The 12th day of beer

A slightly late Christmas present arrived on my doorstep this afternoon: Søren from Denmark had a case of 12 interesting beers sent to me. Thank you! Now, of course, I must drink them all. Immediately.

No, wait, that would be unwise. I shall drink one a night until they are gone. Tonight, I am sipping on Trout Slayer Ale, just because the combination of mighty fish and slaying makes me feel macho.


Mmmm. Mild. Lemony. Not very ferocious at all.

How to afford a big sloppy genome


My direct experience with prokaryotes is sadly limited — while our entire lives and environment are profoundly shaped by the activity of bacteria, we rarely actually see the little guys. The closest I’ve come was some years ago, when I was doing work on grasshopper embryos, and sterile technique was a pressing concern. The work was done under a hood that we regularly hosed down with 95% alcohol, we’d extract embryos from their eggs, and we’d keep them alive for hours to days in tissue culture medium — a rich soup of nutrients that was also a ripe environment for bacterial growth. I was looking at the development of neurons, so I’d put the embryo under a high-powered lens of a microscope equipped with differential interference contrast optics, and the sheet of grasshopper neurons would look like a giant’s causeway, a field of tightly packed rounded boulders. I was watching processes emerging and growing from the cells, so I needed good crisp optics and a specimen that would thrive healthily for a good long period of time.

It was a bad sign when bacteria would begin to grow in the embryo. They were visible like grains of rice among the ripe watermelons of the cells I was interested in, and when I spotted them I knew my viewing time was limited: they didn’t obscure much directly, but soon enough the medium would be getting cloudy and worse, grasshopper hemocytes (their immune cells) would emerge and do their amoeboid oozing all over the field, engulfing the nasty bacteria but also obscuring my view.

What was striking, though, was the disparity in size. Prokaryotic bacteria are tiny, so small they nestled in the little nooks between the hopper cells; it was like the opening to Star Wars, with the tiny little rebel corvette dwarfed by the massive eukaryotic embryonic cells that loomed vastly in the microscope, like the imperial star destroyer that just kept coming and totally overbearing the smaller targets. And the totality of the embryo itself — that’s no moon. It’s a multicellular organism.

I had to wonder: why have eukaryotes grown so large relative to their prokaryotic cousins, and why haven’t any prokaryotes followed the strategy of multicellularity to build even bigger assemblages? There is a pat answer, of course: it’s because prokaryotes already have the most successful evolutionary strategy of them all and are busily being the best microorganisms they can be. Evolving into a worm would be a step down for them.

That answer doesn’t work, though. Prokaryotes are the most numerous, most diverse, most widely successful organisms on the planet: in all those teeming swarms and multitudinous opportunities, none have exploited this path? I can understand that they’d be rare, but nonexistent? The only big multicellular organisms are all eukaryotic? Why?

Another issue is that it’s not as if eukaryotes carry around fundamentally different processes: every key innovation that allowed multicellularity to occur was first pioneered in prokaryotes. Cell signaling? Prokaryotes have it. Gene regulation? Prokaryotes have that covered. Functional partitioning of specialized regions of the cell? Common in prokaryotes. Introns, exons, endocytosis, cytoskeletons…yep, prokaryotes had it first, eukaryotes have simply elaborated upon them. It’s like finding a remote tribe that has mastered all the individual skills of carpentry — nails and hammers, screws and screwdrivers, saws and lumber — as well as plumbing and electricity, but no one has ever managed to bring all the skills together to build a house.

Nick Lane and William Martin have a hypothesis, and it’s an interesting one that I hadn’t considered before: it’s the horsepower. Eukaryotes have a key innovation that permits the expansion of genome complexity, and it’s the mitochondrion. Without that big powerplant, and most importantly, a dedicated control mechanism, prokaryotes can’t afford to become more complex, so they’ve instead evolved to dominate the small, fast, efficient niche, leaving the eukaryotes to occupy the grandly inefficient, elaborate sloppy niche.

Lane and Martin make their case with numbers. What is the energy budget for cells? Somewhat surprisingly, even during periods of rapid growth, bacteria sink only about 20% of their metabolic activity into DNA replication; the costly process is protein synthesis, which eats up about 75% of the energy budget. It’s not so much having a lot of genes in the genome that is expensive, it’s translating those genes into useful protein products that costs. And if a bacterium with 4400 genes is spending that much making them work, it doesn’t have a lot of latitude to expand the number of genes — double them and the cell goes bankrupt. Yet eukaryotic cells can have ten times that number of genes.

Another way to look at it is to calculate the metabolic output of the typical cell. A culture of bacteria may have a mean metabolic rate of 0.2 watts/gram; each cell is tiny, with a mass of 2.6 x 10-12g, which means each cell is producing about 0.5 picowatts. A eukaryotic protist has about the same power output per unit weight, 0.06 watts/gram, but each cell is so much larger, about 40,000 x 10-12g, that a single cell has about 2300 picowatts available to it. So, more energy!

Now the question is how that relates to genome size. If the prokaryote has a genome that’s about 6 megabases long, that means it has about 0.08 picowatts/megabase to spare. If the eukaryote genome is 3,000 megabytes long, that translates into about 0.8 picowatts of power per megabase (that’s a tenfold increase, but keep in mind that there is wide variation in size in both prokaryotes and eukaryotes, so the ranges overlap and we can’t actually consider this a significant difference — they’re in the same ballpark).

Now you should be thinking…this is just a consequence of scaling. Eukaryotic power production per gram isn’t any better than what prokaryotes do, all they’ve done is made their cells bigger, and there’s nothing to stop prokaryotes from growing large and doing the same thing. In fact, they do: the largest known bacterium, Thiomargarita, can reach a diameter of a half-millimeter. It gets more metabolic power in a similar way to how eukaryotes do it: we eukaryotes carry a population of mitochondria with convoluted membranes and a dedicated strand of DNA, all to produce energy, and the larger the cell, the more mitochondria are present. Thiomargarita doesn’t have mitochondria, but it instead duplicates its own genome many times over, with 6,000-17,000 nucleoids distributed around the cell, each regulating its own patch of energy-producing membrane. It’s functionally equivalent to the eukaryotic mitochondrial array then, right?

Wrong. There’s a catch. Mitochondria have grossly stripped down genomes, carrying just a small cluster of genes essential for ATP production. One hypothesis for why this mitochondrial genome is maintained is that it acts as a local control module, rapidly responding to changes in the local membrane to regulate the structure. In Thiomargarita, in order to get this fine-tuned local control, the whole genome is replicated, dragging along all the baggage, and metabolic expense, of all of those non-metabolic genes.

Because it is amplifying the entire genomic package instead of just an essential metabolic subset, Thiomargarita‘s energy output per gene plummets in comparison. That difference is highlighted in this illustration which compares an ‘average’ prokaryote, Escherichia, to a giant prokaryote, Thiomargarita, to an ‘average’ eukaryotic protist, Euglena.

(Click for larger image)

The cellular power struggle. a-c, Schematic representations of a medium sized prokaryote (Escherichia), a very large prokaryote (Thiomargarita), and a medium-sized eukaryote (Euglena). Bioenergetic membranes across which chemiosmotic potential is generated and harnessed are drawn in red and indicated with a black arrow; DNA is indicated in blue. In c, the mitochondrion is enlarged in the inset, mitochondrial DNA and nuclear DNA are indicated with open arrows. d-f, Power production of the cells shown in relation to fresh weight (d), per haploid gene (e) and per haploid genome (power per haploid gene times haploid gene number) (f). Note that the presence or absence of a nuclear membrane in eukaryotes, although arguably a consequence of mitochondrial origin70, has no impact on energetics, but that the energy per gene provided by mitochondria underpins the origin of the genomic complexity required to evolve such eukaryote-specific traits.

Notice that the prokaryotes are at no disadvantage in terms of raw power output; eukaryotes have not evolved bigger, better engines. Where they differ greatly is in the amount of power produced per gene or per genome. Eukaryotes are profligate in pouring energy into their genomes, which is how they can afford to be so disgracefully inefficient, with numerous genes with only subtle differences between them, and with large quantities of junk DNA (which is also not so costly anyway; remember, the bulk of the expense is in translating, not replicating, the genome, and junk DNA is mostly untranscribed).

So, what Lane and Martin argue is that the segregation of energy production into functional modules with an independent and minimal genetic control mechanism, mitochondria with mitochondrial DNA, was the essential precursor to the evolution of multicellular complexity — it’s what gave the cell the energy surplus to expand the genome and explore large-scale innovation.

As they explain it…

Our considerations reveal why the exploration of protein sequence space en route to eukaryotic complexity required mitochondria. Without mitochondria, prokaryotes—even giant polyploids—cannot pay the energetic price of complexity; the lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause. The conversion from endosymbiont to mitochondrion provided a freely expandable surface area of internal bioenergetic membranes, serviced by thousands of tiny specialized genomes that permitted their host to evolve, explore and express massive numbers of new proteins in combinations and at levels energetically unattainable for its prokaryotic contemporaries. If evolution works like a tinkerer, evolution with mitochondria works like a corps of engineers.

That last word is unfortunate, because they really aren’t saying that mitochondria engineer evolutionary change at all. What they are is permissive: they generate the extra energy that allows the nuclear genome the luxury of exploring a wider space of complexity and possible solutions to novel problems. Prokaryotes are all about efficiency and refinement, while eukaryotes are all about flamboyant experimentation by chance, not design.

Lane N, Martin W. (2010) The energetics of genome complexity. Nature 467(7318):929-34.

Apparitions and distractions

Lawrence Murphy was an evil man. He was a Wisconsin priest who molested over 200 boys, and just to make the story particularly deplorable, they were deaf children. Preying on the weakest and most vulnerable was apparently his life’s mission. Furthermore, this was the scandalous case that was reported directly to then Cardinal Ratzinger in his role as the Vatican enforcer; his enforcement involved shuffling the guilty around to hide their crimes and give them fresh opportunities in new hunting grounds.

Well, the Vatican has finally found it in its black (but gold-plated!) and shriveled husk of a heart to do something for Wisconsin: they’ve blessed a ghost sighting as genuine. Woo hoo! That’ll fix everything right up!

The church has declared that a sighting in 1859 of a blond Mary hovering between two trees was real and worthy, and the local Catholic church is now busily expanding their parking lot to cope with the expected influx of gullible suckers pilgrims who will flock to the site to imagine a floating cheerleader for Jesus.


It’s a funny story, too. A Belgian immigrant, Adele, claimed to see this:

As they approached the hallowed spot, Adele could see the beautiful lady, clothed in dazzling white, with a yellow sash around her waist. Her dress fell to her feet in graceful folds. She had a crown of stars around her head, and her long, golden, wavy hair fell loosely around her shoulders. Such a heavenly light shone around her that Adele could hardly look back at her sweet face.

You know what really made it miraculous? Adele was accompanied by two other women, who couldn’t see or hear the floating lady.

” ‘Adele, who is it?” said one of the women. ‘O why can’t we see her as you do?’ said another weeping.

” ‘Kneel,’ said Adele, ‘the Lady says she is the Queen of Heaven.’ Our Blessed Lady turned, looked kindly at them, and said, ‘Blessed are they that believe without seeing. What are you doing here in idleness…while your companions are working in the vineyard of my Son?'”

That settles it. It must have been a magical manifestation if it was invisible. Invisible and blond, just like I always imagined a Middle Eastern Semitic peasant woman. And the statement that you’re blessed if you believe without seeing is pitch-perfect Catholicism.

Another funny thing is that the priests are obviously uncomfortably aware that this all sounds like rather convenient timing.

Catholic leaders described the decree in Wisconsin as a bolt of joy at a trying time for the Catholic church, which is troubled by revelations of sex abuse.

“This is a gift to the believers,” said the Rev. Johann Roten, director of the International Marian Research Institute at the University of Dayton.

“It would be devious to say that this was somehow pulled out of the attic to exorcise the problems of the church today,” Father Roten said in a telephone interview. “But hopefully this will have a beneficial impact on the people, showing them that there are ways of living with faith that are very pure.”

Yeah, how?

Never mind that! We’ve got child-raping priests! This calls for an immediate distraction in the form of invisible blond women, bugger the blatant nature of the ploy, and pass out the platitudes!

Why, that poll is almost virginal!

Atheist Ireland is looking to determine the most fervent believer of the year with an online poll (frivolous topic, frivolous poll), and I was astounded to discover it had hardly been touched. It was an almost virginal poll.

The really, truly True Believer™ of the YEAR 2010

And the winner of 2010 is…

Islamic breast hacking clerics 0% [ 0 ]
Vatican Child Abuse as bad as Ordination of Women. 0% [ 0 ]
God phoning children in Massachusetts. 0% [ 0 ]
Conor Lenihan and the anti science anti evolution book. 100% [ 2 ]
Sheikh Maulana Rape ok in marriage 0% [ 0 ]
Irish Minister for Social Protection pray for the economy. 0% [ 0 ]
Hanging the Christmas elf as a helper of Satan 0% [ 0 ]
Virginia Politician thinking ecurity pat dows are gay agenda. 0% [ 0 ]

Well, I didn’t vote — I just backed away. I like my polls a little more experienced. Don’t let that stop you, though!

BBC gives child rape apologist air time

The Pope had a Christmas message for the world this year: we should forgive Catholic priests for raping children because everyone else was doing it. He invented a peculiar history that bears no resemblance to the late 20th century I lived in.

“In the 1970s, paedophilia was theorised as something fully in conformity with man and even with children,” the Pope said.

“It was maintained — even within the realm of Catholic theology — that there is no such thing as evil in itself or good in itself. There is only a ‘better than’ and a ‘worse than’. Nothing is good or bad in itself.”

The Pope said abuse revelations in 2010 reached “an unimaginable dimension” which brought “humiliation” on the Church.

I grew up in the 1970s. Some of you did, too. Does anyone remember anyone influential saying that child-rape was a reasonable practice? How about anyone on the fringe making vague suggestions that children can give permission to participate in sexual activity? I don’t know of any substantial culture at that time that would have endorsed such a thing; NAMBLA was little more than a freakish collection of perverts who got far more attention than their numbers warranted. If there was anything that was universally reviled, it was the creepy pedophile.

So here’s the Pope pretending that they were living in an environment that somehow condoned child abuse, so the priesthood somehow went along with it? Madness.

I also am not impressed by his regret that the church was humiliated. That’s not an appropriate response at all: church members were the perpetrators of the crime, and the Pope still can’t seem to empathize with the victims…you know, the kids. They always seem to get forgotten when the pontiff pontificates on the abuses of his church.

The other night, I saw this ghastly little documentary called Hell House, about fundagelical nutcases who put on these elaborate morality plays around Halloween, to scare people into Christianity. They have this same moral blindness. I was struck by all the horrible little scenarios they put on: woman goes to rave, is given date-rape drug and is raped; woman gets pregnant, has abortion, bleeds to death; etc., etc., etc. In every case I was struck by the fact that it is the victim who suffers and is abused and dies, and who is then sent to hell for eternal punishment because she doesn’t believe in Jesus. I was expecting in these cases to see them end in an orgy of punishment for the drug-dealer, the rapist, the abortionist (all played by men, by the way), but no…they all get forgotten in the denouement, their behavior isn’t damned, it’s all about the victim being punished for her victimization. That’s religion for you.

Anyway, after listening to this ethical rapscallion invent fantasy stories to justify the abuse of innocents, the BBC, in a fit of moral blindness themselves, offered him a radio spot to blather on some more. What were they thinking? The good news, though, is that he didn’t flaunt his moral turpitude this time. Instead, he highlighted the intellectual vacuity of the church, by talking about the nonsense of their beliefs.

He added that God “often surprises us” in the way he fulfils his promises.

“The child that was born in Bethlehem did indeed bring liberation, but not only for the people of that time and place — he was to be the saviour of all people throughout the world and throughout history.”

It was not a political liberation, achieved through military means, he added, but rather “Christ destroyed death for ever and restored life by means of his shameful death on the cross”.

I just wish people could see through the platitudes and realize that these oft-repeated claims make no freakin’ sense. A guy getting killed 2000 years ago did not end death, you may have noticed, a shameful death is not turned into a point of pride by waving corpses-on-a-stick in our faces, and Christianity has been an agent of ignorance and servility for millennia now, never a cause for liberation.

Shame on the BBC for giving this flabby-brained antique a megaphone and a spot on the airwaves.

Have you still got your Christmas tree up?

Then it’s not too late to get this fabulous ornament for it:


Even if you don’t have a Christmas tree ever or any more, you can still help out with the James Randi Educational Foundation’s fundraising campaign. The JREF has been awarding grants to teachers and students to promote critical thinking, provides lesson plans and curricula, and makes all kinds of tools available to educators, all to help improve the minds of people all around the world. It’s a great cause, and they’re struggling right now like all charities in a bad economy.

I’ve got one of those ornaments on my otherwise entirely squid-based theme of holiday decorations, and it looks great there. The JREF goes well with everything!

I get email

Joe wrote me a letter because he doesn’t think my arguments against creationism are very good. Unfortunately, his arguments are…well, pretty much the standard inconsistent and incoherent tripe I always get from creationists. But at least Joe has an excuse: he’s only 12.

By the way, his email actually was in Comic Sans. Part of it, anyway: a large random chunk in the middle was set in good ol’ Comic Sans.

Hello. This is not Spam. I would like to have a discussion on your post ‘The five best arguments for creationism ever.’ ( Where you try to disprove theory’s made by creationists on a news paper article I left a comment but I feel that your points are not strong and I (being a twelve year old kid) would like to argue them further the other way. Here is the comment that I left (well i changed it a bit from my original comment).

1. We have lots of evidence between evolution with in a species BUT NOT BETWEEN SPECIES its called the missing link!

The “missing link” is copy from tabloid journalism. There is no “missing link”, scientists are not looking for one, and it’s silly to argue that we have to find something that evolution does not predict.

It’s populations that evolve, and we have plenty of examples of transitional forms. Look up ring species, or Tiktaalik, or whale fossils, or any of the hominid fossils. What you are calling the “missing links” are out there, and closing your eyes won’t make them go away.

2.Just because the earth is obviously old doesn’t mean that this point is incorrect as got could have easy created a pre-aged earth (god dint create Adam and eave as babies, he created them pre-aged.

OK, that’s fine; you’ve just invoked a major magic trick by a deceiver god. That is a possibility that would account for the existence of all that evidence for evolution, but then you don’t get to deny the existence of “missing links”; that’s part of the evidence for an old earth that your trickster deity salted in the ground.

3. The compound eye is an example of irreducible complexity so complex that it cannot be any less complex its ether an eye or it isn’t there is no evolution in the middle. Another example of irreducible complexity is blood clotting.

Irreducible complexity is a dead issue, I’m afraid. It’s no obstacle to evolution, the examples of IC that creationists frequently trot out, like the clotting cascade, are explainable by natural processes.

4. It is true that some creationists think that ‘the bible uses allegory to explain the creation of the earth. It is a story, so employs figures of speech and other literary devices to tell the story of how God created man e.g. Genesis “days” could also be read as “ages”.’ but I don’t see what the newspapers point is there.

The newspaper tried to suggest that there were reasonable scientific arguments in favor of a young earth, that is, an earth less than ten thousand years old. It was wrong; there are none.

By the way, you haven’t presented an argument here. Have you run out?

5. Evolutionists have not, cannot ant will not prove evolution… mainly because they have not cannot and will not find the missing link.

This is the same as your first argument. I guess you really are done.

So you’ve managed to come up with a grand total of three arguments: the first is built on a misconception and denial of the evidence; the second simply argues that it was all magic; and the third simply regurgitates an intelligent design creationism buzz phrase. That’s a rather poor performance.


I have a problem with many science teachers teaching evolution. If you are going to teach students evolution you need to teach students all the opposing theories. I

however Evolution and Creation may not be opposite and it may be that they merge together as the book of genesis is taken by many to be a story of figures of speech and literary devices and therefore can mean that evolution may merge into that. And personally given better evidence I may be able to accept that idea however I refuse to believe that man evolved from any other species because man is created in gods image and any other species are not.

Your refusal to believe in the evidence because you don’t like the conclusions is fairly typical creationist thinking, and it’s also illogical and wrong. There is no reason to accept the book of Genesis as a legitimate source of scientific information, and your refusal to consider the possibility that it isn’t a science text and gets all the science wrong puts you out of the realm of scientific thinking.

The molecular foundation of the phylotypic stage


When last we left this subject, I had pointed out that the phenomenon of embryonic similarity within a phylum was real, and that the creationists were in a state of dishonest denial, arguing with archaic interpretations while trying to pretend the observations were false. I also explained that constraints on morphology during development were complex, and that it was going to take something like a thorough comparative analysis of large sets of gene expression data in order to drill down into the mechanisms behind the phylotypic stage.

Guess what? The comparative analysis of large sets of gene expression data is happening. And the creationists are wrong, again.

Again, briefly, here’s the phenomenon we’re trying to explain. On the left in the diagram below is the ‘developmental hourglass’: if you compare eggs from various species, and adults from various species, you find a diversity of forms. However, at one period in early development called the phylytypic stage (or pharyngula stage specifically in vertebrates), there is a period of greater similarity. Something is conserved in animals, and it’s not clear what; it’s not a single gene or anything as concrete as a sequence, but is instead a pattern of interactions between developmentally significant genes.


The diagram on the right is an explanation for the observations on the left. What’s going on in development is an increase in complexity over time, shown by the gray line, but the level of global interactions does not increase so simply. What this means is that in development, modular structures are set up that can develop autonomously using only local information; think of an arm, for instance, that is initiated as a limb bud and then gradually differentiates into the bones and muscle and connective tissue of the limb without further central guidance. The developing arm does not need to consult with the toes or get information from the brain in order to grow properly. However, at some point, the limb bud has to be localized somewhere specific in relation to the toes and brain; it does require some sort of global positioning system to place it in the proper position on the embryo. What we want to know is what is the GPS signal for an embryo: what it looks like is that that set of signals is generated at the phylotypic stage, and that’s why this particular stage is relatively well-conserved.

One important fact about the diagram above: the graph on the right is entirely speculative and is only presented to illustrate the concept. It’s a bit fake, too—the real data would have to involve multiple genes and won’t be reducible to a single axis over time in quite this same way.

Two recent papers in Nature have examined the real molecular information behind the phylotypic stage, and they’ve confirmed the molecular basis of the conservation. Of course, by “recent”, I mean a few weeks ago…and there have already been several excellent reviews of the work. Matthew Cobb has a nice, clean summary of both, if you just want to get straight to the answer. Steve Matheson has a three part series thoroughly explaining the research, so if you want all the details, go there.

In the first paper by Kalinka and others, the authors focused on 6 species of Drosophila that were separated by as much as 40 million years of evolution, and examined quantitative gene expression data for over 3000 genes measured at 2 hour intervals. The end result of all that work is a large pile of numbers for each species and each gene that shows how expression varies over time.

Now the interesting part is that those species were compared, and a measure was made of how much the expression varied: that is, if gene X in Drosophila melanogaster had the same expression profile as the homologous gene X in D. simulans, then divergence was low; if gene X was expressed at different times to different degrees in the two species, then divergence was high. In addition, the degree of conservation of the gene sequences between the species were also estimated.

The prediction was that there ought to be a reduction of divergence during the phylotypic period. That is, the expression of genes in these six species should differ the least in developmental genes that were active during that period. In addition, these same genes should show a greater degree of evolutionary constraint.

Guess what? That’s exactly what they do see.

Temporal expression divergence is minimized during the phylotypic period. a, Temporal divergence of gene expression at individual time points during embryogenesis. The curve is a second-order polynomial that fits best to the divergence data. Embryo images are three-dimensional renderings of time-lapse embryonic development of D. melanogaster using Selective Plane Illumination Microscopy (SPIM).

That trough in the graph represents a period of reduced gene expression variance between the species, and it corresponds to that phylotypic period. This is an independent confirmation of the morphological evidence: the similarities are real and they are an aspect of a conserved developmental program.

By the way, this pattern only emerges in developmental genes. They also examined genes involved in the immune system and metabolism, for instance, and they show no such correlation. This isn’t just a quirk of some functional constraint on general gene expression at one stage of development, but realy is something special about a developmental and evolutionary constraint.

The second paper by Domazet-Loso and Tautz takes a completely different approach. They examine the array of genes expressed at different times in embryonic development of the zebrafish, and then use a comparative analysis of the sequences of those genes against the sequences of genes from the genomic databases to assign a phylogenetic age to them. They call this phylostratigraphy. Each gene can be dated to the time of its origin, and then we can ask when phylogenetically old genes tend to be expressed during development.

The prediction here is that there would be a core of ancient, conserved genes that are important in establishing the body plan, and that they would be expressed during the phylotypic stage. The divergence at earlier and later stages would be a consequence of more novel genes.

Can you guess what they saw? Yeah, this is getting predictable. The observed pattern fits the prediction.

(Click for larger image)

Transcriptome age profiles for the zebrafish ontogeny. a, Cumulative transcriptome age index (TAI) for the different developmental stages. The pink shaded area represents the presumptive phylotypic phase in vertebrates. The overall pattern is significant by repeated measures ANOVA (P = 2.4 3 10-15, after Greenhouse-Geisser correction P = 0.024). Grey shaded areas represent ± the standard error of TAI estimated by bootstrap analysis.

So what does this all tell us? That the phylotypic stage can be observed and measured quantitatively using several different techniques; that it represents a conserved pattern of development gene expression; and that the genes involved are phylogenetically old (as we’d expect if they are conserved.)

Domazet-Loso and Tautz propose two alternative explanations for the phenomenon, one of which I don’t find credible.

Adaptations are expected to occur primarily in response to altered ecological conditions. Juvenile and adults interact much more with ecological factors than embryos, which may even be a cause for fast postzygotic isolation. Similarly, the zygote may also react to environmental constraints, for example, via the amount of yolk provided in the egg. In contrast, mid-embryonic stages around the phylotypic phase are normally not in direct contact with the environment and are therefore less likely to be subject to ecological adaptations and evolutionary change. As already suggested by Darwin, this alone could explain the lowered morphological divergence of early ontogenetic stages compared to adults, which would obviate the need to invoke particular constraints. Alternatively, the constraint hypothesis would suggest that it is difficult for newly evolved genes to become recruited to strongly connected regulatory networks.

They propose two alternatives, that the phylotypic stage is privileged and therefore isn’t being shaped by selection, or that it is constrained by the presence of a complicated gene network, and therefore is limited in the amount of change that can be tolerated. The first explanation doesn’t make sense to me: if a system is freed from selection, then it ought to diverge more rapidly, not less. I’m also baffled by the suggestion that the mid-stage embryos are not in direct contact with the environment. Of course they are…it’s just possible that that mid-development environment is more stable and more conserved itself.

What we need to know more about is the specifics of the full regulatory network. A map of the full circuitry, rather than just aggregate measures of divergence, would be nice. I’m looking forward to it!

The creationists aren’t, though.

Domazet-Loso, T., & Tautz, D. (2010). A phylogenetically based transcriptome age index mirrors ontogenetic divergence patterns. Nature 468 (7325): 815-818. DOI: 10.1038/nature09632

Kalinka, A., Varga, K., Gerrard, D., Preibisch, S., Corcoran, D., Jarrells, J., Ohler, U., Bergman, C., Tomancak, P. (2010). Gene expression divergence recapitulates the developmental hourglass model. Nature 468 (7325): 811-814 DOI: 10.1038/nature09634