Spontaneous generation

[lpetrich]

For all of humanity's history, it was fairly obvious that some organisms are only produced by organisms very much like them. Like human beings. It was also obvious that some other organisms were produced by nonliving matter, like flies from rotting meat. Or so it seemed.

The latter notion is  Spontaneous generation, and it was taken for granted by many people for nearly all of humanity's history. Like Aristotle (385 BCE - 323 BCE):

Now there is one property that animals are found to have in common with plants. For some plants are generated from the seed of plants, whilst other plants are self-generated through the formation of some elemental principle similar to a seed; and of these latter plants some derive their nutriment from the ground, whilst others grow inside other plants ... So with animals, some spring from parent animals according to their kind, whilst others grow spontaneously and not from kindred stock; and of these instances of spontaneous generation some come from putrefying earth or vegetable matter, as is the case with a number of insects, while others are spontaneously generated in the inside of animals out of the secretions of their several organs.

History of Animals, Book V, Part 1

Advancing forward by nearly two millennia, we find a recipe for mice by alchemist Jan-Baptista van Helmont (1580 - 1644). In 1620, he published:

... for if you press a piece of underwear soiled with sweat together with some wheat in an open mouth jar, after about 21 days the odor changes and the ferment coming out of the underwear and penetrating through the husks of the wheat, changes the wheat into mice. But what is more remarkable is that mice of both sexes emerge (from the wheat) and these mice successfully reproduce with mice born naturally from parents? But what is even more remarkable is that the mice which came out were not small mice? but fully grown.

 

[aupmanyav]

Jan-Baptista van Helmont - excellent.

Ayurveda (Sushruta, surgeon; and Charaka, physician):
Books: Sushruta Samhita, Charaka Samhita

Jangama: The world of living.
Jarayuja: Mammals.
Andaja: Eggs, Birds and fish.
Oudbija: Mud, Frogs, etc.
Swedaja: Sweat, Insects.

But, from what they were born was not much relevant to Ayurveda.

 

[lpetrich]

But some people started getting skeptical. Sir Thomas Browne (1605 - 1682) wrote a debunking book, Pseudodoxia Epidemica (in simpler language, "Common Errors"), and he discussed spontaneous generation in it.

Concerning the generation of Froggs, we shall briefly deliver that account which observation hath taught us. By Frogges I understand not such as arising from putrefaction, are bred ....but they let fall their spawn in the water... In this spawn of a lentous and transparent body, are to be discerned many specks, or little conglobulations, which in a small time become of deep black.... Now of this black or duskie substance is the Frogge at least formed; as we have beheld, including the spawn with water in a glass, and exposing it unto the Sun. For that black and round substance, in a few days began to dilate and grow longer, after a while the head, the eyes, the tail to be discernable, and at last to become that which the Ancients called Gyrinus, we a Porwigle or Tadpole. This in some weeks after becomes a perfect Frogg, the legs growing out before, and the tail wearing away, to supply the other behind.

Sir Thomas Browne, Pseudodoxia Epidemica, Book 3, Chap 13, 1672, 6th edition

A good presentation of the lifecycle of a frog.

He also expressed some doubts about the spontaneous generation of mice (Pseudodoxia Epidemica, Book 3, Chap 28). Alexander Ross (ca. 1590 - 1654) responded:

He doubts whether mice can be procreated of putrifaction. So he may doubt whether in cheese and timber worms are generated; Or if Betels and wasps in cowes dung; Or if butterflies, locusts, grashoppers, shel-fish, snails, eeles, and such like, be procreated of putrified matter, which is apt to receive the form of that creature to which it is by the formative power disposed. To question this, is to question Reason, Sense, and Experience: If he doubts of this, let him go to Ægypt, and there he will finde the fields swarming with mice begot of the mud of Nylus, to the great calamity of the Inhabitants.

Alexander Ross, Arcana Microcosmi, Book 2, Chap 10, pp 151-156, 1652

I'll modernize the language:

He doubts whether mice can be generated by rotting. So he may doubt whether worms are generated in cheese and wood. Or whether beetles and wasps are generated in cow dung. Or whether butterflies, locusts, grasshoppers, shellfish, snails, eels, and the like are generated in rotting material, something capable of receiving the forms of the animals that it is inclined to produce. To question this is to question reason, sense, and experience. If anyone doubts this, let them go to Egypt, and they will find the fields swarming with mice that were generated from the mud of the Nile, mice that cause great calamity to the inhabitants.

Or in simpler language:

Is he out of his mind? Spontaneous generation happens all around us. Worms, beetles, wasps, butterflies, locusts, grasshoppers, shellfish, snails, eels, you name it. All you have to do is go to Egypt and look at the mice there -- mice generated by the mud of the Nile.

 

[aupmanyav]

Aledxander Ross - excellent.

 

[lpetrich]

Francesco Redi (1626 - 1697) went a step further. He noticed that rotting meat produces flies -- the same kinds flies that it attracts. So were the flies from meat being produced by the flies that were attracted to the meat?

He decided to do some experiments, and his experiments are classics of experimental design. He tried putting rotting meat into a box. Flies could not get in, and no flies appeared in that meat. He tried putting some rotting meat in a jar with its open end covered with gauze. It attracted flies, but the fiies could not get in. The meat made no flies. But meat that flies could reach was meat that would make flies.

It was a simple experiment, easily repeated and easily extended. But spontaneous generation took two centuries to die. Redi himself believed that gall wasps / gall midges were generated by plant galls, swellings that some plants sometimes get. Also, even if macroscopic organisms were rather evidently produced by other macroscopic organisms, microscopic ones were another story, and it took Pasteur's and Tyndall's experiments to finally discredit spontaneous generation.

 

[Valjean]

Ipetrich appears to be generated of clotted duckweed, in a warm little pond....

 

[lpetrich]

But there is a version of spontaneous generation that has become mainstream:  Abiogenesis

This modern version is usually traced back to Charles Darwin, who speculated in a letter to Joseph Dalton Hooker in 1871 that some ancestral organism may have originated in a "warm little pond, with all sorts of ammonia and phosphoric salts, light, heat, electricity, &c., present, that a proteine compound was chemically formed ready to undergo still more complex changes." He also stated that "at the present day such matter would be instantly devoured or absorbed, which would not have been the case before living creatures were formed."

So he suspected that it would be difficult to work out what happened, because the descendants of its product organism would destroy the evidence of their origin.

The origin of life continues to be an unsolved problem, though research on it goes in both directions, from prebiotic environments to the first organism, and from present-day organisms to the first organism. There are now some hints as to a meeting, though they are still hints and not a well-mapped-out pathway.

 

[lpetrich]

Charles Darwin in his Origin of Species speculated on origin from a few forms or one, and also he stated that the origin of life is almost as impenetrable as the origin of matter. But that was pure hand-waving for a long time.

Organisms too small to see were speculated on for a long time, but such organisms were first observed by Antonie Van Leeuwenhoek in 1673 with an early microscope. In 1866, biologist Ernst Haeckel proposed a division of one-celled organisms into Monera and Protista, what we'd now call prokaryotes and eukaryotes.

Eukaryotes have much more complicated cell structure than prokaryotes, and their origin has long been a mystery. The most success in tracking down eukaryote origins has been with two kinds of organelles, as they are called: mitochondria and chloroplasts (plastids more generally; there are plenty of different-colored ones -- red, orange, yellow, brown, ...). Chloroplasts have been tracked down to blue-green algae, nowadays called cyanobacteria, and mitochondria to alpha-proteobacteria, with such (relatively) close relatives as root-nodule nitrogen-fixing bacteria and Rickettsia (that disease organism). The rest of the eukaryote cell has been more difficult to track down, but what I can find out about it, its ancestry is a mishmash -- the ancestral eukaryote cell was a "chimera", a Frankenstein cell.

Endosymbiosis of mitochondria and chloroplasts was proposed in the early 20th cy., but it was ignored until Lynn Margulis (Carl Sagan's first wife) revived it in the late 1960's. But this hypothesis was not generally accepted until a lot more detail was discovered, including lots of gene and protein sequences.

Gene sequencing enabled resolving the high-level phylogeny of eukaryotes, and also the phylogeny of prokaryotes.

In the 1970's, Carl Woese was working on the phylogeny of prokaryotes with gene-sequencing techniques, when he discovered something weird. He was sequencing genes from bacteria, when he came across a very weird one. It was a methanogen, one that does CO2 + 4H2 -> CH4 + 2H2O to get its energy, one that is thus named after its methane-making. That was weird enough, but he discovered that it branched off way early from the others, about when other bacteria and eukaryotes branched off from each other. He ended up discovering some other members of this deep branch of the family tree of life, and he proposed the name "Archaebacteria", nowadays "Archaea" for them. Ordinary bacteria became "Eubacteria" or "Bacteria".

At first, it didn't seem like much of an issue, but some phenotypic features were eventually found that distinguish most of Archaea and Bacteria, like cell-membrane and cell-wall composition, and also some information-system differences (ribosomes, DNA polymerases, etc.). So Archaea and Bacteria are nowadays accepted as the earliest known split in the family tree of cellular organisms. Woese considered Eukarya coequal with Bacteria and Archaea, but it was since recognized to be some mishmash hybrid of parts from organisms in Bacteria and Archaea -- the eukaryotic information systems are most closely related to Archaea, while a lot of metabolic stuff is most closely related to Bacteria.

 

[bilby]

The origin of life isn't much of a problem; There are several excellent hypotheses, and several of them may be correct. The definition of life is the real problem.

It seems that life/non-life is just another of those common human classification errors - reality simply isn't dichotomous, it's continuous. At least in four dimensions.

The absence of extinct connections at any given point in time is easy to mistake for discontinuity. But it's really, really uncommon for any biological phenomenon to be universally divisible into neat, discrete, and clearly defined sets. Biology is a massive fucking mess, and any biologist worth his salt is aware that every statement of fact in the biological sciences can be improved by appending "... although in reality it is more complex than this".

 

[lpetrich]

The Last Universal Common Ancestor (LUCA) can be partially reconstructed from present-day organisms' genes. It was much like present-day methanogens and some similar organisms, extracting energy by making methane or acetic acid from hydrogen and carbon dioxide. It made all its biological molecules from simple precursors, as plants do, but it was poisoned by oxygen -- it was an anaerobe.

An interesting curiosity of some of the early branchers is their temperature tolerance -- they are thermophiles and hyperthermophiles, some of them being able to survive in temperatures of 100 C and more. This suggests that that temperature tolerance goes back a long way.

But the LUCA was a rather complicated organism, with DNA, RNA, and proteins, DNA and RNA transcription, and RNA translation to proteins. So it would be hard for it to directly emerge from a prebiotic environment. There is an alternative hypothesis, that it already had a lot of evolution behind it. In particular, the RNA-world hypothesis. A RNA-world organism had RNA as both genome and enzymes, and DNA and proteins emerged form it. DNA as a modification of RNA, and proteins as enzyme cofactors assembled for RNA enzymes (ribozymes). Eventually the cofactors became the entire enzymes, with some RNA surviving as cofactors, like some B vitamins.

The RNA-world hypothesis is nowadays widely accepted, and the main criticism I've seen of it is the origin of its RNA. It's rather difficult to make it prebiotically, especially the ribose part.

I've seen the theory that the ribose in RNA had some predecessor, like early proteins (peptide nucleic acid, PNA), or polycyclic aromatic hydrocarbons (PAH-NA).

 

[Wiploc]

But there is a version of spontaneous generation that has become mainstream:  Abiogenesis

Also gods. Many people believe that they don't have ancestors.

 

[lpetrich]

Sources:
Sir Thomas Browne: Pseudodoxia, or Vulgar Errors
Frogs: Browne's Vulgar Errors III.xiii: Frogs, Toads, Toad-stone
Mice: Sir Thomas Browne's Vulgar Errors III.xxviii: Animals - "Whether Mice may be bred by putrifaction as well as univocall production, as may easily be believed, if that receit to make Mice out of wheat will hold, which Helmont hath delivered."

Alexander Ross's Arcana Microcosmi
Spontaneous generation: Arcana Microcosmi, II:10


Flies From Meat and Wasps From Trees: Reevaluating Francesco Redi's Spontaneous Generation Experiments - PubMed

Francesco Redi's seventeenth-century experiments on insect generation are regarded as a key contribution to the downfall of belief in spontaneous generation. Scholars praise Redi for his experiments demonstrating that meat does not generate insects, but condemn him for his claim elsewhere that trees can generate wasps and gallflies. He has been charged with rejecting spontaneous generation only to change his mind and accept it, and in the process, with failing (at least in some sense) as a rigorous experimental philosopher. In this paper I defend Redi from both of these charges. In doing so, I draw some broader lessons for our understanding of spontaneous generation. 'Spontaneous generation' does not refer to a single theory, but rather a landscape of possible views. I analyze Redi's theoretical commitments and situate them within this landscape, and argue that his error in the case of insects from plants is not as problematic as previous commentators have said it is. In his research on gall insects Redi was addressing a different question from that of his experiments on insect generation-the question was not "Can insects come from nonliving matter?," but rather, "Can insects come from living organisms which are not their parents (namely, trees)?" In the latter case, he gave an answer which we now know to be false, but this was not due to any failure in his rigor as an experimental philosopher.

Even in the bad old days of widespread acceptance of spontaneous generation, it was not considered universal, and some advocates of SG considered it possible for organisms to have both origin modes. Like Jan-Baptista van Helmont. He discovered that the mice that were produced with his recipe could interbreed with other mice. But I think that Francesco Redi would have had a few things to say about van Helmont's recipe.

JBvH made another notable contribution to science. I think that he noticed that potted plants don't seem to use up much of the soil that they grow in, and that motivated him to try an experiment. He decided to grow a small willow tree in a pot for a year or so. He weighed the tree and the pot's soil before and after, and when he finished, he found that the tree had gained weight and that the soil had lost weight -- and that it was much more for the tree than for the soil. He concluded that the tree's extra weight came from the water that he watered it with. We now know that that is only partially correct, and that much of the tree's extra weight had come from the air.

 

[skepticalbip]

Those who don't accept spontaneous generation have never battled crab grass and dandelions.

 

[bilby]

Sources:
Sir Thomas Browne: Pseudodoxia, or Vulgar Errors
Frogs: Browne's Vulgar Errors III.xiii: Frogs, Toads, Toad-stone
Mice: Sir Thomas Browne's Vulgar Errors III.xxviii: Animals - "Whether Mice may be bred by putrifaction as well as univocall production, as may easily be believed, if that receit to make Mice out of wheat will hold, which Helmont hath delivered."

Alexander Ross's Arcana Microcosmi
Spontaneous generation: Arcana Microcosmi, II:10


Flies From Meat and Wasps From Trees: Reevaluating Francesco Redi's Spontaneous Generation Experiments - PubMed

Francesco Redi's seventeenth-century experiments on insect generation are regarded as a key contribution to the downfall of belief in spontaneous generation. Scholars praise Redi for his experiments demonstrating that meat does not generate insects, but condemn him for his claim elsewhere that trees can generate wasps and gallflies. He has been charged with rejecting spontaneous generation only to change his mind and accept it, and in the process, with failing (at least in some sense) as a rigorous experimental philosopher. In this paper I defend Redi from both of these charges. In doing so, I draw some broader lessons for our understanding of spontaneous generation. 'Spontaneous generation' does not refer to a single theory, but rather a landscape of possible views. I analyze Redi's theoretical commitments and situate them within this landscape, and argue that his error in the case of insects from plants is not as problematic as previous commentators have said it is. In his research on gall insects Redi was addressing a different question from that of his experiments on insect generation-the question was not "Can insects come from nonliving matter?," but rather, "Can insects come from living organisms which are not their parents (namely, trees)?" In the latter case, he gave an answer which we now know to be false, but this was not due to any failure in his rigor as an experimental philosopher.

Even in the bad old days of widespread acceptance of spontaneous generation, it was not considered universal, and some advocates of SG considered it possible for organisms to have both origin modes. Like Jan-Baptista van Helmont. He discovered that the mice that were produced with his recipe could interbreed with other mice. But I think that Francesco Redi would have had a few things to say about van Helmont's recipe.

JBvH made another notable contribution to science. I think that he noticed that potted plants don't seem to use up much of the soil that they grow in, and that motivated him to try an experiment. He decided to grow a small willow tree in a pot for a year or so. He weighed the tree and the pot's soil before and after, and when he finished, he found that the tree had gained weight and that the soil had lost weight -- and that it was much more for the tree than for the soil. He concluded that the tree's extra weight came from the water that he watered it with. We now know that that is only partially correct, and that much of the tree's extra weight had come from the air.

Indeed. Yet most people, even today, believe that when they lose weight through dieting, the loss is via defaecation and/or urination. In fact, most long-term weight loss is due to the exhaling of carbon in your breath. Short term weightloss can be achieved via loss of water through urine and/or sweat, but this is rarely sustained, as the human body is quite effective at maintaining optimal hydration.

If you want to lose weight, you need to breathe it out.

 

[fromderinside]

Short term weight loss can be achieved via loss of water through urine and/or sweat, but this is rarely sustained, as the human body is quite effective at maintaining optimal hydration.

Obviously you've not experienced  Congestive heart failure.

Diuretics have been a mainstay of treatment for treatment of fluid accumulation, and include diuretics classes such as loop diuretics, thiazide-like diuretics, and potassium-sparing diuretics. Although widely used, evidence on their efficacy and safety is limited, with the exception of mineralocorticoid antagonists such as spironolactone.^[66][68] Mineralocorticoid antagonists in those under 75 years old appear to decrease the risk of death.^[69] A recent Cochrane review found that in small studies, the use of diuretics appeared to have improved mortality in individuals with heart failure.^[70] However, the extent to which these results can be extrapolated to a general population is unclear due to the small number of participants in the cited studies

Taking water pills. Gotta keep my potassium up (bananas, avocado, sweet potatoes, etc). Removal of excess liquid in and around lungs and around heart improve my ability to do simple things like walk a mile or so.

Yeah, I'm looking for my little fiddle.

 

[bilby]

Short term weight loss can be achieved via loss of water through urine and/or sweat, but this is rarely sustained, as the human body is quite effective at maintaining optimal hydration.

Obviously you've not experienced  Congestive heart failure.

Diuretics have been a mainstay of treatment for treatment of fluid accumulation, and include diuretics classes such as loop diuretics, thiazide-like diuretics, and potassium-sparing diuretics. Although widely used, evidence on their efficacy and safety is limited, with the exception of mineralocorticoid antagonists such as spironolactone.^[66][68] Mineralocorticoid antagonists in those under 75 years old appear to decrease the risk of death.^[69] A recent Cochrane review found that in small studies, the use of diuretics appeared to have improved mortality in individuals with heart failure.^[70] However, the extent to which these results can be extrapolated to a general population is unclear due to the small number of participants in the cited studies

Taking water pills. Gotta keep my potassium up (bananas, avocado, sweet potatoes, etc). Removal of excess liquid in and around lungs and around heart improve my ability to do simple things like walk a mile or so.

Yeah, I'm looking for my little fiddle.

Obviously I am talking about humans in good health. That there are disorders which disrupt the ability to maintain optimum hydration is both well known and supportive of the point I am making.

If I said that humans typically have two arms, would you say "obviously you're not an amputee", or would you recognise that I am making a general observation to which there are many well know exceptions?

I seem to recall saying, only a few posts back in this very thread:

...any biologist worth his salt is aware that every statement of fact in the biological sciences can be improved by appending "... although in reality it is more complex than this".

so I pretty much assumed that my readers would understand that I am well aware of exceptions to the statements I make, while being comfortable that those statements are nevertheless broadly true.

Or is your response simply a case of you leaping at the opportunity to talk about yourself and your ailments?

 

[fromderinside]

touchy, touchy, touchy. Just letting my 79er run a little. Hope yours works as well when you mature to one.

FYI I can't leap, wouldn't care to if I could. Oh wait ..... you think ..... talk about jumping.....

Oh, no your thesis being broadly true is just flat wrong. Humans are chronic over compensating biological systems. You will know when you watch the fat lady sing or witness someone flying over the coo coo nest.

 

[lpetrich]

Eukaryote phylogeny:

• Eukaryotes
• The New Tree of Eukaryotes: Trends in Ecology & Evolution - 2019

Courtesy of "phylogenomics" - phylogeny + genomics

The sequencing of large numbers of genes from a large number of organisms has created a gold mine of data - a huge amount of data that one can work from. That has enabled resolving relationships that were previously very difficult to do. But many of these relationships are only supported by gene-sequence comparisons and not by any recognizable shared phenotypic features.

Now to prokaryotes. Their overall phylogeny was mapped out before eukaryote overall phylogeny.

It's fun looking through PubMed for Carl Woese's papers on determining the phylogeny of prokaryotes. He used something called small-subunit ribosomal RNA (SSU rRNA), about 1,500 RNA bases in prokaryotes and chloroplasts, 2,000 in eukaryotes, and 1,000 in mitochondria. He started in the early 1970's, and it was difficult to get long nucleic-acid sequences back then, so he chopped up this SSU rRNA with enzymes and then sequenced the fragments. But that worked well enough for him.

Looking through his papers, he got more and more sequences of prokaryotes, and at first, they seemed like some recognizable group. But then, he sequenced a methanogen, and ... BOOM! It was much farther from other prokaryotes, comparable to their distance from eukaryotes.

That was the first evidence of the oldest known split in known organisms' phylogeny: the Bacteria-Archaea split.

The phylogeny of prokaryotes | Science - back in 1980 - a classic paper on the subject, though mostly using SSU rRNA.

Whole-proteome phylogeny of prokaryotes by feature frequency profiles: An alignment-free method with optimal feature resolution | PNAS is from 2010

Overall, the taxonomic groupings of WPSs by our FFP method agree very well with the reference taxonomy; almost all main groupings agree with the reference taxonomy at several taxonomic levels (domain, phylum, class, and genus), with some minor discrepancies in monophyly and grouping. However, substantial differences in the branching orders of major groups are observed between our proteome FFP tree and trees from other methods based on, for example, SSU rRNAs, orthologous genes, and protein domains.

The more recent branching agrees rather well, but the earlier branching doesn't. Even so, the Bacteria-Archaea split still comes out of this method.

 

[aupmanyav]

lpetrich arrived in the world riding a meteorite.

 

[lpetrich]

Integrated genomic and fossil evidence illuminates life’s early evolution and eukaryote origins

Establishing a unified timescale for the early evolution of Earth and Life is challenging and mired in controversy because of the paucity of fossil evidence, the difficulty of interpreting it, and dispute over the deepest branching relationships in the tree of life. Surprisingly, it remains perhaps the only episode in the history of Life where literal interpretations of the fossil record hold sway, revised with every new discovery and reinterpretation. We derive a timescale of life, combining a reappraisal of the fossil material with new molecular clock analyses. We find that the last universal common ancestor of cellular life (LUCA) predated the end of late heavy bombardment (>3.9 Ga). The crown clades of the two primary divisions of life, Eubacteria and Archaebacteria, emerged much later (<3.4 Ga), relegating the oldest fossil evidence for life to their stem lineages. The Great Oxidation Event significantly predates the origin of modern Cyanobacteria, indicating that photosynthesis evolved within the cyanobacterial stem-lineage. Modern eukaryotes emerged late in Earth history (<1.84 Ga), falsifying the hypothesis that the GOE facilitated their radiation. The symbiotic origin of mitochondria, at 2.053 – 1.21 Ga reflects a late origin of the eukaryotes, that do not constitute a primary linage of life.