Preadapted for multicellularity


#1

Dear all,

I would like to offer up an interesting article for discussion. Titled “Evolution: like any other science it is predictable”, it is written by Simon Conway Morris, professor of evolutionary palaeobiology at Cambridge. I’ve included the citation at the end of this post, and a free pdf version of the article is available here.

The whole article is worth a read, but I would like to focus my attention on two quotes in particular:

The case of the animals, in which we may take at least a parochial interest, is particularly problematic at present. Thus, so far as the fossil record is concerned, the Ediacaran assemblages appear to offer some tantalizing insights into the diversity of early metazoans (and quite possibly other distantly related macroscopic groups), but to date they give no clues as to the transition from more primitive forms. Molecular phylogenies are scarcely more helpful because, while there is strong evidence for the protistan choanoflagellates being the sister group of animals (e.g. Carr et al. 2008), neither they nor related groups that include corallochyteans, ichthyosporeans and ministeriids (e.g. Steenkamp et al. 2006) give many clues as to how the transformation to animals might have been achieved. Certainly, the prior existence of genes linked to cell adhesion and signalling in choanoflagellates (King et al. 2008; Ruiz-Trillo et al. 2008) points to the pre-adaptations for multicellularity. Note, however, that in at least one choanoflagellate, the unicellular(!) Monosiga, the tyrosine kinase signalling apparatus is not only far more diverse than any metazoan (Manning et al. 2008, p. 9678), but as the investigators note this network reveals ‘several common themes that suggest convergent evolution and a limited set of recurring molecular themes favoured by signalling pathways’. (My emphasis)

Choanoflagellates are small, single-celled eukaryotes that use their whip-like flagella to move through the water (these flagella are constructed in a way entirely different from the bacterial flagellum, and the two structures are not believed to be related).

As choanoflagellates are single-celled, they were not expected to contain genes for cell adhesion and signalling molecules. As Nicole King, the biologist who made the discovery, said in an interview: “I was surprised to learn that so much of animal biology was in place before the origin of animals.”

The fact that genes associated with multicellularity should predate multicellular organisms is consistent with, but not expected from conventional evolutionary biology. It is, however, just what we should expect if the first life on earth was engineered with its future evolution in mind.

Okay, but maybe that finding was just a fluke, you think. Not so. As Conway Morris writes:

Perhaps, one day, the entire molecular and morphological transition from protist to animal will be available, but if we enquire what fundamentally is required to make an animal among the most important presumably are: homeotic genes, structural molecules such as collagen, muscles for movement and nerves for the rapid propagation of information. Once again, it is difficult to see what might have prevented them from evolving. Thus, the homeodomain (HD) proteins go deep into eukaryotic history, and their presence in metazoans, fungi, Dictyostelium and plants points to a role in the evolution of multicellularity. Despite this striking association, Derelle et al. (2007) also argued that the last common ancestor of all eukaryotes possessed at least two types (TALE, non-TALE) of HD protein and, echoing the story of the SNARE genes, suggest that the rounds of duplication occurred independently. This leads them to ‘suggest that the eukaryotes as a whole are pre-adapted for multicellularity’ (Derelle et al. 2007, p. 217). In the context of evolutionary likelihoods, if not inevitabilities, it is also important to note that striking structural analogues to the HD proteins occur in the prokaryotes (Treisman et al. 1992; Kant et al. 2002). The independent emergence of more complex homeotic systems does not seem that improbable. (My emphasis)

Homeodomain proteins play a vital role in the development of multicellular organisms, where they are considered part of the development toolkit. The researchers found that homeodomain proteins “are present in all eukaryotic lineages containing multicellular organisms, and absent in exclusively unicellular lineages.” In other words, homeodomain proteins does not appear to play an important role in unicellular organisms.

But the researchers carried out a phylogentic analysis and concluded that the multicellular organisms with homeodomain proteins (animals, plants, algae, and fungi) had all inherited them from a single-celled ancestor, the “Ur-eukaryota”, while those lineages who remained sigle-celled lost their copies through reductive evolution:

As a corollary of ancestral molecular complexity, Ur-eukaryota probably possessed many of the good building blocks, which were subsequently recruited, by convergence in several lineages, to perform the functions required for development of multicellular organisms. In other terms, we suggest that the eukaryotes as a whole are preadapted for multicellularity, which only means that the ancestral complexity of the eukaryote genome and cell biology facilitated multiple acquisitions of multicellularity. (My emphasis)

“Preadapted for multicellularity”. Natural selection is the Blind Watchmaker, with no thought for anything that doesn’t increase the fitness of organisms right now. But thinking about the future, that smacks of teleology.

Thoughts?

References

Conway Morris S., 2010, “Evolution: like any other science it is is predictable”, Philosophical Transactions of the Royal Society B 365 (1537):133-145

Derelle R., et al., 2007, “Homeodomain proteins belong to the ancestral molecular toolkit of Eukaryotes”, Evolution & Development, 9(3):212-219

King N., 2004, “The Unicellular Ancestry of Animal Development”, Developmental Cell 7(3):313-325


#2

Why wouldn’t it be expected that new phenotypes would evolve from the modification of pre-existing genes?

What test could we use to differentiate between evolution and the type of engineering you are alluding to?

In what way are tyrosine kinases not important to the fitness of choanoflagellates as single celled organisms?


#3

Do you or anyone else have any predictions?


(Steve Schaffner) #4

I’m not sure I understand what model of engineering you’re proposing. Are you suggesting that evolution of animals by natural mechanisms was made possible by prior engineering of their ancestors, and that those earlier features didn’t evolve naturally? If so, then no, that’s not what I would expect from engineering.

But nothing here implies that natural selection was thinking about the future. Rather, multicellularity arose where is was possible, and using those molecular tools that were already available.


#5

"Consistent with, but not expected from …"
Before I address specific objections, I feel I should expand on what I mean when I write that the preadaptation for multicellularity is “consistent with, but not expected from” conventional evolutionary biology. I feel this is necessary as I fear that some might confuse my argument with a typical creationist “evolution can’t explain X” argument.

I am not challenging that natural selection (or another conventional evolutionary mechanism of choice) could have produced the features discussed in this thread. Just like natural selection could have produced JCVI-syn3.0 (the artificially synthesized bacteria designed by J. Craig Venter’s lab) through reductive evolution of a Mycoplasma mycoides.

In other words, I am not arguing that conventional evolutionary biology is disproven because genes linked to homedomain proteins, cell adhesion, and signaling are found to be much older than multicellular organisms. I am merely arguing that it was not expected from it.

And that a teleological view exists where these observations were expected.

Was the preadaptation for multicellularity expected?
@T_aquaticus disputes my claim that genes associated with multicellularity should predate multicellular organisms was not expected from conventional evolutionary biology, writing: "Why wouldn’t it be expected that new phenotypes would evolve from the modification of pre-existing genes?

But the issue goes deeper than just nondescript “pre-existing genes” evolving into, say, genes associated with cell adhesion and signaling. After all, those genes might have changed so much so as not to show any identifiable homology with their precursors. And those genes might have evolved much closer to the origin of multicellularity, long after choanoflagellates had branched off from the lineage leading to multicellular organisms.

Another way to put it is that if conventional evolutionary biology predicted this finding, why did the researcher who found it consider it surprising?

Surveys of expressed sequence tags (ESTs) and full-length cDNA sequences reveal choanoflagellates to express multiple members of gene families previously thought to be unique to animals. Despite the apparent simplicity of their lifestyle, choanoflagellates express a surprising diversity of animal signaling and adhesion gene homologs including TKs, G protein-coupled receptors, cadherins, and C-type lectins (King et al., 2003). In addition, several predicted polypeptides from choanoflagellates contain multiple protein-protein interaction domains (e.g., EGF, SH2, TNFR, and CCP) that typically function in animal signaling and adhesion proteins. (King, 2004, my emphasis)

Why would those gene families be “thought to be unique to animals”? And why would the diversity of signaling and adhesion gene homologs be considered surprising?

Differentiating tests
@T_aquaticus also asks what test we could use to differentiate between evolution and my conjecture that the first life on Earth was engineered with its future evolution in mind.

The way I see it, my conjecture is a very fragile hypothesis. If, as the conventional view previously held, genes associated with multicellularity had evolved in tandem with multicellularity, with no sign of deep homology, my view would have a hard time getting off the ground.

Conventional evolutionary biology, on the other hand, is fine either way. When genes associated with multicellularity were thought to be restricted to multicellular organisms, conventional evolutionary biology was perfectly fine with it. And now that those genes have been found to pre-date multicellularity, everything is still a-oh-kay.

So, what would be a sufficient test to differentiate the two views? Is the fact that the teleological view made a risky prediction in an area where conventional evolutionary biology was silent enough? Or am I required to find something that disproves conventional evolutionary biology?

Other objections
@beaglelady asks: “Do you or anyone else have any predictions?”

If you mean in regards to the title of Conway Morris’ article (“Evolution: like any other science it is predictable”), then no. I think he makes a lot of good points, but I do not agree with everything Conway Morris writes. I would be hard put to make predictions about the future course of evolution, except for the trivial “bacteria exposed to penicillin will evolve resistance to it.”

If you mean in regards to my views concerning life having been engineered with its future evolution in mind, I expect to find other examples of genes associated with multicellularity to turn out to be older than multicellular organisms.

@glipsnort writes: “Are you suggesting that evolution of animals by natural mechanisms was made possible by prior engineering of their ancestors, and that those earlier features didn’t evolve naturally? If so, then no, that’s not what I would expect from engineering.”

Is that something you could elaborate on? It might just be me who is daft, but I am not catching your point.

@T_aquaticus asks: “In what way are tyrosine kinases not important to the fitness of choanoflagellates as single celled organisms?”

I am sure tyrosine kinases are important to the fitness of choanoflagellates. Otherwise, natural selection would have removed them long ago. My point is that there is nothing about natural selection acting as the Blind Watchmaker that would make us expect that genes well-suited for multicellularity should have evolved so long before the evolution of multicellularity.

References
King N., 2004, “The Unicellular Ancestry of Animal Development”, Developmental Cell 7(3):313-325


(Steve Schaffner) #6

My main point is that I don’t understand what view you are proposing. What model of engineering would predict that choanoflagellates (and only choanoflagellates) would be pre-loaded with the toolkit necessary for the evolution of multicellular life?


#7

Oh, now I get it. And no, my view isn’t that choanoflagellates (and only choanoflagellates) are frontloaded for multicellular life. Instead I see the first life being an assemblage of cells, some of which contained genes that made the evolution of multicellularity more likely, and some of those genes have been retained in, say, choanoflagellates.


(Steve Schaffner) #8

Good, that was my understanding of your original statement, and my reply then still holds – no, this is not the way I would naturally expect a designer to go about their business. Sure, it could be consistent with a designer, but that doesn’t distinguish it from undesigned evolution.


#9

Humans get things wrong. It happens. I don’t see why our fallibility somehow evidences teleology. Nature surprises us all of the time, but that doesn’t mean that everything in nature is based on teleology.

Again, why shouldn’t we expect multicellularity to evolve from pre-existing genes in single celled organisms?

Those homologous genes are still found in single celled organisms. If these genes were pre-destined to produce multicellularity in a teleological sense, then why are these species who have these genes still unicellular, and why have the remained unicellular for perhaps billions of years?

Where can I find the prediction that we would find these genes in unicellular organisms prior to their discovery? Why wouldn’t conventional evolutionary biology make the same prediction?

That would be the main problem with your thesis. What you are essentially doing is waiting for something to evolve, and then making the argument that you predicted it would evolve after it evolved. That’s not much of a prediction.

Why not?


#10

As in the post above, if these genes were front loaded for multicellularity, why are they still unicellular after hundreds of millions or perhaps billions of years?


#11

So how would you expect designers go about their business? Engineer a complete ecosystem of multicellular organisms from scratch, as well as transforming the atmosphere of the prebiotic Earth to create the oxygen-rich atmosphere needed by complex multicellular life?

As the challenges faced by the first Biosphere 2 project show, just creating a small ecosystem (let alone the organisms in it!) can be a daunting task.

Considering that every mega-complex system we know of - cities, international markets, the internet, etc. - are the product of a long history of gradual modifications by numerous, independent actors, adjusting to the changes made by each other, I say evolution is a process I would very much expect engineers to use if the planet was indeed seeded with life.

As for distinguishing my views from “undesigned evolution”, I’m not that concerned. At this point, my views are merely a conjecture - a hunch, a guess, or a tentatively held working hypothesis - that I pursue in my limited spare time.

One of the things that piques and keeps my interest is the fact that this little conjecture generates insights where conventional evolutionary biology is silent - like the surprisingly long pedigree of multicellular-dependent features. Sure, conventional evolutionary biology can also accommodate that finding, but that’s to be expected. The geocentric model of the solar system with its epicycles could also explain the movements of the planets, although the calculations required where more laborious than those required for by Galileo’s heliocentric model.

My goal isn’t to “disprove evolution”. It’s to see how deep this rabbit hole actually goes.

I don’t think human fallibility is somehow evidence of teleology. In fact, my point - which is quite humble - was spelled out in my previous post:

In other words, I am not arguing that conventional evolutionary biology is disproven because genes linked to homedomain proteins, cell adhesion, and signaling are found to be much older than multicellular organisms. I am merely arguing that it was not expected from it.
And that a teleological view exists where these observations were expected.

As for multicellularity evolving from “pre-existing genes in single celled organisms”, that understates the significance of the finding. Take this phylogeny of the relationship between choanoflagellates and metazoans, from King’s paper (available here):

image

Now, the genes for cell adhesion and signaling could have evolved at the juncture labelled “2”, after choanoflagellates branched off, but before multicellular organisms evolved. What arguments from conventional evolutionary biology would you have used to reject the notion that those genes evolved after the branching off of choanoflagellates, and that they had instead evolved much earlier?

Choanoflagellates still exist because they’re well-adapted to their ecological niche and because they haven’t gone extinct. Having the tools that enable multicellularity doesn’t require that every species takes that journey.

In 2005, when I first started looking into homeodomain proteins (i.e. the developmental tool kit) from a teleological perspective, I expected them to be discovered in unicellular organisms. As I wrote back then:

If we assume that eukaryotes were designed with the purpose of giving rise to multicellular organisms, we can make certain predictions. For one, we would expect the first eukaryotes to have contained a predecessor to the modern tool kit, and it’s possible that some unicellular eukaryotes still possess it. It will probably not be the full set possessed by modern organisms (or rather, full sets, as several organisms differ in the number of genes they have), as some genes may have been generated through gene duplications, but I definately expect genes that are clear precursors to modern tool kit genes to be found in unicellular eukaryotes.

Yeah, I didn’t wait around for multicellularity to evolve. I may not be in the spring of my youth anymore, but I’m not that old.

All kidding aside, my views are about making sense of historical events, not predicting future ones. Do you also want Lynn Margulis, the major proponent of the endosymbiotic origin of mitochondria, to predict the next time a proteobacterium becomes a permanent part of a eukaryote?


#12

The evolutionary argument would have looked at genes in single celled organisms to see what genes they had, and if there were shared genes between multicellular and unicellular life, which is exactly what people have done.

The theory of evolution doesn’t argue for a set path for evolution. The theory of evolution only posits specific mechanisms. There is nothing in the theory of evolution that says genes important for multicellularity can not be found in unicellular organisms.

Then how can you say that these genes were pre-destined to evolve multicellularity?

It seems that the only evidence you have for pre-destined evolutionary pathways is that they happened. It is a very circular argument.


#13

In other words, conventional evolutionary biology does not lead us to expect genes to have a specific age, but accommodates whatever is observed. Which is what I’ve been arguing all along.

No, and I haven’t claimed that either. Again, I’ve been arguing that the findings are “consistent with, but not expected from conventional evolutionary biology”.

I don’t like the word “predestined”. Front-loaded evolution is about probabilities, not destiny.

Imagine you’re part of a team of extraterrestrial engineers, observing prebiotic Earth. You have been tasked with engineering lifeforms so that at some point the planet will be home to multicellular life. You analyze the problem and come to the conclusion - which I’ve detailed in an earlier post - that instead of creating an entire ecosystem of multicellular organisms from scratch, your best bet is to seed the planet with unicellular organisms, engineered in such a way as to make probable the evolution of multicellularity.

So what do you do? You know that as long as your engineered cells experience replication and heritable variation, they will be suspect to natural selection. But how can you be sure that it will lead to multicellularity? We forget it because we’re so used to it, but getting cells to behave like part of a multicellular organism is hard.

You decide to give your cells some tools, to help them along. Maybe some adhesion proteins, to help them stick together, some signalling proteins, to help them communicate, and some homeodomain proteins, to help them differentiate themselves during development.

You’ve given your cells a head start, but does that mean that every lineage will lead to multicellularity? Of course not. Your evolving biosphere will contain lots of ecological niches for unicellular organisms, and natural selection will make sure those niches get filled.

I’ve laid out the reasoning behind my views, and the evidence supporting them, several times. So instead of doing it again, let me ask you this:

What would you consider evidence for the suspicion (not proof) that the earliest life was engineered with multicellularity in mind?


#14

Evolution does not say that multicellularity had to evolve in a specific way. To use an analogy, astrophysics does not say that a solar system has to have a specific number of planets. Each lineage is going to evolve differently just as each solar system is going to form differently. Evolution only proposes a set of mechanisms, and the results of those mechanisms can be nearly infinite. What we see in natural history is only one of a nearly infinite number of possible evolutionary pathways.

Multicellularity evolving from genes not found in unicellular organisms is equally unexpected.

That’s a nice story, but I don’t see how you differentiate this scenario from natural evolutionary pathways. You might as well claim that invisible aliens heat a tiny portion of the atmosphere so that it spawns a hurricane 2,000 miles away, and they do so in such a way that it is indistinguishable from natural processes. You seem to have an unfalsifiable explanation.

A complete discontinuity with unicellular life would be at least a step in the right direction. Finding 1 billion year old labs in archaeological digs would be another big piece of evidence.


#15

You keep refuting points I haven’t made and ignoring the points I have made. It seems that we’re at an impasse, and I suggest agreeing to disagree on whether these findings were expected by (not just consistent with) conventional evolutionary biology.

The point of the story wasn’t to differentiate the scenario from natural evolutionary pathways. The point was to address your misconception that my views require every lineage to evolve multicellularity.

Could you elaborate on what you mean by “a complete discontinuity with unicellular life” and how it would make you suspect that unicellular life was engineered with multicellularity in mind?

So to merely make you suspect teleology, you would have to find a 1 billion year old lab. Thank you, that lets me better calibrate your claims that you don’t find this or that evidence compelling.


(Steve Schaffner) #16

Depends on the designer. If you’re positing designers of unlimited ability (e.g. God), then I would expect them just to build the planet, species, and ecosystem from scratch in the form they wanted. Why go through billions of years of evolution to transform the atmosphere when you can just make whatever you want?

From designers of limited ability (and who is seriously suggesting them?), I would expect that they either would just start the whole show off and let evolution take over, and do whatever it does, or (if they had a particular goal in mind) I would expect them to start building the ecosystem directly, adding and removing and adjusting as they figured out what was going on.

What I would not expect is for them to be able to predict what genes would prove useful for multicellularity, plant them, and then let evolution take over. That’s because predicting how evolution is going to proceed is a lot harder than just putting together an ecosystem by trial and error.


#17

If multicellular life was completely different from unicellular life that would be evidence which would make engineering more attractive to me.

That would certainly be compelling evidence, wouldn’t you agree?


(system) #18

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