No metazoan is an island

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I'm one of those dreadful animal-centric zoologically inclined biologists. Plants? What are those? Fungi? They're related to metazoans somehow. Lichens? Not even on the radar. The first step in fixing a problem, though, is recognizing that you have one. So I confess to you, O Readers, that my name is PZ, and I am a metazoaphile. But I can get better.

My path to opening up to wider horizons is to focus on what I find most interesting about animals, and that is that they are networks of cells driven by networks of genes that generate patterned responses of expression by cell signaling, or communication. See? I'm already a little weird. Show me a baby bunny, and I don't just see a cute little furry pal with an adorable twitchy nose, I see an organized and coherent array of differentiated tissues that arose by a temporal sequence of cell-cell interactions, and I just wanna open him up and play with his widdle epithelial sheets and dismantle his pwetty ducts and struts and fibers and fluids, oochy coo. And ultimately, I want to take apart each cell and ask why it has its particular assortment of genes switched off and on, and how its state affects its neighbors and the whole of the organism.

Which means, lately, that I've acquired a growing interest in bacteria. If I were 30 years younger, I could probably be seduced into a career in microbiology.

There are a couple of reasons why an animal-centric biologist would be interested in bacteria. One is the principle of it; the mechanisms that animal cells use to build complex arrangements of tissues were all first pioneered in single-celled organisms. We have elaborated and added details to gene- and cell-level phenomena, but it's a collection of significant quantitative differences, with nothing known that is essentially new in metazoan cells. All the cool stuff was worked out by evolution in the 3-4billion years before the Cambrian, a potential that simply blossomed in the past half-billion years into big conglomerations of cells. Understanding how the building blocks of multicellularity work individually ought to be a prerequisite to understanding how the assemblages work.

But there's another reason, too, a difference in perspective. It is our conceit to regard ourselves as individuals of Homo sapiens, a body of cells clonally derived from a single human cell. It's not true. It turns out that each one of us is actually a whole population of species, linked by our evolutionary history and lumbering through the world as a team. Genus Homo is also genera Escherichi and Bacteroidetes and Firmicutes and many others.

schematic.jpeg

Physiology

Let's begin with the most widely known factor: we're mostly bacterial in cell numbers, with about ten times as many bacterial cells as human cells. Most of these are nestled deep in our guts, where they are indispensible. In mammals, they help break down complex polysaccharides which we can then absorb through the wall of the digestive tract — these are compounds that would be simply lost without bacterial assistance. Even more dramatically, termite guts contain colonies of bacteria that produce enzymes to break down cellulose. Another insect, aphids, live in plant saps which have negligible protein components, and they rely on gut bacteria that can synthesize nine essential amino acids. One cool feature is that the bacteria can't complete the synthesis of leucine; the last step is carried out by aphid enzymes. The synthetic pathway is split acros two different species!

Another weird twist is that gut bacteria can affect morphology (or vice versa; physiology influences which gut bacteria thrive). Mice with a genetic predisposition to obesity were found to have a different distribution of gut bacteria; fat mice are full of Firmicutes, while lean mice are loaded with Bacteroidetes. Something in the genetics of the obese mice seems to favor the proliferation of that one species. Cause and effect is not so easily separated, though, since doing a fecal transplant and inoculating the guts of germ free mice with the bacteria from obese mice vs. lean mice has a surprising effect: the mice given obese mouse fecal enemas subsequently increased their body fat by 60%. The bacteria promoted more fat storage in the host animal.

So what, you may be thinking, it's mice. However, it turns out that obese humans tend to have reduced amounts of Bacteroidetes species in their guts than lean people, and weight loss is accompanied by an increase in Bacteroidetes. Fecal transplants are not recommended as a weight loss technique…at least not yet.

They have worked for some other problems. Crohn's disease and ulcerative colitis are diseases that involve intestinal inflammation, and they're also associated with imbalances in the species distribution of gut bacteria. Some promising treatments have involved collecting feces from healthy individuals, and using a nasogastric tube to inoculate the guts of Crohn's patients with the stuff. Ick, I know, but it seems to have worked surprisingly well in a small number of patients.

Development

Bacteria are present in the gut from a very early age, and populate the digestive epithelia. There must be interactions going on, and it appears that the bacteria are actually regulating the growth of the gut lining.

Germ-free zebrafish lines have no gut bacteria, and they also have problems. The intestinal lining arrests its development and fails to fully differentiate; the lining also grows much more slowly. They also have difficulty absorbing some nutrients. Add bacteria, though, and growth and differentiation resume. This is a case where the developmental program and the bacterial influences are interdependent, and it makes sense — they've co-evolved.

It's not just fish, either — these are conserved interactions across the vertebrates. Mice exhibit the same dependence on gut flora for development of the intestinal lining.

The very best example of a developmental dependence on bacteria, though, is in squid. The bobtail squid has a light-emitting organ that relies on colonization by a luminescent bacterium, Vibrio fischeri. The animal gleans the bacteria from the water with a special ciliated epithelium and secreted mucus that seems to be just the right flavor for Vibrio, and the bacteria migrate deep into the light-emitting organ. Once colonized, the squid dismantles the harvesting cilia and downregulates the secretion of mucus. If no bacteria of the right species are present, it maintains the cilia. If the bacteria in the organ die, resumes mucus production.

squid_symbionts.jpeg
Bacterial symbionts induce light-organ morphogenesis in squid. A Adult squid (E scolopes). SEM images of epithelial fields before B and after C regression of ciliated appendage. Scale bar, 50 mm. Ciliated appendages are marked by an orange dashed line.

Evolution

If something affects development and physiology, it affects evolution, so evolutionary importance is simply rather unavoidable. However, there's also one somewhat surprising observation (to me, at least — microbiologists probably expect it): different species of related organisms can have different microbial populations, even when raised in identical conditions. Different Hydra species in the lab under controlled conditions have recognizably different populations of bacteria living on their epithelia, and Hydra of the same species collected in the wild have similar distributions of species. The properties of each Hydra species uniquely favor different distributions of bacteria, and the bacteria are also preferentially colonizing particular species of Hydra.

Hydra are wonderful experimental animals in that one can ablate stem cells for a particular tissue type, and still get an animal that develops and lives; do the same thing to a vertebrate, for instance knocking out the mesodermal lineage in the embryo, and you get an aborted blob. In Hydra, you get a tissue that survives and is colonized by bacteria…but the kinds of bacteria populating it is different from the populations in the intact animal. The animal and the bacteria are swapping molecular signals that specify favored relationships. Again, these are coevolved populations that recognize molecular properties of the host and symbiont.

This is all getting very complicated. I'm used to thinking in terms of networks of genes: there are regulatory interactions between genes in a single cell that establish cell-type specific patterns of gene activity; all express a common core of genes, but different cell types, such as a neuron vs. a cell of the digestive epithelia, will also have their own unique special-purpose genes switched on. I'm also comfortable thinking of networks of cells: cells are in constant negotiations with their neighbors, mainting a common pattern of expression within a tissue, and defining interacting edges with other tissues. Cells are continually sending out messages about their state into the system and responding to local and global signals. All this is part of the normal process of thinking developmentally.

Now, though, there's another layer: we have to think in terms of networks of species that cooperate in the development and physiology of individual multi-cellular organisms. Purity is compromised. My precious animalia — they're inconceivable without bringing bacteria into the picture.


Fraune S, Bosch TCG (2010) Why bacteria matter in animal development and evolution. Bioessays 32:571-580.

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We are never ever alone from PJZen's The Big Picture on July 22, 2010 8:48 AM

PZ Myers is still writing.  Get ready for some poop. “It is our conceit to regard ourselves as individuals of Homo sapiens, a body of cells clonally derived from a single human cell. It’s not true. It turns out that each one of us is actual... Read More

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Elio Schaechter had a little piece on this recently in which he tracked down the claim that the ratio of endogenous to commensual cells is 10:1.

I mean of course the other way round…

There’s been a lot of work lately on the human “microbiome” of symbiotic microoganisms … but just recently I’ve been seeing reports of early work on a complementary “virome”. It seems the complex human microecology also includes an extensive set of viruses – and they may well be a necessary component of the whole.

That makes me just stare off into space: “HOW?” How can an obligate parasite be a good member of the community? Well, for sure this is fun stuff.

John Wilkins said:

Elio Schaechter had a little piece on this recently in which he tracked down the claim that the ratio of endogenous to commensual cells is 1:10.

Do remember that they’re largely prokaryotes, which are several orders of magnitude smaller than our eukaryotic cells. But still that’s interesting.

Not to mention all those beautifully useful bacteria that live within our metazoan cells and which we call mitochondria. Bacterial symbiosis goes way, waaay back to the very early stages of biological evolution.

It is our conceit to regard ourselves as individuals of Homo sapiens, a body of cells clonally derived from a single human cell. It’s not true. It turns out that each one of us is actually a whole population of species, linked by our evolutionary history and lumbering through the world as a team.

This notion has fascinated me for decades. It is not even possible from a physicist’s perspective to see most living organisms as a single, highly complex system. Rather, it makes far more sense thermodynamically to see living systems as collections of hundreds, if not thousands, of subsystems existing in a highly coordinated arrangement.

That coordination is kept going by a number of subsystems that supply quasi-periodic “signals” that are quite temperature sensitive (that’s a significant clue).

For example, given all the chemical binding energies of bones, tissues, genes, etc. that are on the order of 1 eV, we still have nervous systems with activation energies on the order of 0.070 eV. Such systems operate within only very narrow temperature range, shutting down at low temperatures (hypothermia) and going chaotic at high temperatures (hyperthermia).

One of the reasons I find misconceptions about thermodynamics frustrating is that these fundamental concepts, properly understood, can guide the research into complex assemblies of multiple systems. The misconception about information having something to do with thermodynamics is clearly a science-stopper in this area.

To get from abiogenesis to complex, coordinated assemblies of separate systems means pulling apart the thermodynamic environments in which each of these subsystems are able to remain intact. It means understanding the “signaling systems” that work only within narrow energy windows. There are many examples of such systems in nature. The trick is to learn the kinds of environments in which these come together and survive. Most likely one will find these to be “pumped and shuttled” environments.

There was an interesting article in Science News recently about C-section babies being colonized by relatively weird and potentially nasty hospital bacteria rather than mom-vaginal-tract bacteria and how this might be a reason for giving C-section babies a dose of mom-bacteria right after birth.

I can’t get the code to work right, but here’s the citation: http://www.sciencenews.org/view/gen[…]_birth_route

Mike Elzinga said:

The misconception about information having something to do with thermodynamics is clearly a science-stopper in this area.

There’s a “human thermodynamics” wiki online that I was poking through – it tends to be more than a layman can digest, but really took a dim view of using “information” as a concept in thermophysics.

I’m acquiring a real distrust of anyone who uses the term “information” in any context where it doesn’t seem pertinent. The term is ambiguous, it’s been badly mishandled by crackpots, and using it just helps feed the crackpots.

Let’s begin with the most widely known factor: we’re mostly bacterial in cell numbers, with about ten times as many bacterial cells as human cells. Most of these are nestled deep in our guts, where they are indispensible.

I’ve seen this claim that gut bacteria are indispensible more than once. What’s the evidence to support it?

Researchers can generate bacteria-free axenic mice. They may not be completely normal, but they thrive & reproduce. If gut bacteria aren’t indispensible in mice, how do we know they’re indispensible in humans?

(psst - plants have differentiated tissues, too)

Does this imply that todays parasites beyond bacterial in size, for instance, worm, tick, mite, might evolve into a mutually beneficial relationship?

The very best example of a developmental dependence on bacteria, though, is in squid.

Okay, show of hands, who didn’t see that coming. :-)

There must be a more hygienic – or at least less aesthetically offensive – way to introduce Bacteriodetes into a patient?

fnxtr said:

The very best example of a developmental dependence on bacteria, though, is in squid.

Okay, show of hands, who didn’t see that coming. :-)

Well, you see, I was facing in another direction at the time. Only way I could’ve missed it.

Wonderful post, PZ! You have inspired me to offer my services as a feces donor to the local hospital. Let’s hope they’ve heard of these studies and don’t lock me up in their psych ward…

PZed - going on strike has been beneficial. This is the best written post I’ve read from you for some time. Although I should stand up for the fungi, who must laugh at this:

Hydra are wonderful experimental animals in that one can ablate stem cells for a particular tissue type, and still get an animal that develops and lives; do the same thing to a vertebrate, for instance knocking out the mesodermal lineage in the embryo, and you get an aborted blob.

And Hydra can’t even make beer.

Very nice post, PZ! I’m continually fascinated by host/microbe interactions. Thanks for pointing to that article; I’ll have to get that and read it now.

My name is Ryan and I’m an angiospermaphile who can’t be bothered with “primitive” ferns or bryophytes.

“Show me a baby bunny, and I don’t just see a cute little furry pal with an adorable twitchy nose, I see an organized and coherent array of differentiated tissues that arose by a temporal sequence of cell-cell interactions, and I just wanna open him up and play with his widdle epithelial sheets and dismantle his pwetty ducts and struts and fibers and fluids, oochy coo.”

Sir, I must warn you that this kind of attitude will not make you popular at dinner parties. I recommend either professional help or keeping very quiet about it.

Futhermore please extend my deepest sympathies to any collections of organized and coherent array of differentiated tissues that arose by a temporal sequence of cell-cell interactions, or “pets” as I call them, in your household.

could anyone elaborate? when a hydra loses a tissue type, is it resurrecting an ancient relationship with bacteria that existed when tissues were colonies of unrelated species? (rather like completing the signal to V’Ger)

PZ -

Mice exhibit the same dependence on gut flora for development of the intestinal lining.

This is quite interesting, as a fair number of models of immunodeficient mice exist, which are typically raised in quite sterile conditions. Do you have a reference? I hadn’t heard of it before.

PZ Myers Wrote:

So I confess to you, O Readers, that my name is PZ, and I am a metazoaphile. But I can get better.

I hope so, given that the unidentified, unembodied, possibly deceased designer has an inordinate fondness for bacteria, “irreducibly complex” flagella and all.

Roger said:

Sir, I must warn you that this kind of attitude will not make you popular at dinner parties.

Unless Hassenpfeffer is on the menu.

This comment has been moved to The Bathroom Wall.

This comment has been moved to The Bathroom Wall.

Frank J -

I hope so, given that the unidentified, unembodied, possibly deceased designer has an inordinate fondness for bacteria, “irreducibly complex” flagella and all.

You forgot to say “possibly alien platypus”. Anything but evolution!

Note that since the typical human eukaryotic cell probably has around 100 times or so the volume and mass of a typical human-inhabiting prokaryotic bacterial cell, we are still probably more human than bacteria on a biomass basis. (There are tiny eukaryotic algae cells with diameters in the 2 micron range, making them similar in size to prokaryotic cells, and there are very large bacteria, but even human spermatazoa are much larger than a typical prokaryotic cell.)

John Kwok -

He refers again and again to it as some kind of refutation of “Darwinism”, completely clueless as to understanding that humanity is engaged in a pharmaceuticallly-driven coevolutionary arms race with Plasmodium.

Also an underlying pre-pharmaceutical “arms race”, that explains why so many people in the world are suffering from sickle cell anemia or sickle trait, as well as many odd features of pathogenic Plasmodium species.

And of course, if he was right, the particular “designer” he adulates would be one that deliberately inflicts humans - including many small children - with malaria.

This comment has been moved to The Bathroom Wall.

I’ve always wondered how gut bacteria get in there in the first place. I suspect it’s related to Adam Savage’s iconic statement, “There’s poo everywhere!” but I’ve always wondered for sure.

Why are all of Kwok’s comments being moved to the bathroom wall? They seem quite reasonable to me? or is it that Kwok has rubbed so many people the wrong way?

In a similar thread, one of my projects deals with a ‘plant’ toxin that might only be partially made by the plant, while the toxin may actually be finalized (if you will) by a fungus that lives on the plant.

PZ and JK have history. I do not blame PZ.

Ntrsvic said:

In a similar thread, one of my projects deals with a ‘plant’ toxin that might only be partially made by the plant, while the toxin may actually be finalized (if you will) by a fungus that lives on the plant.

I knew about lichens in terms of plant-fungi symbiosis – I was surprised to learn it was Beatrix Potter who discovered that, and that the plant and fungi components can be grown separately under careful conditions – but I was really startled to find out how common symbiosis between truffles and mushrooms on one side and plant root systems on the other really are.

I was also reading a note in SCI-AM Online about a researcher, I think with the USDA, who was improving the temperature tolerance of crop plants by infecting them with fungi obtained from plants growing under extreme warm conditions. Even more surprising, he had to add a virus to the infection to get the full effect. “OK, my mind is blown.”

Please. Kill any of my responses now.

I would classify “Beebee” Byers as an “aimless rambler”.

But you know, taxonimists are noted for quarreling over their work. I don’t think “troll” is useful in the naming system because in this case that’s at the family level.

Hmm, somehow I recall Roadrunner / Coyote cartoons: “Roadrunner (hot-roddicus supersonicus)”.

MrG said: But you know, taxonimists are noted for quarreling over their work. I don’t think “troll” is useful in the naming system because in this case that’s at the family level.

Too true. While some have stayed vaguely on the post topic, those isolated bits of data are not sufficient to overturn the plethora of evidence supporting your proposal to put ‘troll’ at the family level. Carry on. :)

Yeah, the problem with “troll” as a classification element is that it doesn’t provide a distinction among them.

I thing Beebee might be better called an “aimless babbler”. And then there’s the “BS degree”, archetypically a computer scientist with a program that disproves evo science (but don’t ask him if he’s going to submit a paper to the appropriate journals); and “off the meds”, Ray Martinez being a classic example – the kind of people one feels embarrassed to argue with because they’re clearly dysfunctional.

MrG said:

Yeah, the problem with “troll” as a classification element is that it doesn’t provide a distinction among them.

I thing Beebee might be better called an “aimless babbler”. And then there’s the “BS degree”, archetypically a computer scientist with a program that disproves evo science (but don’t ask him if he’s going to submit a paper to the appropriate journals); and “off the meds”, Ray Martinez being a classic example – the kind of people one feels embarrassed to argue with because they’re clearly dysfunctional.

Today’s “featured article” on Wikipedia is “Confirmation Bias”. Perhaps we can start referring to Robert “Confirmation” Byers. :)

This comment has been moved to The Bathroom Wall.

This comment has been moved to The Bathroom Wall.

MrG said:

I think I’m going to gradually put together a zoology of creationists. This one’s the “incoherent ranter”, furiously tossing out all kinds of mad claims that barely make sense and demanding answers.

Then there’s the “chapter & verse”, who responds to any question by citing scripture.

However, I have a strong suspicion that somebody over on talk.origins has actually done this. I’ll have to poke around.

There’s TO’s FAQ on the “kinds” of creationism.

Also TO’s Jargon File, while dated, discusses regular anti-evolution posters of the ’90s and their techniques.

Keep in mind that the Internet stalkers are representative neither of the professional anti-evolution activists or evolution-deniers in the general public, most of whom never heard of TO, PT, much less anything PZ discusses in his article above.

Hygaboo Andersen said:

MrG said:

Hygaboo Andersen said:

This is only because intelligent design is rejected by Darwiniacs on apriori grounds.

Hmm … if “a priori” means “rejected out of hand” then … yeah, given an explanation that relies on a Designer who is completely unspecified – anyone can specify any Designer they like, or refuse to specify one at all (gee do people do that?) – that refuses to specify what the Designer did, and whose only support is negative arguments of ignorance … I guess I don’t have a problem with that.

I must admit to being disappointed, however, in the poor reception I have got for my theory that complex machines like PCs or cars can only operate through the intervention of unseen gremlins.

So, since you can not verify the existence of unseen gremlins you have concluded that cars and PC’s got here by random explosions? Why not try that experiment at home. Get some dynamite and blow a few tons of steel and see if cars and PCs appear. If it works, it will be the first real evidence for Darwinism.

What stupidity! Natural selection does not involve explosions. It is not a random process, or it wouldn’t be called natural SELECTION!

MrG:

Note: The article in my first link was based on an early version of NCSE’s “creation-evolution continuum.” The latter was later updated as ID showed itself to be a “big tent” scam, and not just a more common-descent-friendly version of OEC.

Eh, waddya expect – explosions, crocoducks, whatever.

Frank J said:

There’s TO’s FAQ on the “kinds” of creationism.

I was thinking more in terms of the styles of creationists that show up on PT to put on a song-&-dance. There is definitely a correlation to ideology – a “chapter & verse” is by good odds likely to be a YEC (less likely an OEC), while a “BS degree” is very likely to be an ID proponentsist.

It’s actually hard to determine any particular flavor from an “incoherent ranter” – they just seem to hate evo science and not really think much about creationism – and can be very difficult with an “aimless babbler”, because it’s so hard to figure out what they’re saying.

I think we all understand that Bugaboo Ericson or whatever he called himself is a parody, but still…

Yeah, and the believer’s in the godless sodomite religion of Darwinism think it all just came together by random chance. If that’s true why don’t new life forms emerge when an explosion occurs? Boy are evolutionits stupid!

Creationists are the ones who believe that everything appeared suddenly. Why are you calling creaionism the “godless sodomite religion of Darwinism”? There’s no need for homophobic language. We all know the creationist track record.

http://en.wikipedia.org/wiki/List_o[…]ist_scandals

Yes, homeostasis requires a finely-tuned environment, why can’t we create it in a random explosion?

Ask a creationist, they’re the ones who say that every single type of organism just appeared suddenly.

This is only because intelligent design is rejected by Darwiniacs on apriori grounds.

That would be unfair. Let’s fix that. I’m going to forget about the theory of evolution and pretend I never heard of it. What’s the evidence for intelligent design?

Hygaboo Andersen said:

I am completely unacquainted with the last forty years of scientific responses to creationism, but i thought everyone would be really amazed by something i heard kent hovind say

you need to try really really hard to understand that nobody is interested, or impressed, or swayed. readers here aren’t just scientifically literate; they are also intimately familiar with the evolution-creationism conflict, which you are not. you think we can’t tell, but we can. the responses to you might suggest that you have engaged in debate, but it’s a simple reflex action … people have been doing this so long they can’t let the stupid stuff go. maybe you’re thirteen years old and starting out on your first battles in the name of jeebus; maybe you’re a fully grown imbecile; but you need to try really really hard to understand that you can’t usefully battle the forces of sodom without learning a bit about the topic

I think that Hygaboo Andersen’s homophobic slur against those who accept evolutionary science (see his link in http://pandasthumb.org/archives/201[…]mment-224846 ) entitles him/her a perminant ticket to the BW.

dpr

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This page contains a single entry by PZ Myers published on July 21, 2010 8:04 PM.

Dean Kenyon: a young-earth creation scientist who was later relabeled an intelligent design proponent was the previous entry in this blog.

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