a gel that can keep out most larger molecules, like a membrane. But if encountered by another F-G-rich protein, this gel lets it right through, like a pat of butter through oil. It also tends to let small molecules through quite easily. The nuclear pore is quite permeable to the many chemicals needed for DNA replication, RNA production, etc.

Summary from current paper, making the case that peroxisomes use PEX13 to make something similiar to the nuclear pore, where targeted proteins can traverse easily piggybacked on carrier proteins, in this case PEX5. The yellow spaghetti is the F-G or Y-G protein tails that congregate in the pore to make up a novel (gel) phase of matter. This gel is uniquely permeable to proteins carrying the same F-G or Y-G on their outsides, as does PEX5. "NTR" is short for nuclear targeting receptor, to which nuclear-bound cargoes bind.

Peroxisomes are sites for specialty chemistry, handling some relatively dangerous oxidation reactions including production of some lipids. They combines this with protective enzymes like catalase that quickly degrade the resulting reactive oxidative products. This suggests that the peroxisomal membrane would need to be pretty tight, but the authors state that the gel-style mechanism used here allows anything under 2,000 Daltons through, which certainly includes most chemicals. Probably the solution is that enough protective enzymes, at a high local concentration, are present that the leakage rate of bad chemicals is relatively low. 

Experimenters purify large amounts of the Y-G protein segments from PEX13 and form macroscopic gels out of them. In the center is a control, where the Y residues have been mutated to serine (S). N+YG refers to the N-terminus of the PES13 protein plus the Y-G portion of the proteins, while Y-G alone has only the Y-G segment of the PEX13 protein.

For its gel-containing pore, the peroxisome uses (on a protein called PEX13) tyrosine (Y) in place of phenylalanine, resulting in a disordered gel of Y-G repeats for its structure. Tyrosine is aromatic, (thus hydrophobic) like phenylalanine and tryptophan, and apparently provides enough distinctiveness that nucleus-bound proteins are not mistaken in their destination. The authors state that it provides a slightly denser packing, and by its composition should help prevent nuclear carriers from binding effectively. But it isn't just the Y-G composition that directs proteins, but a suite of other proteins around the peroxisomal and nuclear pores that, I would speculate, help attract their respective carrier proteins (called PEX5 in the case of peroxisomes) so that they know where to go. 

Evolutionary conservation of the Y-G regions of PEX13, over a wide range of species. The semi-regular periodicity of the Y placements suggests that this protein forms alpha helixes with the Y chains exposed on one side, more or less, despite general lack of structure. 

The authors show some very nice experiments, such as making visible gels from purified / large amounts of these proteins, and then showing that these gels indeed block generic proteins, and allow the same protein if fused to PEX5 to come right through. The result shown below is strikingly absolute- without its peroxisome-specific helper, the protein GFP makes no headway into this gel material at all. But with that helper, it can diffuse 100 microns in half an hour. It is like making jello that you can magically pass your hand through, without breaking it up ... but only if you are wearing the magic glove.

Experimental demonstration of transport. Using macroscopic gel plugs like those shown above, the diffusion of green fluorescent protein (GFP) was assayed from a liquid (buffer) into the gel. By itself (center, bottom), GFP makes no headway at all. But when fused to the PEX5 protein, either in part or in whole, it diffuses quite rapidly into the Y-G gel.

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• Humanism.
• Humanism.
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One Pump to Rule ... a Tiny Vesicle

Synaptic vesicles are powered by a single pump that has two speeds- on and off.

While some neural circuits are connected by direct electrical contact, via membrane pores, most use a synapse, where the electrical signal stops, gets turned into secretion of a neurotransmitter molecule, which crosses to the next cell, where receptors pick it up and boot up a new electrical signal. A slow and primitive system, doubtless thanks to some locked-in features of our evolutionary history. But it works, thanks to a lot of improvements and optimization over the eons.

The neurotransmitters, of which there are many types, sit ready and waiting at the nerve terminals in synaptic vesicles, which are tiny membrane bags that are specialized to hold high concentrations of their designated transmitter, and to fuse rapidly with the (pre-) synaptic membrane of their nerve terminal, to release their contents when needed, into the synaptic cleft between the two neurons. While the vesicle surfaces are mostly composed of membranes, it is the suite of proteins on their surfaces that provide all the key functions, such as transport of neurotransmitters, sensing of the activating nerve impulse (voltage), fusing with the plasma membrane, and later retrieval of the fused membrane patches/proteins and recycling into new synaptic vesicles.

Experimental scheme- synaptic vesicles are loaded with a pH-sensitive fluorescent dye that tells how the V-ATPase (pink) is doing pumping protons in, powered by ATP from the cytoplasm. The proton gradient is then used by the other transporters in the synaptic vesicle (brown) to load it with its neurotransmitter.

The neurotransmitters of whatever type are loaded into synaptic vesicles by proton antiporter pumps. That is, one or two protons are pumped out in exchange for a molecule of the transmitter being pumped in. They are all proton-powered. And there is one source of that power, an ATP-using proton pump called a V-type ATPase. These ATPases are deeply related to the F-type ATP synthase that does the opposite job, in mitochondria, making ATP from the proton gradient that mitochondria set up from our oxygen-dependent respiration / burning of food. Both are rotors, which spin around as they carefully let protons go by, while a separate domain of the protein- attached via stator and rotor segments- makes or breaks down ATP, depending on the direction of rotation. Both enzymes can go in either direction, as needed, to pump protons either in or out, and traverse the reaction ADP <=> ATP. It is just an evolutionary matter of duplication and specialization that the V-type and F-type enzymes have taken separate paths and turn up where they do.

Intriguingly, synaptic vesicles are each served by one V-type ATPase. One is enough. That means that one molecule has to flexibly respond to variety of loads, from the initial transmitter loading, to occasional replenishment and lots of sitting around. A recent paper discussed the detailed function of the V-type ATPase, especially how it handles partial loads and resting states. For the vesicles spend most of their time full, waiting for the next nerve impulse to come along. The authors find that this ATPase has three states it switches between- pumping, resting, and leaking. 

Averaging over many molecules/vesicles, the V-type ATPase pump operates as expected. Add ATP, and it acidifies its vesicle. The Y-axis is the fluorescent signal of proton accumulation in the vesicle. Then when a poison of the ATPase is added (bafilomycin), the gradient dissipates in a few minutes.

They isolate synaptic vesicles directly from rat brains and then fuse them with smaller experimental vesicles that contain a fluorescent tracer that is sensitive to pH- just the perfect way to monitor what is going on in each vesicle, given a powerful enough microscope. The main surprise was the stochastic nature of the performance of single pumps. Comparing the average of hundreds of vesicles (above) with a trace from a single vesicle (below) shows a huge difference. The single vesicle comes up to full acidity, but then falls back for long stretches of time. These vesicles are properly loaded and maintained on average, but individually, they are a mess, falling back to pH / chemical baseline with alarming frequency.

On the other hand, at the single molecule level, the pump is startlingly stochastic. Over several hours, it pumps its vesicle full of protons, then quits, then restarts several times.

The authors checked that the protons had no other way out that would look like this stochastic unloading event, and concluded that the loss of protons was monotonic, thus due to general leakage, not some other channel that occasionally opens to let out a flood of protons. But then they added an inhibitor that blocks the V-ATPase, which showed that particularly (and peculiarly) rapid events of proton leakage come from the V-ATPase, not general membrane leakage. They have a hard time explaining this, discounting various theories such that it represents ATP synthesis (a backwards reaction, in the face of overwhelming ratios of ATP/ADP in their experiment), or that the inactive mode of the pump can switch to a leakage mode, or that the pump naturally leaks a bit while it operates in the forward direction. It appears that only while the pump is on and churning through ATP, it can occasionally fail catastrophically and leak out a flood of protons. But then it can go on as if nothing had happened and either keep pumping or take a rest break.

Regulation by ATP is relatively minor, with a flood of ATP helping keep the pump more active longer. But physiological concentrations tend to be stable, so not very influential for pumping rates. These are two separate individual pumps/vesicles shown, top and bottom. It is good to see the control- the first segment of time when no ATP was present and the pump could not run at all. But then look at the bottom middle trace- plenty of ATP, but nothing going on- very odd. Lastly, the sudden unloading seen in some of these traces (bottom right) is attributed to an extremely odd leakage state of the same V-ATPase pump. Not something you want to see, generally.

The main finding is that this pump has quite long dwell times (3 minutes or so) under optimal conditions, and switches with this time period between active pumping and an inactive resting state. And that the pumping dwell time is mostly regulated, not by the ambient ATP concentration, but by the proton gradient, which is expressed by some combination of the charge differential across the vesicle membrane and the relative proton concentration gradient (the chemical gradient). It is a bit like a furnace, which has only two speeds- on or off, though in this case the thermostat is pretty rough. They note that other researchers have noted that synaptic vesicles seem to have quite variable amounts of transmitter, which must derive from the variability of this pump seen here. But averaged over the many vesicles fused during each neuronal firing, this probably isn't a big deal.

The behavior of this pump is a bit weird, however, since most machines that we are familiar with show more gradual breakdowns under stress, straining and slowing down. But here, the pump just decides to shut down for long periods of time, generally when the vesicle is fully charged up, but sometimes when it is not. It is a reflection that we are near the quantum level here, dealing with molecules that are very large in some molecular sense, but still operating at the atomic scale, particularly at the key choke points of this kind of protein that surely involve subtle shifts of just a few atoms that impart this regulatory shift, from active to inactive. What is worse, the pump sometimes freaks out completely and, while in its on state, switches to a leaking state that lets out protons ten times faster than the passive leakage through the rest of the vesicle membrane. The authors naturally urge deeper structural studies of what might be going on!

• Our soylent future.
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• A war within.
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Empty Skepticism at the Discovery Institute

What makes a hypothesis scientific, vs a just-so story, or a religious fixation?

"Intelligent" design has fallen on hard times, after a series of court cases determined that it was, after all, a religious idea and could not be foisted on unsuspecting schoolchildren, at least in state schools and under state curricula. But the very fact of religious motivation leads to its persistence in the face of derision, evidence, and apathy. The Discovery Institute, (which, paranthetically, does not make any discoveries), remains the vanguard of intelligent design, promoting "skepticism", god, alternative evolutionary theories, and, due to the paucity of ways to attack evolution, tangential right-wingery such as anti-vaccine agitation. By far their most interesting author is Günter Bechly, who delves into the paleontological record to heap scorn on other paleontologists and thereby make room for the unmentioned alternative hypothesis ... which is god.

A recent post discussed the twists and turns of ichthyosaur evolution. Or should we say biological change through time, with unknown causes? Ichthyosaurs flourished from about 250 million years ago (mya) to 100 mya, with the last representatives dated to 90 mya. They were the reptile analogs of whales and dophins, functioning as apex predators in the ocean. They were done in by various climate crises well-prior to the cometary impact that ended the Cretaceous and the reign of dinosaurs in general.

Bechly raises two significant points. First is the uncertain origins of Ichthyosaurs. As is typical with dramatic evolutionary transitions like that from land to water in whales, the time line is compressed, since there are a lot of adaptations that are desirable for the new environment that might have been partially pre-figured, but get fleshed out extensively with the new ecological role and lifestyle. Selection is presumably intense and transitional fossils are hard to find. This was true for whales, though beautiful transitional fossils have been found more recently. And apparently this is true for the Ichthyosaurs as well, where none have been found, yet. There is added drama stemming from the time of origin, which is right after the Permian exinction, perhaps the greatest known extinction event in the history of the biosphere. Radiations after significant extinction events tend to be rapid, with few transitional fossils, for the same reason of new niches opening and selection operating rapidly.

Ichthyosaur

Bechly and colleagues frequently make hay out of gaps in the fossil record, arguing that something (we decline to be more specific!) else needs to be invoked to explain such lack of evidence. It is a classic god of the gaps argument. But since the fossils are never out of sequence, and we are always looking at millions of years of time going by with even the slimmest layers of rock, this is hardly a compelling argument. One thing that we learned from Darwin's finches, and the whole argument around punctuated equilibrium, is that evolution is typically slow because selection is typically not directional but conservative. But when selection is directional, evolution by natural selection can be startlingly fast. This is an argument made very explicitly by Darwin through his lengthy discussions of domestic species, whose changes are, in geological terms, instant. 

But Bechly makes an additional interesting argument- that a specific hypothesis made about ichthyosaurs is a just-so story, a sort of hypothesis that evolutionary biologists are very prone to make. Quite a few fossils have been found of ichthyosaurs giving birth, and many of them find that the baby comes out not only live (not as an egg, as is usual with reptiles), but tail-first. Thus some scientists have made the argument that each are adaptations to aquatic birth, allowing the baby to be fully borne before starting to breathe. Yet Bechly cites a more recent scientific review of the fossil record that observes that tail-first birth is far from universal, and does not follow any particular phylogenetic pattern, suggesting that it is far from necessary for aquatic birth, and thus is unlikely to be, to any significant extent, an adaptation. 

Ha! Just another story of scientists making up fairy tales and passing them off as "science" and "evolutionary hypotheses", right?  

"Evolutionary biology again and again proves to be an enterprise in imaginative story-telling rather than hard science. But when intelligent design theorists question the Darwinist paradigm based on empirical data and a rational inference to the best explanation, they are accused of being science deniers. Which science?" ... "And we will not let Darwinists get away with a dishonest appeal to the progress of science when they simply rewrite their stories every time conflicting evidence can no longer be denied."

Well, that certainly is a damning indictment. Trial and sentencing to follow! But let's think a little more about what makes an explanation and a hypothesis, on the scientific, that is to say, empirical, level. Hypotheses are always speculative. That is the whole point. They try to connect observations with some rational or empirically supported underlying mechanism / process to account for (that is, explain) what is observed. Thus the idea that aquatic birth presents a problem for mammals who have to breathe represents a reasonable subject for an hypothesis. Whether headfirst or tailfirst, the baby needs to get to the surface post haste, as soon as its breathing reflex kicks in. While the direction of birth doesn't seem to the uninitiated (and now, apparently to experts with further data at hand) to make much difference, thinking it does is a reasonable hypothesis, based on obvious geometric arguments and biological assumptions, that it is possible that the breathing reflex is tied to emergence of the head during birth, in which case coming out tailfirst might delay slightly the time it takes between needing to breathe and being able to breathe. 

This argument combines a lot of known factors- the geometry of birth, the necessity of breathing, the phenomenon of the breathing reflex initiating in all mammals very soon after birth, by mechanisms that doubtless are not entirely known, but at the same time clearly the subject of evolutionary tuning. And also the paleontological record. Good or bad, the hypothesis is based on empirical data. What characterizes science is that it follows a disciplined road from one empirically supported milestone to the next, using hypotheses about underlying mechanisms, whether visible or not, which abide by all the known/empirical mechanisms. Magic is only allowed if you know what is going on behind the curtain. Unknown mechanisms can be invoked, but then immediately become subjects of further investigation, not of protective adulation and blind worship.

In contrast, the intelligent design hypothesis, implicit here but clear enough, is singularly lacking in any data at all. It is not founded on anything other than the sentiment that what has clearly happened over the long course of the fossil record operates by unknown mechanisms, by god operating pervasively to carry out the entire program of biological evolution, not by natural selection (a visible and documented natural process) but by something else, which its proponents have never been able to demonstrate in the least degree, on short time scales or long. Faith does not, on its own, warrant novel empirical mechanisms, and nor does skeptical disbelief warrant them. Nor does one poor, but properly founded, hypothesis that is later superceded by more careful analysis of the data impugn the process of science generally or the style of evolutionary thinking specifically.

Imagine, for example, if our justice system operated at this intellectual level. When investigating crimes, police could say that, if the causes were not immediately obvious, an unnamed intelligent designer was responsible, and leave it there. No cold cases, no presumption of usual natural causality, no dogged pursuit of "the truth" by telegenic detectives. Faith alone would furnish the knowledge that the author of all has (inscrutibly) rendered "his" judgement. It would surely be a convenient out for an over-burdened and under-educated police force!

Evolution by natural selection requires a huge amount of extrapolation from what we know about short time scales and existing biology to the billions of years of life that preceeded us. On the other hand, intelligent design requires extrapolation from nothing at all- from the incredibly persistent belief in god, religion, and the rest of the theological ball of wax not one element of which has ever been pinned down to an empirical fact. Believers take the opposite view solely because religious propaganda has ceaselessly drilled the idea that god is real and "omnipotent" and all-good, and whatever else wonderful, as a matter of faith. With this kind of training, then yes, "intelligent" design makes all kinds of sense. Otherwise not. Charles Darwin's original hypothesis was so brilliant because it drew on known facts and mechanisms to account (with suitable imagination and extrapolation) for the heretofore mysterious history of biology, with its painfully slow yet inexorable evolution from one species to another, one epoch to another. Denying that one has that imagination is a statement about one's intelligence, no matter how it was designed.

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• With a wonderful soundtrack, including NDN Kars.
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• California is dumbing down math, and that will not help any demographic.