Here’s the last bit of the three-part interview I did at the July TAM with Joel Guttormson, Outreach and Event Coordinator for the Richard Dawkins Foundation for Reason and Science.
By the way, since I’ve read Addy Pross’s short book What is Life? How Chemistry Becomes Biology, I’ve realized that abiogenesis (the origin of life from nonlife) and the subsequent evolution of life are really not separate issues, for abiogenesis surely involved the same kind of competition between replicating systems that characterizes things we’re comfortable calling “alive.”
I have said that evolution started with the first successful self replicating molecule. There would be variation in its replicates, and thus natural selection would occur. I’m not sure how well thought out that is.
Jerry, your anecdote about your first classroom experiments with fruit flies brings to mind something I’ve wondered about.
Is there room in evolutionary biology for amateurs to do meaningful work?
Particle physics, of course, is something that you need a massive collider for…but there’re lots of amateur astronomers doing real work with relatively modest equipment.
Are there questions needing to be answered that somebody with a generic college-level education and modest resources and a corner of the home and a bit of time could work on?
I should quickly note: while I’d love in principle to do something like that, I’ve got enough other projects of more importance on my plate that it’s not something I could personally seriously consider for at least a couple years. But, if there’s anybody else here who might draw inspiration….
Cheers,
b&
I’m not Jerry, but there certainly are citizen science projects in Biology. Like this.
I suppose Jerry’s answer might depend on what you are driving at, but all biology is evolutionary biology when you think about it.
I obviously had something more lab-type in mind, but, once I get my garden in place, counting birds would certainly seem to be a natural (especially since a big part of the plan is to create a wildlife-friendly habitat).
Thanks!
Jerry, I’d still love to hear your thoughts, too — along with anybody else who’d like to chime in!
Cheers,
b&
I’d say that a lot of evo-bio questions that currently haven’t been answered haven’t even been asked yet. So, as usual, the way to be a good scientist is to Keep Asking questions.
…of course, that assumes that one is sufficiently familiar with the questions that’ve already been asked to not reinvent the wheel.
At the same time, reinventing the wheel might not be such a bad idea — that is, independently recreating experiments in order to verify the results. I imagine that might not be such a terrible place to get started, either….
b&
I strongly disagree about abiogenesis and evolution being separate issues. This is a common mistake that Creationists make; they try to knock down the theory of evolution by arguing that our understanding of abiogenesis is woefully incomplete, but the two are separate issues. We have very strong evidence to show modern species evolved from a common ancestor; what we still lack right now is an understanding of how that common ancestor came into existence. If you define evolution as “change in the genetics of a population across generations” which is one of several definitions I’ve heard but seems to be a good one, then it’s something that applies strictly to life as we know it. Abiogenesis, by contrast, is a chemistry problem — what conditions and sequence of reactions led to a system that harnesses spontaneous (negative Gibbs free energy) processes to drive thermodynamically-unfavorable synthesis of monomers and polymers in a regulated way? We don’t have the answer to that question yet…
I’m afraid it is often an infinite regress problem.
If you point to chemistry as the origin of life some believers simply refuses to entertain the idea because they don’t like thinking of themselves as things.
Human life is sacred.
And, coincidentally enough, the explanation for why these humans should think so can be found with a simple anagram of the last word of that sentence.
b&
Fearful to the degree of creating self inflicting horrors to be fearful about.
But hey, what about all the good things it does?…;-)
I think the point is that, though, yes, genetic molecules are the foundation of modern life, the same fundamental principles of inheritance apply in other situations as well. All you need, really, is for something to duplicate itself but imperfectly, and Darwin takes over from there.
That something doesn’t have to be sophisticated or complex; it just needs those two properties: duplication and variation. And there’s a lot of reason to think that there are, indeed, such sorts of structures that basic chemistry would cause to spontaneously assemble…and, so long as there isn’t any extant life to hoover up such structures as food, they would seem to have pathways of increasing complexity that eventually result in superior lifeforms such as Felis silvestris catus.
Looking even further back, astrophysicists rightly use the term, “evolution,” to describe the big-scale changes in stellar- and galactic-scale phenomenon — though, of course, this evolution is of a different type from Darwinian biological evolution. But the earliest stars were exclusively hydrogen and helium, and their life cycles resulted in both the creation of heavier elements as well as conditions which would inevitably result in the birth of new, slightly different stars…in a process in which the creation of stellar systems rich in heavier elements (such as our own) was inevitable, and it is the same physics at different scales that transitions into the phenomenon we label, “life.”
Cheers,
b&
The distinction you make here seems to come down to whether or not the replicator is alive. If it is alive, its called biology and therefore evolution, and if it is not alive it’s called chemistry and therefore not evolution.
So maybe it comes down to preferred meanings for words. But there are myriad chemical processes that respond to differences in their environment by going down different paths, that evolve (little ‘e’) and that replicate.
That being the case the next question is, where do you draw the line between life and chemistry? Getting people to agree on a definition of life is far worse than getting people to agree on a definition of species. The problem of where to draw the line between life and chemistry seems about pefectly analagous to the problem of where to draw the species line between organisms. If you look at it from far enough away, low resolution, it is fairly easy to justify significant differences. But as you zoom in, higher resolution, it becomes more and more difficult to do so.
To put specifics to it: most (but not necessarily all) would agree that bacteria are alive. Whether or not viruses are alive is the subject of no small debate. Prions are generally not considered alive, but non-trivial arguments can be put forth that they are, indeed, alive…and prions are merely particular protein isomers; if you’re going to say that prions are alive, you’ll have a hard time distinguishing prion proteins from non-prion proteins.
It’s the same problem as trying to draw a dividing line on the spectrum between blue and green. Though “blue” and “green” are very, very useful labels, trying to use them with precision is a fool’s errand. Rather, refer to a spectral power distribution graph if that’s the sort of thing you need. Same with biology v chemistry; when the two get close enough that they overlap, arguing over which is which is counterproductive, and you’re much better off simply describing what’s going on in direct terms.
Cheers,
b&
Not a problem for me:
1) Bacteria are alive
2) Viruses are not really alive because they are parasitic replicators that require enzymes from a host not coded for in their own DNA/RNA. Thus, they aren’t a self-contained life form. A virus particle without a host cell will forever look like a dead package of nucleic material and undergo no replication.
3) Prions are definitely not alive but simply proteins that fold into different energetically allowed conformations that have secondary protein structure.
Ask yourself, what’s the difference between a dead bacterium and an alive one? The answer is metabolism–energy used to maintain the integrity of their structure (self vs. environment), house the replicator (DNA), and maintain energy imbalances (e.g ionic strength) between self and replicator. And the replicator must reproduce.
Next to last sentence should have read “…between self and environment”
Your objection to viruses not being alive can equally apply to any other organism that’s dependent either for life or for reproduction on some other organism.
Including, most emphatically, humans (mitochondria and the microbiome) as well as plants that depend on specific pollinators. And what of other parasites?
Again, you’re trying to draw the line between green and blue at precisely 495.000nm, when there’s not even any meaningful visual difference between 494nm and 496nm.
Cheers,
b&
Viruses are the only sort of parasite that depend on the host not just for food or reproduction, but for metabolism as well. A virus particle has no power supply; it’s entirely passive (and subject to entropic decay) until it encounters a biochemical environment that can unpack and activate it. And even then, the host cell provides the power source and does all the work; the viral DNA is a passive free rider on that existing metabolic system.
So if we consider metabolism and actively maintained chemical disequilibrium to be a defining character of life, then it seems reasonable to conclude that viruses are not alive by that definition.
On the other hand if all we require of life is replication (assisted or otherwise), then I guess chain letters and Facebook memes are alive.
While that would be a good argument against life, there’re equally strong arguments in favor of life. In particular, viruses are highly evolved and evolving and even swap genetic material amongst themselves — and they’ve been evolving for billions of years.
Imagine an outsider test of biology. If we had nothing like viruses on Earth and discovered them in some alien ecosystem, I’m pretty sure we’d classify them as alive, as ultimately efficient parasites. And if that would be a reasonable conclusion for other biospheres, then it’d certainly be one for ours as well.
Cheers,
b&
Exactly.
I think life is best defined at the cellular level. Humans are alive only as long as our cells are alive (and organ systems etc). Yes, the fingernails of a dead person can grow, other parts of a braindead human are still alive, etc. So I’ll take the liberty of defining life at the unicellular level because multicellular critters can be “partially dead” or be alive with dead cells or be dead with living cells and it’s a worthless discussion.
Again, that viruses mutate and evolve (they are the most basic of replicators that come in a plain brown wrapper) does not imply alive. They are aberrant genes that happen to have evolved a self-sealing envelope, the barest replicator imagineable. Without host polymerases and energy, a planet could be filled with virions and we would detect no evidence of life. Oligos: yes, life: no. It’s no different than me taking DNA, PCR amplifying it repeatedly (copying errors will occur), and transfecting that DNA into a living bacterium to see what proteins are made and what they do. I added the DNA polymerase and nucleotide building blocks, and energy and allowed transcription and translation.
“Your objection to viruses not being alive can equally apply to any other organism that’s dependent either for life or or reproduction on some other organism.”
Totally false. All single and multicellular parasitic organisms are alive whether their host feeds them or spreads their genes/DNA. Mitochondria are not alive, the microbiome (bacteria) are. But enough of this.
The larger point that I would make (as a chemist) is that I dislike the metabolism-first models because whatever redox chemistry inside a lipid drop occurs must still link up with ribonucleotides at some point. I fail to see how that chemical energy becomes directed towards RNA replication.
“Yes, the fingernails of a dead person can grow…”
I believe what actually happens is that the fingers shrink, giving the illusion of fingernail growth.
“…biology v chemistry; when the two get close enough that they overlap”
chemology? biolistry? stew?
Ice cream!
…and it’s even in Chicagoland, for those who happen to be there:
Cheers,
b&
The argument put forward in the Pross book is that solving that “chemistry problem” will necessarily entail importing many of the concepts of biological evolution: replication, differential survival, kinetic stability of information as opposed to thermodynamic stability of individual molecules, and so on. So the earliest stages of biological evolution are continuous with the chemical origins of those patterns of stability. Just as there’s no single organism you can point to and say “This is the first chicken,” there’s no molecule you can point to and say “This is the first gene; biology starts here.”
I disagree. We should be able to explain (and grow closer all the time) how ribose and deoxyribose were formed prebiotically and as single enantiomers. We know how the nucleoside bases form (that’s easy). Now how could they polymerize (replicate) to make oligonucleotides? How do we arrive at the RNA world hypothesis?
The first replicator was likely RNA. How it “became alive” is the hard question (formed cell membranes, used energy, etc) How genes worked is easy. We don’t need to know what the first gene was–just how it was formed and survived in a niche that can be found in our galaxy.
That’s the point that Torbjorn has been making: the first replicator almost assuredly wasn’t RNA, although the last universal common ancestor very likely was. But that organism almost certainly evolved from earlier protein-based replicators which didn’t use RNA, and those would have evolved from even more primitive replicators not even based in protein, and so on.
RNA isn’t something that’s going to spontaneously coagulate out of the goo, complete with an instruction set capable of self-replication; it itself is quite complicated and sophisticated that only could have arisen as the end product of a long and torturous evolutionary development.
Cheers,
b&
Thanks for the discussion Ben. I disagree with Torbjorn. Sure there could have been pre-RNA world replicators that were supplanted in time by RNA and then DNA. But I would expect to see chemical “fossils” of these replicators. In other words, the ribosome still has RNA built into it after billions of years. Why not all protein? Why do both DNA and RNA persist? My final point is a bit Occam’s razor but reduces to starting material availability. Chiral L amino acids are found in space on asteroids as are the nucleobases (and easily made on Earth) and there are hints of sugars (like ribose) in space too. Whatever pre-RNA world replicator one might invoke must be made from the simple available stuff found on space rocks or in common primordial Earth niches. Given that RNA building blocks are out there makes the pre-RNA world sound like an infinite regress that we would observe vestigial traces of and haven’t.
I’m not clear on which part you’re disagreeing with. If the first replicator (be it RNA or something else) was not alive, that puts it in the domain of chemistry, which would seem to indicate agreement on your part that chemical evolution is continuous with biological evolution.
Or perhaps what you mean is that there was such a thing as “the first gene”, but biology didn’t start there. In which case I think we’re in substantial agreement there too. Regardless of whether genes appeared gradually or suddenly, it takes more than genes to make life. You need metabolism, or what Pross calls “dynamic kinetic stability”, to maintain the energy disequilibria that power life (and I suspect that developed gradually as well).
Or perhaps I’ve misunderstood your point somehow.
Given that Jerry changed his mind after reading the book he mentioned, perhaps you should read it too before disagreeing so strongly?
That is classical darwinian evolution, and it is a good definition for extant biological life. (That is, you want to constrain to biochemistry (wetware) because of those pesky software/hardware analogs out there.)
But the mechanisms of evolution continues into chemical life, as pointed out in other comments.
And vice versa! For example:
As has been pointed out elsewhere, extant life has exactly the same traits of using spontaneous processes as chemistry does. [“Turnstiles and bifurcators: The disequilibrium converting engines that put metabolism on the road”, Branscomb and Russell, Biochim et Biophys Acta 2013]
ATP is produced in cells by non-equilibrium processes that are ~ 20 times away from cellular thermal energy. (Because differences in Gibbs FE isn’t an energy as such but measures the distance from equilibrium as – dG/kT.)
Criticizing Darwin, Miller, Sagan, and Ben Goren here, these astrobiologists notes that near equilibrium soup (“food”) theories doesn’t spontaneously iterate into disequilibrium chemistries. Because the existence of an equilibrium in the first place tells us so.
What is needed is from the outset is a disequilibrium process. And an “Atwood machine” a geared, turnstile, engine that links larger such processes to a cellular disequilibrium process.
AHV theory supplies both, a chemical gradient between an acidic ocean and an alkaline vent fluid, and the smallest possible engine in the form of electron bifurcating atoms – metals such as Mo & T – that can elevate one electron in potential by lowering another.
The AHV mound inorganic cells are likely homologous to the earliest metabolism that have been derived phylogenetically (a CO2/CH4 mixed metabolism that is ancestral to both methanogenes and acetogenes), to the pH difference between cells and environment, to the root import part of chemiosmosis and (in the Archean) to the CHNOPS ratios of cells.
So I claim that we have an answer to the “chemistry problem” and that it is consistent with a phylogeny and darwinian small step processes. But to say that we have _the_ answer is premature. [And really, if Russell et al predicted the existence of AHVs ~90 and the first one was discovered -00, it would be rapid progress in any case.]
You’ll get no argument from me that some sort of energetic gradient and a way to exploit it is an absolute requirement for biogenesis.
And the various experiments and proposals seem to be converging around a rough cluster of basic ideas more than ample to be confident that they’re all in the right ballpark even though it’s unlikely anybody yet has the perfectly right answer.
I am starting to think, though, that we may well see in the not-too-terribly-distant-future a modern equivalent of the Urey-Miller experiment that demonstrates evolutionary progressions from some particular known early conditions all the way to nucleic acids. Once there, the question can be definitely considered settled, even if there remain reasonable doubts as to whether or not that was the exact pathway that terrestrial life actually did take.
Cheers,
b&
Certainly, as I believe I’ve noted before, Russell has got 8 MUSD to experiment in AHV simulacrum reactors with. I think they started 2010, but I’m not up to speed on the results, except that they _have_ shown the spontaneous assembly of inorganic membranous cells.
I don’t think they will get to nucleic acids that way. These compartments reproduce without, and the type of attempts that probes early phylogenies deepest FWIW all predicts that early cells had metabolism and proteins before they adopted RNA as genetic material.
– AHV theory itself, with reproducing inorganic cells with metabolism and early inorganic catalysts. The same catalysts are now incorporated in (mostly AFAIK) proteins, while the metabolic carriers of carbon (coenzyme A) and energy (ATP & NADH) are nucleic acids.
– Protein fold families predicts that the earliest folds were metabolic, and that tRNA coupling enzymes were adapted from such metabolic origins.
– Under Archean conditions of no oxygen and reduced soluble iron, the oldest preserved RNA (intron type II, its autosplicing RNA function now adopted as spliceosome “knife”, and the ribosome functional core, an early molecular switch) are free electron metabolic catalysts; modern RNA is not.
And it seems the RNA sugar and its bases could have been selected because they stabilize early organic membranes, and conversely such lipids stabilize them. Since organic membranes would be beneficial for leaky inorganic cells, maybe they were adopted in that way. And there is a nucleotide metabolic enzyme pathway from such constituents to RNA, meaning selection could have bootstrapped autocatalysis on the road to ribozymes. [Ref: Joyce, IIRC.]
But the central problem is still how to get the sugars and bases, which is very hard chemically as I understand it.
One likely solution is recently suggested, but it is a metabolic CHN cycle all by itself. Sure, it could have been driven by the suggested AHV carbon and phosphate pathways, fed by AHV ammonia. But to get from two relatively simple and predictive metabolic open chains (carbon assimilation, ortophosphate production) to couple in a third, cellular type of recycling…
The coupling between disequilibrium processes and genetic processes is still very much an open question (in my mind at least). “Genetic takeover”? Maybe.
In my mind the bottom line of Lane’s & Martin’s proposal is that we don’t need to go there anymore. It is perhaps unnecessary “anthropomorphic” nucleic acid chauvinism.
If we are lucky we already know what geochemical systems are our most distant cousins. Then we will have as little principal need (but of course always curious desire) to fill in the exact pathways between, as we need to do between the flagellum homologs and the flagellum assembly, or between the other hominins and us.
Considering how sophisticated nucleic acids are, that would seem to make sense.
But that would also be a most fascinating thing to explore: self-replicating metabolic cellular “organisms” using something simpler than nucleic acids for the work of replication. Even if they don’t have any luck organically evolving that sort of thing in the lab, if they could manufacture something like that (using, perhaps, techniques that draw inspiration from the work of Craig Venter)…that would be pretty huge as well and extremely fascinating.
It could also offer a good midpoint stage to play around with; modify these proto-organisms in various ways to see if they make better or worse fits with hypothetical earlier and later stages of evolutionary development.
The best thing about this is that it’s something that we can reasonably hope to succeed at doing in the lab. I’m pretty sure the chemistry and microengineering required isn’t radical by modern technological standards.
Cheers,
b&
It is also interesting to follow the disequilibriums back in time, similarly to Ben following the evolution of systems. The AHV disequilibrium is a result of serpentinization so mostly crustal subduction.
[With a potential stagnant lid in the Archean, still ~ 10 % of the time the crust had to have subducted, see “Stagnant-lid tectonics in early Earth revelaed by 142Nd variations in late Archean rocks”, Debaille et al, Earth and Plan Sci Lttrs, 2013. This ups the chances for abiogenesis in similar stagnant-lid regimes of planets, eg Mars!]
That goes back to how the disequilibrium of differentiation works on siliceous but ferrous terrestrials under planetary formation.
Moving back, we hit the final disequilibrium of gravitational aggregation of matter. This in turn is a product of quantum fluctuations during inflation (the seed for galaxies) and disequilibrium of halting inflation (the necessary seed for matter-antimatter imbalance is temporary absence of matter-radiation equilibrium, together with two putative symmetry breakings of standard particles).
We can blame life, as indeed the observable universe at large, on inflation.
…and, since Saint Reagan placed the blame for inflation on Carter, does that mean that Jimmy is God?
…sorry….
b&
Professor Ceiling Cat said “dog”.
Out of curiosity, will you write more about Addy Pross’ book? I think I mentioned in the “books of 2013” post that I found out about it here at WEIT, ordered it, and read it. I thought it was very interesting, and clearly written (speaking as someone not in the biology/chemistry field). I would love to hear your comments about it.
I once was asked by someone interested in the origin of life whether natural selection applied during the process. Knowing basically nothing about the relevant chemistry, I found myself saying that the different theories in one way or another involved chemicals encouraging each others’ production or persistence. So sort-of-alive systems have sort-of-natural-selection. It’s like knowing when you’re outdoors or knowing when you’re underwater. The change is actually continuous, but for most purposes, in most situations, you can model it by saying you’re either in or out.
Isaac Asimov already trod this path decades ago (as he did in so many things). He discussed the Miller-Urey experiment and then extrapolated into protein-like molecules that auto-catalyze copies of themselves, and “eat” other molecules to get the energy and atoms to do this. He realized that there would be natural selection at work even at this primitive stage.
I think this essay was collected either in Only a Billion or in View From a Height.
Agreed, there was a continuity, presumably a fine-grained one of darwinian small steps.
For example, in the popular (I think) AHV [alkaline hydrothermal vent] theory, Russell et al proposes that chemical evolution continues into Lamarckian evolution between the inorganic cells of the AHV mound. [Or, I would think, between mounds as the infestation of new chemistry can spread by seeding.]
That in turn continues into Darwinian evolution of genetic replicators.
Mostly a separation has been made re creationists, that fails evolution for not incorporating all of abiogenesis. But the situation seems to me to be akin to masses vs gravitation. General relativity isn’t responsible for all mass mechanisms (re, say, the Higgs mechanism). But there is a relativistic mass contribution where gravitational processes are essential.
So you can’t tease them apart. But you also can’t say that relativity/evolution theory is dependent on predicting mass/root cellular populations.
I think that’s exactly backwards.
Creationists point to the lack of a solid theory for abiogenesis as a serious criticism of evolution, precisely because they consider the two continuous.
Responding supporters of evolution (with wildly varying levels of understanding on the subject) then claim that they are two separate issues entirely. Evolution has nothing to do with the origin of life, they say.
The creationists are right here. It’s the same topic, and the lack of a good theory for how life began is absolutely a weakness. It’s just not even remotely fatal as weaknesses go, and prospects look better every year for overcoming it.
My response to the splitters is that saying evolution has nothing to say about the origins of life is like saying linguistics has nothing to say on the origins of language.
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