Patient Scientists Elucidate Origin of Eukaryotes

Guest post by John Tillman

In 1962 paper, Roger Stanier and C. B. van Niel established the division of cellular organization into prokaryotes and eukaryotes, defining prokaryotes as those organisms, such as bacteria, which lack a cell nucleus.

Ernst Mayr (1904-2005) called the evolution of eukaryotes–cells with nuclei–“perhaps the most important and dramatic event in the history of life”. Eukaryotic cells also contain various organelles, such as mitochondria, their powerhouses, and in plants and algae, photosynthetic chloroplasts, which use sunlight to make sugar from water and carbon dioxide. This momentous milestone probably occurred between 1.8 and 2.2 billion years ago, but possibly longer.

In 1966, Lynn Margulis (1938-2011), the first Mrs. Carl Sagan, proposed that eukaryotic cells resulted from endosymbiosis, via engulfment of the ancestor of mitochondria by another prokaryote. Experimental evidence for this hypothesis came in 1978, when Robert Schwartz and Margaret Dayhoff demonstrated the descent of mitochondria from bacteria and of chloroplasts from cyanobacteria. During the 1980s, the DNA of mitochondria and chloroplasts was found to differ from their host’s nuclear genetic material, which validated endosymbiosis as a real evolutionary process.

Meanwhile, in 1977, Carl Woese (1928-2012) and George Fox defined Archaea as a third domain of life, with fellow prokaryotic Bacteria and with the much more complex Eukaryota.

In 1999, M. W. Gray, et. al., found strong phylogenetic evidence that an alphaproteobacterium was the ancestor of the mitochondrion. This left open the question of what kind of prokaryote engulfed the first proto-mitochondrion. Similarities in the membranes of archaea and eukaryotes suggested that the endosymbiosis wasn’t between two bacteria, but was a union of two separate domains. If so, then phylogenetically, there were arguably only two domains, not three, since the nuclear DNA of us eukaryotes descends from archaea.

In 2017, various researchers identified the Asgard superphylum as the closest archaean relatives of eukaryotes, but this group was known only from its DNA, recovered from seafloor sediments. Without knowing what Asgard archaeans even look like, let alone their behavior, scientists couldn’t shed light on how endosymbiotic events might have happened.

But now long, hard work by real scientists has helped to unravel this mystery. Thanks to the remarkable persistence and painstaking practice of Japanese microbiologists, science now knows enough about one member of the Asgard superphylum to form an educated hypothesis regarding ancient endosymbiosis and the origin on unicellular eukaryotes and their multicellular descendants, ie animals, fungi and plants.

Please read this Science article for the fascinating details:

https://www.sciencemag.org/news/2019/08/tentacled-microbe-could-be-missing-link-between-simple-cells-and-complex-life

This discovery offers another instance of the importance to life in general of all kinds of symbiosis. We eukaryotes swim in a sea of microbes, most of which aren’t parasites or pathogens. Many make our lives possible. Even the simplest animals–sponges–often form symbiotic relationships with oxygen-producing cyanobacteria. Similarly, lichen are mutualistic partnerships between fungi and algae or cyanobacteria. “Coral symbiosis is a three-player game”:

https://www.nature.com/articles/d41586-019-00949-6

While H. sapiens relies less on gut prokaryotes than do termites, ruminants and other animals needing to break down cellulose, our bodies still contain about 1.4 microbes for each human cell.

Gut prokaryotes: not just for methane any more!

[Edit Addendum sent by John Tillman.

Might add that it appears that eukaryotes developed only once.  Soon after the origin of eukaryotes, sexual reproduction evolved, perhaps in response to reactive oxygen species produced by pre-mitochondria.  Since both photosynthetic and heterotrophic eukaryotes have sex, this development seems to have occurred after proteobacteria (a major gram-negative phylum) were engulfed to become pre-mitochondria but before the inclusion of cyanobacteria as pre-chloroplasts.
From last year:
Advertisements

199 thoughts on “Patient Scientists Elucidate Origin of Eukaryotes

  1. Oops!

    “Now” for “know” in 7th paragraph.

    Should know better than to write on an auto-filling phone.

    [fixed ~ctm]

  2. Sounds complicated. Very complicated. More than complicated, cells and cellular life appears to have design, purposeful design.

    • Only a very unintelligent designer would have engineered the Rube Goldberg apparatuses of molecular and organismal biology.

      Eukaryote sexual reproduction is a good example of processes far more complicated than a good chemical engineer would have designed. As with all else in biology, sexual reproduction makes sense only in the light of evolution, as famously noted by devout Orthodox Christian geneticist Theodosius Dobzhansky.

      • Rabbits were not designed to be eaten by foxes. The natural world, social and political systems were not designed to be the way they are now. Sh!t happens.

        • True.

          The ancestors of rabbits lived in the Eocene. Surely some predator then ate them. The carnivores might even have been related to foxes.

          The canid family of order Carnivora does indeed date from the late Eocene, but it didn’t evolve specifically to prey upon lagomorphs.

          True foxes didn’t evolve until much more recently.

          • The “ancestors of rabbits” as well as those of foxes lived in all eras (and eons). That’s the point. Lazy phrasing just contributes to the dumbing down we see all around us.

          • Kurt,

            Of course you’re right. I should have said the first lagomorphs evolved in the Eocene.

            I shouldn’t post in haste from work.

          • “The carnivores might even have been related to foxes”

            Of course they were. How could they be unrelated?

          • Tty,

            Again, I meant more closely related than to other members of the canid branch of carnivores, ie already differentiated from more distant canrnivore ancestors.

      • I would become more convinced that life could originate through random (unintentional) processes if scientists could create life in a laboratory. Since they can’t do that yet using all the accumulated knowledge (e.g. the structure of DNA was discovered way back in 1953) and the incredibly sophisticated technologies now available, I have a hard time believing it could happen under the primitive conditions of 4+ billion years ago, with no intelligent guidance or assistance.

        • Ralph Dave Westfall
          I have a hard time believing it could happen under the primitive conditions of 4+ billion years ago, with no intelligent guidance or assistance.

          “I cannot imagine it, therefore it is not possible” is not a convincing argument.

        • Ralph,

          They’re working on it. Recently funding has become available.

          Jack Szostak estimates five years, but IMO he’s optimistic. Other origin of life labs say 10 to 20 years.

          But there have been great strides in just the past five years. Simple experiments have yielded profound advances in understanding.

        • Life is created by, decided by and proliferated by mistakes. A few mistakes will be beneficial, while many are not or will have no effect at all. Which ones win and which lose is determined when opportunity meets capability.
          And, remember is it not survival of the “fittest”, but survival of the “fit enough”.

          • A good example is the evolution of nylon-eating bacteria from sugar-eaters. The simple point mutation which enables nylon consumption must have occurred repeatedly during billions of years, but was always fatal until nylon entered the environment. Then it became a beneficial mutation.

        • Why would the results of intense, decades-long, mostly unsuccessful, directed research and experimentation convince you of the possibility of “random (unintentional) processes”?

          • Origin of life research is not now and never has been intense. It’s conducted in a few labs scattered around the globe.

            Its many recent successes give me reasonable assurance that eventually researchers will find at least one way in which the ubiquitous precursors of life might have first polymerized and replicated via abiotic chemical evolution. There is probably more than one pathway from biomonomers to replicating polymers.

      • Evolutionary thinking has a lot of similarity to the junk science that is so prevalent in the global warming thinking among climatologists. This is easy to fall into, because if you have something that you can’t test, then all of a sudden just an active imagination is the primary driver of the “science”.

        And when a science becomes primarily driven by imagination, and becomes political, to the point of driving out any one who disagrees, then you see the current situation with both evolution and climate who will often ignore evidence against their views.

        It is not unusual for evolutionists to take a small piece of evidence, such as the pig’s tooth, and modern indian skull that was used to imagine the Piltdown Man. (this was was the evidence used in the Scopes trial to help prove evolution). These two items were sufficient evidence for evolutionists to paint entire pictures of these mythical creatures, complete with their tools and society structure.

        And this goes on today, with things like the Rodhocetus whale fossil, that was the replacement for the debunked horse evolution. These were touted as the best proof of evolution, until later finds show that they were just imagining mythical creatures based on very scant fossil evidence.

        “Science is supposed to work this way-it self corrects” is the typical reply. But, in reality, what is done is that junk science is touted as undeniable, and anyone who disagrees is considered science deniers.

        • Science did work properly in the case of “Piltdown Man”. It was scientists who showed it a fake. Its hold on paleontology delayed recognition of the validity of Raymond Dart’s discovery of the first australopithecine fossil in the 1920s.

          Recent discoveries in whale evolution weren’t invented to replace horse evolution, which has not been “debunked”. Fossil horses and whales are facts, ie scientific observations of nature.

          Whale descent from terrestrial artiodactyls is evident not only in the fossil record, but in anatomy, genetics and every other line of evidence.

        • I’m not really capable of responding very patiently to this kind of junk non-science, but I’ll try.

          First, evolution has long been a fact about only disputed by those who prefer a literal biblical reading of Genesis (the book). Everybody else, including Christian priests of many sects, think that Genesis is not a literal description of a creation. Now this not an argument on who’s right, but on who are people keeping the stagnant ‘argument’ going on.

          Second, the problem of abiogenesis, which is hard-to-explain, is not really much a problem to evolutionary thinking. There are, generally, stuff that people don’t understand. It has been so, and will be so. There is nothing new under the Sun, pun intended.

          Third, the evidence of evolution is so completely covering areas like animal, plant, fungi morphology, taxonomy, physiology, metabolism, ontogenesis, cell biology, paleontology, genetics, etc that you really can’t seriously study biology or its relatives like medicine if you fail to study evolution.

          Fourth, the Piltdown forgery scandal is a ‘bit’ outdated piece of non-science. Please enter the 21st century. The forgery proves nothing about evolution, what it shows is that science proceeds eventually despite hoaxters. That you keep talking about it means that you don’t have very good arguments.

          And fifth, as everybody familiar with the USENET knows, there has been no progress in the arguments creationist use for the last 40 years. But the knowledge on evolutionary development has increased a lot. We have now tools to sequence genetic material, and evolutionary predictions hold over and over again. There have been Eucaryotes about 1850 million years. That is an awful lot of time for single cell evolution, which has been running for billions of years. We know now it is probably much less than 14 billion, but still more than 3,000,000,000 years. Generation by generation, the fittest continued to live and outcompeted those which did not reproduce.

          • The vast majority of Christians belong to denominations which accept the fact of evolution. It’s a lot easier to read evolution into the Bible than it is astronomy, physics, chemistry, geology and other aspects of biology.

            Even in AD 400, theologian Augustine, who invented the doctrine of original sin (based upon his misunderstanding of Greek), recognized that the contradictory creation myths in Genesis 1 and 2 and elsewhere in the Bible should not be taken as literally true. He felt that insisting on the biblical flat and solid-domed Earth, as did early Church Fathers, hampered the spread of the religion among educated pagans.

            Protestant divine John Calvin also knew that Genesis wasn’t to be taken literally. Christian sects which insist on biblical inerrancy or literalism miss the whole point of their professed religion.

          • I am curious if Neo-Darwin evolution is 100% true and factual, why was there a conference at the Royal Society a couple of years ago about the problems with the current synthesis? (see https://evolutionnews.org/2016/12/why_the_royal_s/). When you refer to “creationists” are you talking about young earth creationists and not about BioLogos or Reasons to Believe or to all Christians?

            I am not familiar with USENET. Is it the repository all human knowledge?

            When you stated, “evolution has long been a fact” are you saying it is “settled science?”
            Asking for a friend…..

          • Mike,

            Evolution, like gravitation, is a fact, ie a repeated observation of nature, with a body of theory seeking to explain how it works. Evolution is much better understood than gravitation, but still contains competing theoretical opinions as to its function.

            The conference you mention, and many others, feature discussions between, for example, those who consider directional evolution, for instance driven by natural selection, more important than stochastic evolutionary processes, such as speciation by reproductive isolation and genetic drift.

            But the attendees all know that evolution is a scienctific fact, ie an observation of nature. In 1858, it was an insight by Darwin and Wallace, but now so many instances of new species and genera evolving in the wild and being created or recreated in the lab that evolution is known to be “true and factual”. Not all details of its explanatory theory however are agreed upon, nor should they be. Science in this sense is never settled. But we do now know that the Earth goes around the Sun, for instance, contrary to the Bible and Ptolemy.

          • Mike,

            Not much in the way of information in your link, but lots of misinformation.

            No one at the RS conference tried to argue against the fact of evolution. Rather, as I pointed out, evolution theory is always subject to change.

            Here is what Gerd Müller actually said:

            https://royalsocietypublishing.org/doi/full/10.1098/rsfs.2017.0015

            Just because nobody knows what gravity is, doesn’t mean it’s not a fact. The theory of universal gravitation has changed a lot since Newton published the Principia 332 years ago, but that doesn’t mean that physicists no longer regard gravitation as a valid observation, ie a scientific fact.

            Same goes for changes in evolution and its theoretical development since the Modern Synthesis–the fusion of evolution with genetics–in the first half of the last century.

            https://www.encyclopedia.com/earth-and-environment/ecology-and-environmentalism/environmental-studies/modern-synthesis

    • It might look intelligent until you work out just how many potential evolutionary pathways died out to leave the one that exists…

      The earliest life is about 4.5billion years old. But it’s easier to just use life since sex evolved at ~2billion years. If we assume 3 generations a year, then there are approximately 2^(3*2billiob) = ~10^2billion evolutionary pathways that didn’t make it … (and about a million that did … 2billion -1million is still essentially 2billion)

      So, in order to “prove” intelligent creation, you have to prove that the chances of us arriving is less that 1 in 1(with 2billion zeros) …

      So, let’s assume that each possible evolutionary path were represented as a separate “planet” … how does that compare to actual space where there are about 1,000,000,000,000,000,000,000 stars in space, or about 10 raised to the 21 … only 2billion -21 less zeros.

      So, even if every star in the Universe had its own earth like planet, then the range of evolutionary pathways that exist on each planet (assuming we all started the same when sex evolved), would still be absolutely minuscule… indeed essentially too small to be stated as a normal number …compared to the possible evolutionary pathways.

      I cannot conceive of a way to disprove the “default” hypothesis of natural evolution … so unfortunately your hypothesis of intelligent design has about as much credibility as the “we can’t explain what caused the warming so something intelligent must have done it” of the climate cult.

      • Don’t forget the extinction events that culled the herd so to speak, although this may have removed the weak lines and reinforced the lines that ultimately became us quicker than if they hadn’t occured.

        • The most massive extinction event of all time was the Oxygen Catastrophe inflicted on the anaerobic world by the rise of photosynthetic Cyanobacteria.

          But anaerobes managed to survive, and now we aerobes can enjoy abundant oxygen.

        • The “weak ” lines were only weak in particular circumstances .

          When the asteroid hit 66 million years ago most large animals, particularly land animals, were wiped out. Large size, a competitive advantage for many creatures 5 minutes before impact became a fatal disadvantage 5 minutes after impact.

          Contingency

      • Nobody is questions the “evolutionary process” – it is alive and well. But …

        The simple issue is this:
        The smallest self-replicating prokaryotic DNA is over 100,000 cells long.
        All attempts to find or produce a smaller “living cell” have failed.

        From Information theory, a 100,000 long chain of DNA that contains information decoding
        working proteins and self-replication, which did’t evolve from a much much much smaller “machine” cannot be the outcome of any random process.

        This has nothing to do with “intelligent design” just a minimal-size working DNA machine and the likelihood of it being generated out of thin-air, literally.

        • basically this.
          even with the number of galaxies and the stars and planets around them. The natural process of getting the first living reproducing cell is so astronomically small that according to the math it would require trillions rather than billions of years of random chemical events to come about…

        • By 100,000 “cells”, I assume you mean base pairs. A genome that small might imply perhaps 100 genes, ie sequences coding for proteins.

          But the first protocell would have been far simpler even than such a minimal modern prokaryote. It might have had only a single gene, such as coding for a protein enzyme that separates replicated RNA strands. RNA itself both stores information and catalyzes reactions.

          To get to the human genome’s now estimated 19,000 genes (possibly fewer) would thus require only fewer than 15 doublings, ie one per less than 267 million years over the past four billion years. Assuming that the first protocell in our galaxy arose on Earth rather than in space 10 billion years ago.

          • 1. Yes, “cells” was suppose to be base-pairs.
            2. What are you trying to imply by “the first … would have been”?

            It is up to Science to provide an explicit DNA sequence that is small enough to be self-replicating, and suggest that, statistically speaking, it has likely been formed “randomly” somewhere in the universe.

            Once again: with the smallest known self-replicating DNA being 100k base-pairs long,
            Science has completely failed on the issue.

            Even if we find a “DNA creature” with 10,000 base-pairs, there is still ZERO chance it has been created by a random process. 4^10,000 or 1 and 60,000 zeros after it(!) cannot be “likely random” even with 10^20 microseconds & 10^20 earth-like planets, etc.

            Evolution *is* a DNA-based ALGORITHM. Unless the first/smallest/small-enough self-replicating DNA is demonstrated, “evolution” is absolutely meaningless in explaining the TRUE origin of life.

            So for what we have is this:
            1. some basic molecules (RNA, amino acids etc) are produced “randomly/naturally”
            2. once a self-replicating DNA-based cell occurs, an evolutionary process produces more complex cells/animals/humans.

            This is nice. But, it misses the critical issues of life’s origin or design.
            (I’m agnostic, BTW)

          • Life was probably originally RNA-based, or even started with a different nucleic acid.

            The genomes of DNA viruses vary through four orders of magnitude in size, but the smallest yet recorded is in Circovirus SFBeef, with just 859 base pairs.

            Modern organisms naturally have much larger genomes than the first protocell. Remarkably short single (unpaired) RNA strands show biological activity. I’ve heard tell of functionality in a mere 5-mer, but here is a useful 110-mer snippet of RNA:

            https://www.ncbi.nlm.nih.gov/pubmed/17459888

            RNA, unlike DNA, can fold in ways similar to proteins. Hence its enzymatic capability.

            There is no good reason to assume that protocells could not have had very small genomes, and every reason to hypothesize that they did. A single gene with on the order of 100 base pairs is perfectly plausible. Maybe even ten bp.

          • You might as well argue that Bleriot could not have flown across the English Channel in 1909 with a 25 horsepower engine because today trans-Pacific flight is possible with jet airliners.

            Modern prokaryotes are far more advanced than their Hadean ancestor protocells.

        • In 1952 Stanley Miller and Harold Urey conducted a simple experiment in their lab (reproduced later my many high-school students) which showed that amino acids, one of the basic building blocks of proteins in living organisms, could be easily synthesized by electric discharges in a flask containing simple inorganic compounds (air and water).
          https://en.wikipedia.org/wiki/Miller–Urey_experiment

          This immediately started a huge wave of speculation that life itself could have started from compounds simply created by lightning in Earth’s primitive atmosphere.

          Fast forward to now. No one has shown how DNA, the essence of Reproduction, could have evolved. All living creatures contain DNA (not counting viral RNA. Can’t auto-reproduce).

          And DNA is not found naturally in any non-living sources. (Except one: dead creatures and plants.)

          Furthermore, higher forms of life, vertebrates etc depend on being self-aware (‘consciousness’) to create models in their minds to carry out ‘willful’ actions, such as reproduction, tool-making and obtaining nourishment.

          I am not aware of any credible theory that explains how all of this arose to create and sustain Life for billions of years.

          It is like asking how long would it take a monkey to type out Hamlet, at random? Well, I downloaded the play here (and created a file called hamlet.txt):
          http://shakespeare.mit.edu/hamlet/full.html

          Then I wrote a little Python script to compute a histogram of the characters needed to render the play in a readable form (including spaces, punctuation, carriage returns etc). [Dots are to preserve indentation]

          from collections import Counter
          with open(‘hamlet.txt’) as f:
          …c = Counter()
          …for x in f:
          ……c += Counter(x.strip())
          print c

          From this I learned that there are 65 character tokens, for a total of 180,720 characters. The most frequent character is space ” “. (Remember, this is poetry, and must be properly formatted to be appreciated). The top 15 characters are, FYI:
          ‘ ‘: 26629
          ‘e’: 14430
          ‘t’: 10944
          ‘o’: 10395
          ‘a’: 8720
          ‘s’: 7900
          ‘n’: 7758
          ‘h’: 7715
          ‘i’: 7410
          ‘r’: 7229
          ‘l’: 5340
          ‘d’: 4869
          ‘u’: 4085
          ‘m’: 3631
          ‘\n’: 3271

          So, the probability of typing the first character ‘T[he Tragedy of Hamlet…”] is 1/65. So the probability of typing the whole document perfectly on the first try is 1/10^180720.

          Yes, that is 10 with 180720 zeros. If the monkey typed one letter per second it would take about 10^180720 seconds to have an even chance of success. Recall that the current age of the Universe (rounded up) is only 10^18 seconds.

          Assume for the sake of argument, that the monkey is incapable of realizing that he has typed anything meaningful. So we cache is output in a Universe-sized server. So, after 10^180720 seconds we stop the monkey and search the cache to see if he has succeeded.

          The complexity of the search in itself is on the order of O(180720*10^180720), which means checking the answer is even more ‘intractable’ than typing itself.

          I think we should agree that randomly creating life (i.e. DNA, consciousness and human will) surely will be even more ‘complex’ than typing Hamlet randomly.

          • Short chains of RNA (oligomers) form spontaneously under various conditions, to include in ice. As noted, nucleobases, ribose sugars and phosphate groups all occur naturally in meteorites. Nature makes them readily. Same goes for hundreds of amino acids, of which life on Earth uses 21 (only 20 are coded by DNA and RNA).

            Once you have RNA, it’s a simple step to DNA, the sugar of which has just one less oxygen atom than does ribose. This lack allows it to form its characteristic double helix, making it a more stable library of genetic information than RNA.

            Novel nucleic acids can be synthesized in the lab. Some researchers think that another naturally occurring nucleic acid might predate RNA.

          • @Tillman
            “Once you have RNA, it’s a simple step to DNA…”
            If it is so simple, why do we not see isolated DNA forming in nature? Instead, it is only found in living (or dead) organisms.

            Spontaneous synthesis of amino acids and oligomers is a no-brainer. The pieces combine according to simple laws of chemistry. But DNA is more complex, a brain-spawner, holding designs that can spawn the brains needed to build rocket ships to the Moon!

            I don’t think DNA evolved ‘spontaneously’, by random “trial and error”. That would be an extremely ‘noisy’ process. Where is the ‘debris’ from the failed trials? It should be everywhere.

            Evolution theory says species evolve from random mutations to genes. But random genetic changes are tantamount to “defective” genes. So, ironically, it is the genetic ‘defects’ which survive and are called the “fittest”. While the ‘normal’ genes are called ‘extinct’.

            I think there is a yet-to-be-discovered ‘life principle’, which will better explain the physics and intrinsic ‘design’ of life. I think all living organisms, even plants, are ‘conscious’, more or less, in the sense that they ‘notice’ their surroundings and intrinsically formulate actions (from trivial to extraterrestrial) to sustain their lives with respect to their surroundings.

            Yes, this sounds like I am getting into religion, but I’m not. I think living self-awareness can all be explained by science, through observation and experiment. Life has a more extensive design than we realize. We are self-aware because it is part of nature. I believe we humans will soon be collaborators (in an evolutionary sense) in discovering the actual mechanisms of consciousness and extending it to group consciousness.

          • DNA doesn’t need to exist outside organisms for it to have arisen by RNA’s losing an oxygen atom and substituting one of four nucleobases for another.

            RNA does exist outside organisms, so it’s even possible for a short chain of RNA to mutate into DNA, but oligomers don’t last as long as polymers.

            There is no need to posit a life principle beyond ordinary chemistry. Biochemistry is still chemistry.

            Neither RNA nor DNA developed via random trial and error. RNA self-assembles naturally from its constituents, ie nucleotides composed of a ribose sugar, a phosphate group and a nucleobase. All these components occur naturally on Earth and in space. And, as noted, once you have RNA, it’s easy to make DNA.

            What remains for origin of life researchers is to make a polymer, ie long chain, of RNA without a biological enzyme. Oligomers of RNA aren’t stable, although even a little 5-mer has biological activity.

            And then they have to separate the replicated strands, again abiotically or with an abiotically produced enzyme, either of RNA or a peptide, ie amino acid oligomer.

            It has recently been discovered that it is easier to form peptides directly from amino acid precursors than by bonding together complete amino acids.

          • There is no such thing as normal genes. All genes, ie sequences coding for proteins, are subject to mutations of all kinds. Mutations can be positive, negative or neutral in their selective effects, and formerly deleterious mutations can be beneficial in changed environments.

            Mutations in non-coding sequences can also affect fitness, ie reproductive success.

          • Vertebrate consciousness doesn’t exist apart from our brains. Plants, fungi and animals without brains can respond to stimuli and exhibit behavior without enjoying what we might consider consciousness. So can unicellular eukaryotes (protists) and prokaryotes.

          • There isn’t a more embarrassing way to demonstrate the total lack of understanding of life than to engage in calculations of combinatorial complexity based on the number of bases in the genome. I don’t mean to insult you — it’s just an observation (and a tired one). No superior demonstration of ignorance has been invented yet. Simply saying you don’t know anything about it is not nearly as powerful or spectacular as professing it to be something irrelevant.

            Your calculation is off by a factor of about ∞ in one direction, and about as badly off in the opposite direction. You can’t even know how wrong you are because the task of gauging your error is intractable. You are overestimating because life does not have the degrees of freedom you imagine — for sure, the ones you are implying are not there. Only a minuscule fraction of your imaginary code space is physically possible, and only a tiny fraction of that which is possible makes any difference whatsoever. That is true of the smallest genomes such as a flu virus or a λ-phage, which you can write out on a single page and more-or-less predict the effects of their variations; even more so in large genomes. You don’t have the freedom to change things at random. You don’t have the freedom to decide what parts of your code stay put and what parts are simply spliced out, never to be seen again.

            On the other hand, you are underestimating it because iterating an alphabet doesn’t even begin to emulate the repertoire of transformations available in life. Real genomes get spliced, duplicated, transposed, and inverted. Segmented genomes get re-assorted, translocated, conjugated, fused, and broken up — all of which happens recursively. On top of that, genomes allow double entendre, or more appropriately, double lecture (or triple, or sextuple, as the case may be — check out the Hep B virus). But that’s not all. Life is not just about things in the genome; it’s about making things from genomic templates. Therein lies complexity you can’t begin to imagine without at least a few hints form biology. That additional complexity is also constrained in hilariously arcane ways.

            What did you mean to achieve by bringing up the typing monkey metaphor? How is it relevant to anything, even to a typing monkey, which would be a biological phenomenon entirely unfit for that metaphor?

          • @Selkov
            “What did you mean to achieve by bringing up the typing monkey metaphor? ”

            “Scottish Sceptic” brought up the notion of combinatorial probabilty first. I was merely trying to demonstrate how unlikely ‘spontaneous’ creation is.

            So I guess it is somewhat like thermodynamics. At the macro level events like breaking an egg seem non-reversible, i.e. the egg might ‘spontaneously’ roll off a shelf and get smashed, but there is no way that smashed egg will ‘spontaneously’ put itself back together (even with the help of all the king’s men).

            But at the atomic level a completely different situation emerges. All molecules are separated by empty space from each other and seem to be free, more or less, to move in all directions. In other words there are no intrinsically ‘irreversible’ kinetic vector motions at this level. All you need is sufficient energy to get pushed in any ‘desired’ direction.

            Boltzmann provided the key equation (S=k*log(W)) here, which explains this paradox, and provides a ‘bridge’ between the macro and micro worlds. Yes, all the molecules surrounding a lit candle could theoretically line up in the same direction and spontaneously blow out the candle. But statistical mechanics reveals the probability is so infinitesimally small that it won’t happen in the lifetime of this Universe. The Second Law rules our Universe: disorder tends to always increase.

            So why does Life, at first glance, seem to increase order at the expense of disorder? I realize that, if you analyze and add up the entropy of our ‘exhaust’ fumes and detritus, this is an illusion. But the origin of Life is still mysterious. It really does seem (at our ‘macro’ level) that Life somehow created itself out of ‘ordinary’, inorganic stuff.

            Someone else here disputed the notion of an ‘Intelligent Designer’ because it did not explain how the Designer was created. So I have the same complaint, DNA holds the key to the design of life forms and (seemingly) their “purpose” in the Universe. But there is no convincing explanation of how that came about. ‘It just happened, by accident’ is not very believable. We know Hamlet was not written by an immortal random monkey. We know Shakespeare wrote it in his relatively short lifetime. But how did Shakespeare get here in the first place?

            For example, it seems to me (at my macro level) that humans were somehow (waving my hands here a bit) ‘destined’ to leave this planet and ‘infest’ other worlds. Just like other social animals and bugs, but on a much, much larger scale. Why did Evolution give us brains big enough to escape Earth’s gravity and travel to other planets? To escape from predators? Would not being able to find a clever way to hide in a cave or tree provide enough ‘fitness’ to allow us to continue our primitive genetic pathways?

            Your explanations of how this happened just sound like ‘it works because it works’ to me.
            Please explain: What is ‘consciousness’ ? It is not some ‘imaginary’ process in our brains. It is real (i.e. is sensitive to external stimuli and injuries). it is responsible for how we move, learn and plan our actions. Without it we would have to be ‘scripted’ by a program to determine our anticipated responses to external stimuli. Robots do that now. But robots can’t imagine how the Universe works or how to explore it with no a priori knowledge or instructions.

            Sorry if these sound like ‘stupid questions’ to you. I would really like to hear your thoughts on this.

          • “It works because it works” is almost standard biological explanation. The correct version of it is, “It works because there is nothing to prevent it from working”.

            Life does not seem to increase order even at first glance; to me, it doesn’t. I see it as a quasi-stationary flow. Note that as you grow old, you develop conditions called “disorders” and “complications”. That is not a linguistic co-incidence. You acquire new components and go through new states because it is really hard not to. It is impossible.

            I did not mean to give an explanation for the origin of life, although I do think that people whose thoughts revolve around spontaneous polymerization and vesicle formation are on to something. I just want to correct misconceptions about what it presently is. Not knowing about the origin is not a good excuse for not knowing what’s relevant and what isn’t. Random combinations are not relevant. Gas-phase thermodynamics are not relevant. We’re made of solid-state ratchets driven by reciprocating engines. The engines are driven by chemical gradients, of which there are lots on this planet. Pretty much every place that is not at uniform equilibrium is exploited. Each little engine shuttles between a source and a sink (Fe II – Fe III, or what have you), ratcheting something up another gradient. It is the invisible coupling between the engines and their loads under opposing gradients that creates the illusion of magic. But there is no magic. Just lots of engines, ratchets, and couplings, and all of that irreversibly moves forward, down the invisible gradient of local disequilibrium. The best general explanation for why that works is because there is nothing to stop it.

            For emphasis, imagine a weeding campaign in a garden or the effort required to get rid of mold in a shower. That is an uphill battle. For weeds and mold, it is downhill.

            Back to the question of origins, even though it was not my point and I have little to contribute to that discussion, I don’t think anyone should be surprised seeing orphaned structures and mechanism of unknown genesis. Two pervasive aspects of life unappreciated by non-biologists are redundancy and competition. Everywhere you look, you will see analogous mechanisms of different nature doing the same thing. Many such redundant mechanisms compete with each other. You will also see dynamic equilibria between opposing actions. Typically, letting one of the opponents win is disastrous. You are kept in one piece by a crowd of machines that break things and another crowd that repairs the damage. Even a slight imparity between the two crowds can be lethal. You develop by building scaffolds that are used to erect temporary structures that are then used to build something else and then dismantled. Building temporary things to be destroyed is a very common pattern in life, to the extent that pretty much everything in your body is temporary, even on a short time scale. That, with redundancy and competition, supports the idea that more than one type of life could co-exist in the same place and what were’s seeing now is the remnants of the winner. The losers in that hypothetical competition could have provided the scaffold for building what we are now.

            A failure to reproduce should not be taken too seriously either. First, no one knows what to reproduce. Then, many biological experiments, even those that are well-described and whose outcomes are well-known are notoriously hard to reproduce.

            One thing you can be certain about is that whatever happened at the dawn of life was a downhill motion and there was nothing to oppose it. That’s a good summary of modern biology: everything you learn indicates life is headed downhill and is unstoppable.

          • @Selkov
            “It works because there is nothing to prevent it from working”.

            So, summarizing what you said, that really is your answer to how life (“DNA”) originated. You really do not know. And furthermore, you claim that knowing how it evolved is not as important as appreciating the amazing components and functions of this finely crafted, unstoppable machine (ratchets, gradients etc).

            So here’s another question: Which came first, the chicken or the egg?

            The answer is: neither.

            Obviously the chicken’s DNA came first, which is the design of the chicken, egg, and the mechanism which allows the chicken to produce the egg and also allows the egg to produce the chicken. It’s all inside the DNA. This particular mechanism has been running successfully for millions of years now.

            So I guess you were right, it was unstoppable, in the sense that there was nothing to prevent it from working.

            But I think it illustrates that knowing the origin of DNA is much more important than knowing how the chicken or the egg works.

          • I can’t see how ideas about the origin of life can be more important than the knowledge of how it works. I am in the business of recommending chemotherapy to cancer patients. They rely on my knowledge of how it works, not how and where it originated.

            I am curious about the origin, and that’s that. I don’t expect it to ever be explained. But I can provide easy corrections to obviously faulty explanations rooted in ignorance. Counting bits is obviously wrong. You have no idea what you’re counting. Every time someone says the word “random” in this type of conversation, I know he has no clue. Random means “equal chances”. You will struggle hard to find a pair of alternatives in life that are observed at equal frequencies. The closest you’ll ever get to parity will be in sex balancing, but that is a tightly controlled feedback mechanism; nothing in it is left to chance, and it is not always at parity when balanced.

            My recommendation is, if something is important to you, invest in the acquisition of relevant knowledge. It will be hard and it may take more than a lifetime, but it is more fun than fiddling with irrelevant numbers based on speculation.

    • And that runs into the paradox. If complex life crew requires an intelligent designer, where did the intelligent designer come from?

      • Mass/energy space/time all came into existence at a finite point in the past. Despite what Stephen Hawking said, if you have nothing, you get nothing. What or whomever created the universe is outside of it, an uncaused first cause. It was always there.

        “A commonsense interpretation of the facts suggests that a super intellect has monkeyed with physics, as well as chemistry and biology, and that there are no blind forces worth speaking about in nature. The numbers one calculates from the facts seem to me so overwhelming as to put this conclusion almost beyond question.”
        – Fred Hoyle

          • Spacetime did not exist prior to the big bang. What you are suggesting is that if you have space time and matter you get space time and matter. Big whoop. However, prior to the big bang none of those three existed.

          • Chad,

            Spacetime did exist before the Big Bang. As presently conceived, it, all energy and mass was concentrated in a hot, dense Singularity. The Big Bang was when the Singularity started expanding.

            There isn’t much agreement on what came before the Singularity, but possibly the Big Crunch of a previous Universe.

            Physics shades into metaphysics at this point now, but as time goes on we might have sufficient evidence to peer or at least peek into the deep past and project the deep future.

        • OK, you’ve convinced me. The Evolutionary Hypothesis has too many holes to explain lions and tigers and bears, or humans and tardigrades and Archaea and DNA. Much less tell us if there are other places in the Universe with life or if we are alone on this little planet in an obscure corner of an unimpressive galaxy.

          So, how does this ID Hypothesis work? I’m willing to stipulate that The ID (I’ll use Id for Id’s pronoun so as to avoid giving people funny ideas about gendered entities with beards and such) is omnipotent, omniscient, eternal and invisible to humans, except on special occasions. Let’s put aside the whole issue of Time, too, although I’m willing to stipulate that The ID is unconstrained by time, if that makes it easier to understand the theory.

          So, does The ID puppet master each and every subatomic (and maybe sub-sub atomic—it’s turtles all the way down) particle every sub-nanosecond of what we perceive as time? Does Id move every molecule in every living thing all the time? Or does Id just set initial conditions of physics (like the strong and weak forces, gravity, electromagnetism and time), then push the big red Big Bang button, retreat to the Half-Astral Plain and enjoy the show?

          Maybe The ID pokes in from time to time and changes direction or throws in a miracle to confuse observers. How often does Id interfere? Like only once, creating DNA and tossing it onto only one planet to see how it works out? And in that case, how would we distinguish between evolution as we see it and Evolution as the Work of The ID? What experiments could we run to test the hypothesis?

          And what does that mean for Free Will? If The ID runs the show, as opposed to setting off the fireworks and watching over us, does Id run a fully double-predestinarian Universe, where every subatomic particle has had its place preordained from the Big Bang to the Eschaton? Does Id get bored with such an arrangement? How would we go about discovering the Real Story if that’s the case?

          • Yikes, I have no idea how the entity you have labeled ID sustains the universe. Like you do not know how life came from non-life. I am sure that you will point to what scientists (presumable intelligence) have done in their labs but if you are honest that is experiments run under ideal conditions.

            If all you have is a brain derived from lower life forms, can you “think” at all, as your “thoughts” would be the result of random molecular reactions.? You would be a “moist robot.” You might what to check this out:https://evolutionnews.org/2019/07/egnor-how-to-test-materialist-theories-of-mind/

            All I am saying is pure scientific naturalism can not explain all of nature. My mind is open, is yours?
            Hope you have a great day.

  3. I am sorta surprised the Japanese researchers didn’t name the Archaea after something from Shinto mythology, rather than Greek.
    More things that have emerged in the subject since I left school in 1978.

    • The phyla in the Asgard superphylum of archaeans are all named for Norse gods.

      The domain of Archaea wasn’t even recognized as distinct from Bacteria until 1977, originally based upon the structure of their ribosome subparts. Ribosomes are complexes of RNA and protein in which amino acids are stitched together into protein under RNA direction.

      • The Asgard was presumably warriors whom the main gods got to watch their backs in battle 😉

        Great article. A complex subject condensed down enough to maintain the reader’s attention. Not something I would normally have been motivated to look into. Very interesting.

        • Glad you liked it!

          To keep my material shorter, I let the link speak for itself rather than also describing the researchers’ discoveries regarding the archaean and bacterium they managed to grow.

  4. The origin of eukaryotes from bacteria and archea I thought has been known for years.
    The news is that these guys have finally cultured it. That is big, but it doesn’t change anything as far as our understanding of evolution.

    • The host had been hypothesized to be an archaean, but only in 2017 was Asgard DNA shown to be the closest group to us.

      Besides culturing an Asgard member, the researchers also discovered its close symbiotic relationship with a bacterium and how a unicell about the same size could engulf another similarly small microbe. Tentacles!

      The behavior of the cultured archaean also shed light on how the cell nucleus evolved.

  5. Point of clarification. The idea of symbiosis producing eukaryotes was not the original idea of Lynn Margulis. The idea was originally put forth in lectures and discussions as a speculative idea by the Russian Constantin Nerezhkowsky in 1905. Scientists of his day regarded as crazy. She is the one who popularized the idea among English speaking scientists and the general public in her highly accessible and excellent books. As far as I know she never claimed it her idea and she was very explicit about giving credit to the originator including in his obituary especially later in life, correcting those who gave her the credit. (see “The Tangled Tree”, David Quammen.)

    • I should have said the idea was popularized by the then Lynn Sagan. She was able to adduce more data than had previous endosymbiosis speculators. Many of her older colleagues savaged the young academic, but further discoveries supported the hypothesis.

      • Indeed, her first paper on the subject was submitted to about 15 journals before being accepted for publication and it took about another 10 years for the theory to be accepted. I believe that she once received a response to a proposal that her research “was crap”. Interestingly the symbiotic event that gave rise to chloroplasts has been shown to have occurred at least three times yielding different versions.

        • Stories like this make me wince whenever I hear we’re not supposed to question climate change because 97% of scientists agree it is real.

    • As I noted in the comments there, some water bears have evolved a gene that repairs X-ray damage to DNA.

      Some have rudimentary arthropod-style eyes.

        • True. Sexual reproduction might have evolved in order to do so.

          But the tardigrade X-ray repair gene hasn’t yet been found in other organisms.

  6. Yes complicated. Nucleated cells have restricted growth patterns un like the the the others. Complex live needs only so may liver cells, pancreas cells eyeballs and teeth etc. Made from the dna recipes for thousands of proteins. The complexities of which, we only recently with DNA decoding could grasp, Collagen has 1055 amino acid building blocks. Twenty amino acids needed in vast quantity and all left handed ones. Only bonded left left handed ones will fold. Twenty t RNA preteens needed for the assembly, ribosomes,etc. Think of thechallenge for an automated system to send a signal of what protein is needed to a protein device that has to make a copy of the DNA recipe that is needed. It has to unwind the DNA to make the copy. That copy is then edited before it is taken out of the nucleus to the ribosome in the cyctoplasm. There the amino acids are strung together with out error. The string then is taken to a folding device. If it does not fold it is disassembled and the parts are reused. Once it is folded into a protein it is encapsulated and taken to where it is needed.
    Now encase hormones like insulin, The cell produces proteins it does not need but the body does. Note also that the stem cells produce things related to where they are. How many types of teeth do you have.It is by design you have only two eyeball, but how, how does it keep it so straight. When liver cells are found though out the body that is cancer. It amazes be how seldom cells loose track of just how may om themselves are need!

    I amm so amazed.

    Google protein syntheses. If you look long enough there is a electron microscope showing the the process with the Prophesier in that back ground saying this is live.

    This is such an exciting time to live, thanks for the article.

    • Thank you!

      It is indeed exciting. Every time people have thought that there was nothing more to learn, things turned out just to be getting started, with the most exciting bits yet to come.

      But it takes real science to provide the excitement.

    • “This is such an exciting time to live, thanks for the article.”

      I agree. Life is amazing. So many questions!

  7. Life?… Need to figure out prebiotic chemistry before you can even ask questions about life, evolution and fast cars. Modern science can’t even create or emulate the conditions for the creation of simple proteins, carbohydrates, nucleic acids or lipids from prebiotic chemistry let alone figuring out what self organizing set of laws arranges these biomolecules to form cells….. No random process can do this.

    There is simply not enough time in the universe to do it. 14 billion years is not even close, let alone 4 billion years for the probabilities of random processes to create life in a puddle… and time is your enemy with synthetic chemistry. To get certain chemical outcomes they require very strict time, temperature and ph control and then a physical process to stop the reaction….. and then cold storage before recombining the next steps, which are even more time and environmentally constrained because of the fragility of the chemical arrangements, etc.

    Forget the mystery of life…. Just try figuring out prebiotic chemistry.

    ….. Yet here we all be. Quite amazing really.

    • Prebiotic chemistry has been figured out as far as the monomers of life and well into the oligomers, if not yet long polymers.

      Modern science most certain has created and emulated the conditions for the autosynthesis without biological enzymes of simple proteins (peptides), carbohydrates, nucleic acids and lipids from prebiotic chemistry. It is working on how to polymerize amino acids to build proteins and nucleotide chains to make RNA and DNA. Recent work by Nobel Laureate Jack Szostak and his Harvard team has showed how lipid vesicles could evolve into cell membranes.

      “Random processes” most certainly do produce naturally essential biomolecules such as amino acids, nucleobases, sugars, phosphate groups and lipids. We have long known this to be the case, since meteorites have brought all these precursors of life to Earth. In fact, they carry many times as many amino acids as are used by life here. Organisms use only 21 of the hundreds of amino acids delivered from space.

      There has been plenty of time in the universe for the monomer constituents of biological polymers to form the long chains of nucleic acids and proteins found in living things. It’s possible that life first arose in space ten billion years ago, as soon as stellar nucleosynthesis made oxygen, nitrogen, carbon and other vital elements available, to go with the primordial hydrogen. But I’m still of the old school that terrestrial life arose right here on our own planet, from the precursor compounds delivered from space and produced here. The trillions of reactions per second on early Earth for 100 or 200 million years offer plenty of opportunity for polymerization to occur via a number of possible avenues in various environments.

      So, there is no mystery as to prebiotic chemistry. And figuring out how to get from the monomers and oligomers (short chains) of biomolecules to polymers (long chains) is simply a chemical engineering problem, liable to be solved during the lifetimes of most readers.

      RNA is remarkable in being both a storehouse of genetic information and an enzyme. It also spontaneously self-assembles into oligomers with enzymatic activity in a variety of conditions, such as the pockets of liquid water in ice. As noted, we’ve long known that the five nucleobases of RNA and DNA must self-assemble, but we now know how they do that. It was easy for the most important nucleobase adenine, but more challening for the other four. In 1961, Joan Oro showed that adenine could be made simply by heating the ubiquitous compound HCN in aqueous solution. In 2015 the Sutherland lab discovered the abiotic synthesis pathway for last two hardest to create nucleobases. Plus, the same chemical reactions in a cyanosulfidic protometabolism make RNA, protein and lipid precursors:

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568310/

      As noted, however, we already knew that these and other constituents of the polymers of life occur naturally in space. Recent research just shows how they’re made prebiotically.

      • No, not quite right. The closest synthetic chemists have come to actually creating the building blocks of biomolecules from constituent chemicals was the creation of some ribose by passing hydrogen cyanide gas, carbon dioxide and formaldehyde through an electric current… and even there it was in a concentration that required a mass spectrometer to measure it. Certainly not enough for being useful for chemistry. This was done in the early sixties…. There has been little progression in the actual creation of these biomolecules from constituent chemicals in the laboratory at all since…. There has been quite large advances in other nanoparticals using different solvents, but nothing using H2O as a solvent.

        • Yours is hardly an adequate argument against the role of chance in this process. MotherNature had billions of yrs to experiment. Belief in Creationism is facilitated by a disbelief in the Power of Large Numbers. MotherNature cares nothing about her own failures; only her successes count.

        • Nope.

          Origin of life researchers have discovered how to create abiotically all the monomers of life, to include amino acids, nucleobases, ribose sugars, phosphate groups and lipids.

          And, as noted, scientists have long known that these monomers spontaneously form, since they arrive here on meteorites.

          But wait! There’s more! Short chains (oligomers) of amino acids and nucleotides (a nucleobase attached to a ribose sugar and a phosphate group, the building block of RNA and DNA) also self-assemble. So too do lipid vesicles.

          I don’t know where you got the idea that these constituent components of proteins and nucleic acids don’t form naturally, but they do.

        • An amazing lecture from a leader in his field – a must view for anyone who thinks that the problem of biogenesis is nearly solved and that given sufficient time anything can happen.

          • LOL, he just wants someone to show him the chemistry, in that lecture he does not mention his beliefs in regard to the chemistry. Watch it, you might learn something. But I am guessing you will not, as his conclusions would cause concern within your religion.

          • Mike,

            I did watch it.

            Many biochemists and molecular biologists could show him what he clearly doesn’t want to see, because of his religious beliefs.

          • Since Dr. Tour is a Christian so therefore his science is suspect. Please, his science disagrees with your worldview (religion) and is therefore wrong according to you. Dr. Tour can say the sky is blue and you would say because of his beliefs he must be wrong. Sounds a bit closed minded to me.

          • Mike,

            Dr. Tour is not a Christian. He’s Jewish.

            His argument isn’t faulty because of his religious beliefs. It’s just that his faith has cancelled out his ability to practice the scientific method with regard to the origin of life.

          • He was Jewish growing up but became a Christian in college. I think he talks about his faith at some point in this video. The first part of the video is him talking about some of the research coming from his lab’s work with graphene. There is no doubt that he is a very good synthetic organic chemist.

    • Forget the mystery of life…. Just try figuring out prebiotic chemistry.

      ….. Yet here we all be. Quite amazing really.

      Indeed. Inability of replication ‘spontaneous’ creation of life, where we have all substrates and basic components of life plus highly controlled environment is something astonishing. What I’ve heard some scientists actually giving up on trying to figure out how life actually originated – that may be a perpetual mystery. Even if in the future we are able to observe ‘spontaneous’ emergence of life out of non-living matter that cannot prove that in the past the same process occurred. In terms of origin of life what we have here is basically secular way of saying “and then a miracle happened…”

      And here we are.

      • The mystery seemed impenetrable in the last century, even to one proponent of the RNA World hypothesis. Now, not so much. There have been huge advances in this century, to include the discovery that RNA self-assembles under various naturally occurring conditions, such as in pockets of liquid water in ice. While cold reactions are slower, thus concentrating the constituent chemical compounds facilitates their bonding together.

        • The mystery seemed impenetrable in the last century

          Quite contrary, I would say, in the last century, with simplistic view of the cell machinery solving the puzzle seemed to be within the reach. As we’re gradually unravelling complexity of inter- and extracellular signalling, fine tuning of cellular machinery purely naturalistic origin of first cell seems to be ‘fool errand’. More we know about complexity of life, less likely naturalistic scenarios look. What’s the minimal required complexity for a single cell what we know from empirical evidence? Few hundreds genes or so plus supporting machinery? We cannot simplify further without killing a cell. Surely, you can imagine such steps but if you go to a laboratory and try to prove it you shall fail miserably. Or photosynthesis – supposedly very early occurrence in the history of live. By exploiting quantum effects and storing energy harvested from light in the chemical form this process exhibits sophistication and efficiency greatly exceeding anything produced thus far in the field of photochemical engineering.

          Researches have started to realise what actually needs explaining. It’s not just chemistry, it’s far more than that. As physicist Paul Davies pointed out secret of life resides in the informational properties of the living organisms. Origin of information that drives cellular processes – that needs explaining. Miss this point and you try to explain origin of a meaningful text only by invocation to chemical composition of ink and paper. Ink and paper do not have powers to organise themselves into a meaningful text.

          • Nope. Improved understanding of molecular biology has helped science unravel the origin of life.

            For instance, details of the structure of ribosomes hint at the importance of tRNA in abiotic chemical evolution. Ribosomal structure also suggests that nucleic acids and peptides (protein precursors) may have co-evolved.

            I could site many other instances of improved understanding in this century. Nor in the last century did scientists imagine that cells were simple.

            While the smallest modern bacterial genome might have only 182 genes (if that still be the record), a protocell could have had only one, yet still be able to replicate itself.

            IIRC, some viruses have just four or possibly fewer genes. A protocell surrounded by yummy organic molecules might have gotten by with few genes, living akin to a modern parasitic virus.

            Indeed without the need for a proteinaceous case and infection apparatus, a protocell could get by with even fewer genes than a modern virus.

        • In 1981, Nobel Laureate Francis Crick stated, “An honest man, armed with all the knowledge available to us now, could only state that in some sense, the origin of life appears at the moment to be almost a miracle, so many are the conditions which would have had to have been satisfied to get it going.” Being a devout materialist, he put his faith in Darwin’s notion that given the right location and sufficient time anything could happen, but his candid statement is worthy of reflection.

          Nearly 40 years later, nothing much has changed. A review article written in 2018 by over 30 OOL scientists (Steel, E. J., et al. 2018. Cause of Cambrian Explosion – Terrestrial of Cosmic? Progress in Biophysics and Molecular Biology. 136) continues to invoke miracles, stating, “The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle.” Again, being materialists, they cannot accept the miraculous. So, being confronted with the compelling fact that life could not have originated on earth, they propose a scenario that life emerged elsewhere in space.

  8. I’m not a biologist (studied paleontology as part of geological science) but this was an entrancing read for me for some reason! I think its because real science is quite beautiful, forensic and telling about the passionate minds of real scientists.

    This research is classical the contributions by relatively few individuals over time. It is not of this unhappy post normal world of gangster science that has abandoned and even torqued the scientific method to create ‘science’ for ulterior and selfish purposes.

    It was refreshing for another reason, too. Biology was the first science to be corrupted and weaponized for political purposes (à la Ehrlich and his eugenic “Population Bomb” in America and Lysenko in USSR 30yrs before that). Sociology is terminally corrupted by the politics of the left and so I thought was biology until I read this wonderful story.

    • “Gangster science” is apt. Waged by GIGO computer gamers bent on world domination from the academic equivalent of their moms’ basements.

    • Paul Ehrlich was a prof of mine in 1971. Most of his undergrad students recognized that he was a Marxist prophet of doom. The only one of his apocalyptic predictions which came to pass was that a plague would come out of the tropics to threaten the developed world, aided by air travel.

      He’s good on butterfly populations. Humans, not so much.

      • Ehrlich was not all that great on butterfly populations either as I understand it, but thanks for the interesting link and discussion. One thing that always bothers me about origin of life and eukaryotic life hypotheses is why they seem to be limited to some single time in the distant past. One commentator claims that chloroplasts seem to have originated at least three times. The complex symbioses we call lichens seem to have originated multiple times. If RNA leading to DNA is so simple, why hasn’t it continued to occur over time? Ditto for eukaryotic life styles. Lots of obligate endocellular alphaproteobacteria are out there and although many are disease causing organisms some seem to confer definite advantages to their hosts. Was there some golden age of endosymbiosis?

        • The similarities among both archaea-descended nuclear and mitochondrial DNA across all eukaryotic phyla support a single origin. That three different lines might have acquired distinct cyanobacterial symbionts wouldn’t be surprising, if true.

          It’s not so much a Golden Age of endosymbiosis but that once a protocell-eukaryote existed, that more complex cellular space was taken. The fused lineage underwent evolution to develop our meiosis-mitosis-mixis system of reproduction, then to acquire further organelles, such as chloroplasts, and become multicellular three times, leading to plants and the more closely related heterotrophs animals and fungi.

    • Biology is of course subject to the same pressures as sociology, but being a hard science to some extent immunizes it against PC as compared to the social “sciences”, each of which assumes an unspportable model of human behavior in order to support its particular delusions.

      • Mousa: [as Rambo prepares to play Afghan game ‘buzkashi’] God must love crazy people.
        Rambo: [getting on horse] Why?
        Mousa: He make so many of them! [laughs]

      • Remember what J B S Haldane said, when asked what he could say about the Creator, based on his knowledge of nature:

        “The only thing I’m sure of is that he has an inordinate fondness for beetles”

    • Intelligent design? – took 4.5billion years to design something that could move bit of wood around a 8×8 checker board with odd names like “rook”.

      Human design – took ~4.5 decades to design a machine that could beat the most intelligent thing designed by “intelligent design”.

      The smartest thing in any room these days is usually the phone!

      • Yes but no phone or machine would be smart enough to dip a Mars bar in deep chip fat.

        Great article and another example why reading WUWT is so worthwhile.

    • The great American philosopher-statistician George Carlin explained it thus:

      “Think of how stupid the average person is; and then realize half of them are stupider than that!”

      • Mathematically incorrect. Half of the people are stupider than the median person, not the average person. Carlin was no statistician, but he was funny.

        • Ken – picky picky – we all know that stuff – median vs mean vs mode and all that.
          https://www.thoughtco.com/the-mean-median-and-mode-2312604

          But if I recall correctly (and it’s been a very long time), in a Normal Distribution, are not the Median and the Mean essentially the same?

          And is it not also well-known that human stupidity is Normally Distributed? 🙂

          I feel it necessary to defend the mathematical expertise of the late great George Carlin, since sadly, he is no longer here to defend himself.

          I suggest, for example, that Carlin was vastly more statistically competent than those paragons of green virtue, Mann, Bradley and Hughes of MBH98 “hokey stick” fame and all their admiring minions at the IPCC – who have a perfectly negative (i.e. 100% WRONG!!!) predictive track record.

          And one’s predictive track record is the best objective measure of one’s scientific competence.

          And yes, we can agree that Carlin was funny – very funny.

          • The “normal distribution” is a mathematical construct used to develop statistical analysis methods. There is nothing in it that makes any collection of data about the real world magically fit it. Some naturally occurring real-word data collections fit it in useful ways, but it is a mistake to assume normal distribution when doing statistical analysis of a real-world problem.

            Being an amateur cynic (Carlin was a full-time professional cynic), I would wager that the curve on human intelligence is heavily skewed toward the mentally limited side, which means that more than half of the population are well below average. By the way, “Heavily skewed” means it does not fit a normal distribution.

  9. Endosymbiosis: “symbiosis in which one of the symbiotic organisms lives inside the other.”

    Do scientists know enough about this process to reproduce it? Can they turn bacteria or archea into eukaryotes in the lab using endosymbiosis? Or is a process like this, that occurred by random chance, too complicated for scientists to replicate by design?

    Engulfment is one thing, but once engulfment has taken place, what would cause the organism to not only make use of this new enhancement but to duplicate it for its offspring when it reproduced? It would seem to require an awfully complicated series of events for this to occur.
    eukaryotes from bacteria and archea

    • Until just this year, science had no living examples of the archaean superphylum related to the ancestor of eukaryotes with which to conduct research. But our very first observation of living members of the Asgard superphylum convincingly showed how the endosymbiosis probably occurred.

      The engulfment conferred tremendous selective advantage on the symbiotic relationship between archaean host and its similarly small engulfed protebacterial symbiont.

      The relationship is transmitted to the next generation through the process of mixis, which is one aspect of the complex sexual reproductive system of us eukaryotes. In multicellular eukaryotes, ie animals, fungi and plants, mixis is called fertilization, since the two haploid cells which merge to form the diploid zygote are of different sizes, ie eggs and sperm. But among eukaryote unicells, the merging cells can be of similar size.

      As you may know, you inherit your mitochondria from your mom, because they’re in the egg, so much bigger than the specialized sperm.

      BTW, the closest unicell relatives of animals are the choanoflagellates, a group of free-living, often colonial flagellate eukaryotes. Choanoflagellates are collared flagellates having a funnel shaped collar of interconnected microvilli at the base of a flagellum. They’re practically identical to choanocytes, the feeding cells of sponges. They also strongly resemble sperm.

      Common origins of RNA, protein and lipid precursors in a cyanosulfidic protometabolism

      https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568310/

      • “But our very first observation of living members of the Asgard superphylum convincingly showed how the endosymbiosis probably occurred.”

        I suppose that now scientists are convinced how endosymbrosis probably occurred, they will try to reproduce the process where eukaryotes are produced from bacteria and archea. That would prove once and for all that they have a workable theory. Let me know if they are successful.

        • The particular species of Asgard archaeon and alphaproteobacterium involved probably no longer exist. Nor do the conditions of two billion years ago, although researchers could try to recreate them.

          Still, worth a try if the closest extant archaeon can be cultured.

          • Although, it did take about two billion years of archaea and bacteria living together for the unique endosymbiosis to occur, so obviously it was a rare event and might be hard to replicate in a lab in a reasonable time.

  10. For those that need it much simpler:
    https://www.youtube.com/watch?v=FGnS-Xk0ZqU

    We don’t know much about the process. Don’t even know if the engulfment hypothesis is correct. It could have evolved from endoparasitism. Amoebas have lots of parasites, and parasitism is the predominant form of live. Every non-parasite has multiple parasites and many of these have their own parasites.

    • Javier,

      Parasitism of an archaean by a bacterium was an attractive hypothesis for the origin of eukaryotes. But now we know what at least one Asgard archaean looks like and how it behaves, which new information strongly supports the engulfing hypothesis.

      True, a parasite doesn’t have to be smaller than its host, but mitochondria are tiny compared to modern eukaryotic cells. Culturing an Asgard archaean shows that it and its symbiont bacterium are about the same size, and that the host forms tentacles. These facts support the engulfing hypothesis.

      Further, tentacle formation helps explain how the cell nucleus might have arisen in eukaryotes.

  11. If indeed there is a “” Creator”” then he or she must be the original
    “”Mad scientist””, to have created such a complicated life form as we have today.

    We needed one who believed in the “”Keep it simple stupid” thinking.

    Seriously a very interesting article, although many levels above my I.Q.

    MJE VK5ELL

    • “Keep it simple stupid” – If there is a great designer, He also must have created the ridiculously complicated “structure” of sub-atomic physics, and the incomprehensible “big bang” origin of the universe, not to mention the “dark matter/dark energy” conundrum. And, oh yes, what about the origin of the many “constants” in science. Get one of those wrong, and nothing can exist.
      All good reasons why the ultimate understanding of nature probably lies in the field of philosophy, not science.

  12. Was it really likely to have been “..engulfment of the ancestor of mitochondria by another prokaryote”?
    I have more often thought it likely to have been an invasive infection of one by the other. It liked the new environment, didn’t kill the host, and the two co-evolved to eventually become essentially one life form.

    • Please see my reply to Javier.

      Now that we know what an Asgard archaean looks like, how it behaves and that it exists in a symbiotic relationship with a bacterium, the engulfing hypothesis is supported.

  13. Hey John,

    Great summary, thanks for that. Your title is a gross exaggeration though, I reckon. Scientists in fact have not ‘elucidated origin of eukaryotes’ though their work on existing microbes is no doubt impressive. Consider following statements from the article you pointed:

    could be missing link’ […]

    may be an important discovery about how complex life evolved’ […]

    ‘they say could explain how simple microbes evolved’ […]

    ‘which may have helped it corral’ […]

    ‘The team hypothesizes that, eons ago, an archaeon encircled the protomitochondrion and put it to work.’ […]

    And most importantly:
    ‘And even if this one doesn’t prove to be the ancestor of eukaryotes’ […]

    Thus, what we’re basically seeing is a stack of speculations rooted into another stack of speculations. Nothing wrong with that but that’s far cry from actually proving or indeed observing evolution of eukaryotes.

    Besides, argumentation from similarities always makes me a little bit puzzled. A gene sequence from one organism is very similar to a gene sequence from another organism. Presto, that is an excellent proof of evolution! I reckon there are quite few missing links in this reasoning.

    • Given what can now be observed, the best supported hypothesis is that eukaryotes arose via endosymbiosis between an archaean in the Asgard superphylum and an alphaproteobacterium (a member of Class Alphaproteobacteria in Phylum Proteobacteria).

      Scientific papers always and news reports usually are couched not in definite language but discuss probabilities and possiblities. There is no “proof” is science, as in math, but only “falsification”, ie showing an hypothesis false, or confirmation of a testable prediction made based upon the hypothesis.

      The discovery of this archaean and its bacterial symbiont confirms the endosymbiosis hypothesis, but of course can’t “prove” it.

      As for genomic similarities among species, it’s now possible to see past evolutionary events in the genetic material of organisms. Of course you’re free to conjecture that God for some reason on purpose made tarsiers, New and Old World monkeys, lesser and greater apes all with our vitamin C gene broken in the same way. But the best scientific rather than supernatural explanation is that these primates share a common ancestor which suffered this deleterious mutation, leaving us vulnerable to scurvy, unlike the vast majority of mammals, still able to make their own ascorbic acid.

      Likewise, the best explanation of the relative genetic closeness of species is that they share derived traits from common ancestors. Humans are genetically closest to chimps and bonobos among living species, then to gorillas, then to orangutans, then to gibbons and other lesser apes, then to Old World monkeys, then to New World monkeys, then to tarsiers, then to lemurs and lorises, then to other mammals, etc. The closer together, the more shared mutations inherited from common ancestors.

      Only a stupid designer would have made our feet as they are, for instance. A sophomore engineering student could do a much better job. The best explanation is that it’s a jerry-rigged derivative of a grasping foot, first adapted for climbing in trees, then to walking upright.

      • Scientific papers always and news reports usually are couched not in definite language but discuss probabilities and possiblities.

        Depends what subject and what evidence is presented. Consider official climate science where most of the scientists here claim that AGW is proven beyond any reasonable doubt, in similar manner as gravitation or evolutionary theory.

        Japanese scientists were in fact very modest. What we are observing is interesting symbiotic relationship between different strands of microbes. Based on that scientists speculated that in the distant past such kind of relationship may have evolved into something different, some kind of ‘fusion’ of two organisms. Still, we never observed such fusion neither in the wild nor in laboratory. We don’t even know how such fusion could happens in details. Surely, we may speculate building different scenarios, often contradicting each other. But building speculative scenarios is far cry from actually observing that happening.

        Only a stupid designer would have made our feet as they are, for instance. A sophomore engineering student could do a much better job.

        Not sure about that. How long modern humans exist? ~200k years? And still, through countless generations, in different races and in different environments humble feet do the job. You can stay, you can walk, you can run or even dance using them. Our sophomore student could get a hefty price for such achievement.

        • The feet of Australopithecus were just about as well adapted for plantigrade walking as are ours. There hasn’t been much improvement in millions of years. That’s because there is a limit to how much a grasping foot can be adapted to upright walking. Further improvement must await fortuitous mutation. Or possibly genetic engineering now that we are capable of that.

          Same goes for our having too many and too large of teeth in our reduced jaws. They are still getting smaller and rear molars are on their way out, but dentistry is interfering with natural selection. Which is a good thing. In a state of nature, chronic infection from my impacted wisdom teeth might have finished me off before I had a chance to reproduce.

    • “Elucidate” means “to shed light on”, which IMO is an appropriate description of the effect of these research findings.

    • My guess is that most worlds with life are prokaryotic. But given the plethora of stars and galaxies in the universe, more complex unicells and even multicellular organisms must have evolved many times.

      • seeing as even the best scientists have no clue how life came from non life on this planet, that is just an opinion. I am of the opinion that the only life in the universe is on earth, but that is just my opinion because we have no idea.

        I do think it would be more fun if we had lots of aliens like in Star Wars.

        • The best scientists have lots of clues to the origin of life. There are several possible pathways.

          Life is probably inevitable under the requisite conditions.

  14. John – very interesting article.
    Can you answer a few unrelated biology questions:

    1) What is horizontal gene transfer.?
    2) Tyrosine (UAU) pairs with Isoleucine (AUA) whereas Tyrosine (UAC) pairs with Methionine (AUG). Any significance to this?
    3) In the genome, only 5% maps to proteins. Any significance to this/

    Thanks,
    Walt

    • Horizontal gene transfer occurs when one organism, possibly not even of the same species as the other, directly transfers all or part of its genome to another. It’s the common method of “sex” in prokaryotes, but also happens to a lesser extent in eukaryotes.

      Humans for instance have incorporated a lot of virus DNA into our genome.

      I was not aware of the difference in bonding during polymerization into peptides which you describe for tyrosine coded by UAU v. UAC. I do know however that tyrosine is both polar (forming hydrogen bonds as a proton donor or acceptor) and amphipathic (found at the surface of proteins or lipid membranes), while methionine is amphipathic and hydrophobic (normally buried inside the protein core).

      I could only speculate upon the significance of the coding association. How 64 nucleobase triplets came to code for the 20 amino acids is however a fascinating study.

      IMO the significance of the low percentage of protein-coding sequences is that humans and other organisms have a) picked up a lot of junk during our evolutionary history, and 2) control sequences are very important to how development occurs. For instance, corn (maize) is identical to its wild ancestor teosinte in protein-coding terms. The great phenotypic differences between them are all down to sequences controlling how the plants grow and develop.

      Similarly, many of the obvious differences between humans and chimps owe to control sequences. Both species have the same number of follicles per square inch of skin, but our body hair grows short and theirs long. Our legs and their arms grow longer.

      Junk DNA can prove useful if beneficial mutations arise in it.

      • A recent discovery from interdisciplinary researchers at UDub:

        https://www.sciencedaily.com/releases/2019/08/190812155502.htm

        As origin of life research has progressed, scientists have come more and more to appreciate that nucleic acids and proteins co-evolved, both during prebiotic chemical evolution and later biologically.

        This paper describes how fatty acid (lipid) vesicles, acting as proto-membranes for proto-cells, were stabilized by amino acids, the monomers of protein polymers. It had previously been shown that lipid bilayer vesicles (basically soap bubbles), which form naturally due to having water-loving and water-hating ends, act to concentrate RNA segments.

        • Probably only tangentially related, I heard this from the protein wizard supreme Viktor Morozov. He died recently, so if you don’t hear it from me, you’re unlikely to hear it from anyone.

          A protein in solution will crystallize or not depending on the presence or absence of a free amino acid. That is more-or-less common knowledge. There are papers published on the mechanisms of co-crystallization for some proteins and some amino acids. What is not known is that a protein can be identified by testing it against all common amino acids and noting which amino acids promote its crystallization. The tests Morozov developed based on this observation beat protein sequencing and other methods both in speed and accuracy.

          That may only be a curiosity at this point, but it suggests a few things about amino acids:
          * They are sticky
          * There is specificity in their stickiness
          * Weak binding can result in strong effects

          • Gene,

            Thanks very much for that.

            Russians, once freed from Communism and Lysenko, have made great strides in our understanding of biology and climate.

    • My best guess is that the odds of eukaryotes’ descending from the fusion of an archaean and a bacterium are around 99%. That it was via dendritic endosymbiosis, with an Asgard archaean engulfing an alpaproteobacterium of about the same size, rather than, say by a parasitic bacterial invasion, I’d now, thanks to this and other recent discoveries, venture well over 50:50.

  15. While it is often believed that only eukaryotes use sex to exchange DNA, it isn’t really so. It seems all life is capable of swapping packages of genes in various ways and this likely predates the eukaryotes. Meiosis is just one form of gene swapping which is very efficient at mixing up the pool of genes.

    In meiosis only the DNA in the nucleus is actually divided up, the DNA in the mitochondria is reproduced in full – so even in meiosis only some of the DNA (the nuclear) is “swapped”.

    If the human eukaryote cell can be thought of as “swimming” in a sea of other cells, then the mitochondria can be thought of as a separate life form swimming inside a eukaryote.

    Oh, and they used to believe that in mammals, only the female’s copy of mitochondria are passed on – turns out this isn’t always true either. Sometimes the male’s mitochondria is passed on – so much for using mitochondria DNA to determine the entire tree-of-life back to Eve.

    Life is incredibly messy it is a wonder that it works at all!

    • Robert:
      One of the tenets of evolutionary theory was that acquired characteristics were not passed along to future generations. However, I remember a PBS documentary about a study in Iceland about acquired characteristics being passed on to future generations in mitochondrial DNA. ( I seem to recall something about the abundance of food during the early teens of the grandmother affecting the longevity of the grandchildren). Do you know anything about this?
      Thanks,
      -Walt

      • John, I am not a biologist, just a physicist. Thanks for your running dialogue with this post and the time you took,your passion for te subject is obvious. I think I have learned a lot and have other avenues to explore.

        • You’re welcome.

          My employer might not approve of the time I’ve invested.

          I’m in awe of the hard, diligent work put in by authors of this paper and wanted to share their discoveries.

  16. It seems the evolution of evolution involved reducing its inherent randomness through such means as the evolution of sexual reproduction, which allows for the appearance of a community of gene sharing organisms. In such a community evolution through random mutation is allowed to proceed in a multitude of directions simultaneously and reversibly, whereas every asexually reproducing organism is essentially its own species, doomed to a speedy extinction. Sexual reproduction speeds up the evolutionary process considerably, allowing for the comparably long lived multicellular organisms (years vs. minutes) to attain evolutionary rates maybe surpassing those of their single celled ancestors.

    On the teleological extremes we have simple cause and effect determinism on the one hand and perpetual external interference on the other (with no natural cause and effect discernible by whatever definition). The quest for an effect without a cause (the middle position) is a holy grail indeed; some of Newton’s contemporaries charged him with making God obsolete. As Einstein said, either everything is a miracle or nothing is.

    God knew better than these biological statisticians how big the bang would have to be to end up with machines that wondered what happened after 15 billion years. The question is, how do you get a machine to wonder? –AGF

  17. Thank you for this article and the link to the Science article. We have suspected for a long time that Archaea + Procaryote == Eucaryote and had a good idea of the Procaryotes involved…but this finding from growing an Asgard archae organism is stupendous.
    I had always assumed that ‘outside in’ would be the mechanism, but the long dendrites of this organism, and its existing postulated symbiotism with an ‘outside’ methane-producer, does make it seem that an ‘encirclement’ of the bacterium by pseudopods from the archaem (sp?) might have been ‘what happened’.

    Jan

  18. Hey John,

    A protocell surrounded by yummy organic molecules might have gotten by with few genes

    Compared with that official climate science is the example of hard, settled science. Much fewer ‘mighthaves’ and ‘couldhaves’.

    Synthetic chemistry can indeed produce all building blocks required by living cell. What we cannot do however is assembly all those components back into working, living cell. Even if we have all required components, in proper proportions in highly controlled environment and without any interfering substances and factors. Life simply do not jump out of such tube. It’s like Humpty-Dumpty problem:

    Humpty Dumpty sat on a wall,
    Humpty Dumpty had a great fall.
    All the king’s horses and all the king’s men
    Couldn’t put Humpty together again.

    In our story origin of life researches play the role of ‘all the king’s horses and all the king’s men’. You may have all required components and all tools and techniques provided by newest technology and you still cannot put Humpty together again. Seems to be that there is a some kind of ‘entropy barrier’ that is very difficult to overcome, even with very heavy interference from researches. Even if eventually our technology becomes advanced enough to manipulate macromolecules in order to put Humpty all together and actually create a living cell that will only prove that life does indeed requires intelligent agent.

    • When and if a protocell replicates in a lab, that will show on the contrary that no “designer” is necessary for the origin of life. It will demonstrate one way in which naturally occurring conditions might have produced the first organism, capable of evolving into prokaryotes, then eukaryotes and multicells like us.

      Szostak’s lab has already found, through simple experiments, how lipid vesicles, ie protocell-membranes can split, and how they can evolve into more advanced barriers. Others have discovered pathways for the abiotic synthesis of biomolecules. Science is getting close. Competing scenarios are being investigated.

      The history of science teaches us never to say that results are impossible.

      • When and if a protocell replicates in a lab, that will show on the contrary that no “designer” is necessary for the origin of life.

        If we actually assemble a living cell from basic components that will be enormous achievement of bioengineering, massive milestone something that will hit all headlines in all mass media. Scientists who do that will make a grand history. At this point we can start ‘play God’. Such breakthrough, at very minimum, will confirm possibility that life could have been intelligently created, casting further doubts on naturalistic scenarios that blind forces of nature can do anything close to it. Examples of fine engineering work cannot be used as proof for lack of engineering work.

        • Not so.

          The whole point of origin of life research is to find prebiotic conditions under which life could have arisen.

          It’s as if proponents of supernaturalism are getting ready for whatever happens, ie either no lab-made life or successful creation of replicating protocells. I’m reminded of creationists who always say, whenever “gaps” in the fossil record are filled, that now there are two gaps where before there was but one.

          My personal favorite example is Morganucodon, which protomammal has both the “reptilian” and mammalian jaw joints, just as predicted by the fact of evolution, but previously scoffed at by creationists. When this widespread Triassic genus was first discovered in a Welsh coal mine, then around the world abundantly and well preserved, contrary to repeated assertions by creationists, the usual antiscientific suspects just blithely said, OK, now show all the species intermediate between the ancestors of Morganucodon with the reptilian condition, ie two small bones at the back of their lower jaws besides the dentary, and the mammalian condition, with those two bones now in the middle ear.

          Morganucodon and other protomammals at its level of evolutionary development had already started using those two bones to improve hearing, while they were still attached to the dentary, before they migrated into the skull to become the mammalian middle ear. In Morganucodon, the main jaw joint is already between the dentary (the bone with teeth) and the skull.

          • Hey John,

            The whole point of origin of life research is to find prebiotic conditions under which life could have arisen.

            We can create such conditions relatively easy. What we never observed is a process that creates living cells. We don’t know what happens in the future but my bold prediction is we will never observe such naturalistic process. The only hope is bioengineering and that one day our knowledge and technology will be advanced enough to actually assemble from basic components, via carefully designed processes, a living cell. But that would only prove that for life you need an intelligent agent.

            I like your optimism but the matter of fact is that as we discover new layers of complexity embedded in the cell our understanding how life could emerge actually recedes. More we know about cells less likely naturalistic scenarios of ‘spontaneous’ emergence of life look like. Handwaving and reassurances that ‘science makes progress’ cannot cover that.

            Science is all about “might”. It’s not about religious certitude.

            You’ve got it wrong, I’m afraid. Science nowadays is always painted as hard, objective knowledge in contrast to subjective religious believes. After all ‘faith is confidence in what we hope for and assurance about what we do not see’. That’s, by the way, very accurately describes evolutionary speculations as well.

            But evolution is a fact. Catastrophic anthropogenic climate change is not a fact, or even a well supported hypothesis. Indeed, it was born falsified.

            Really? Pay attention to that:

            “Global warming can no more be “proven” than the theory of continental drift, the theory of evolution or the concept that germs carry diseases.” (Livescience).

            You give yourself a privilege to reject mainstream science with respect to climate science (quite rightly so) yet react quite harshly to those who are skeptical about some claims of evolutionary theory (‘antiscientific suspects’). Not very consistent approach. Good timing though – WUWT just posted summary from an article form the Nature. And authors are crystal clear:

            Since the early 2000s there has been little disagreement among scientific experts over the fundamental evidence supporting the existence, origin, and societal significance of anthropogenic climate change […]. Yet, while an anthropogenic cause is supported by an overwhelming majority of climate change scientists […]

            So, it’s matter of perspective: from the perspective of mainstream science your position on global warming is classified simply as antiscientific. Methinks bit more modesty wouldn’t hurt.

          • Science doesn’t do proof. It does observation, hypothesis, prediction and testing.

            “Continental drift” however can be directly observed now. Geologists have discovered new tectonic plates moving around, thanks to GPS signals.

            The germ theory of disease is confirmed using Koch’s postulates.

            Evolution likewise is an observation of nature, a consequence of reproduction. It’s a fact, not a speculation as you baselessly assert. Speciation and the evolution of new genera have been repeatedly observed in nature, created and recreated in lab.

            Whether the born-falsified hypothesis of catastrophic anthropogenic climate change is “mainstream” or not, I can’t say. No survey of opinions on the hypothesis all the world’s scientists has yet been taken. But consensus or no, opinion isn’t how science works.

            There is no actual evidence supporting the alarmist hypothesis, which is why so many scientists, including the best, reject it.

            OTOH, as noted, evolution is a scientific fact, not an evidence-free, GIGO computer game-based, politically-motivated hypothesis. So there’s no basis for comparing unfounded climate change alarmism with the reality of evolution.

          • <<<>>>

            Can you provide some links? Would not something created in a lab be intelligence based creation?

          • Mike,

            Sure. Be happy to.

            This from Harvard’s Szostak Lab is already outdated, but still will give you the idea. Their simple experiments showed how lipid vesicles can split and evolve into versions of modern cell membranes.

            http://exploringorigins.org/

            Some scientists now think that volcanic hot springs on land offer advantages over deep sea vents as incubators of life, thanks to their wet and dry cycles:

            Earliest signs of life on land preserved in ca. 3.5 Ga hot spring deposits.

            https://www.ncbi.nlm.nih.gov/pubmed/28486437

            A goal of origin of life research is to create life by recreating conditions on the early earth, then letting compounds known to exist then react, without human intervention. No intelligent design required. Some researchers aim to find at least one environment in which nucleotides form RNA polymers with abiotic enzymes, then replicate and split apart. Same goes proteins forming from bonded amino acids or directly from their precursors.

            Others, like the Sutherland Lab at Cambridge, have discovered how the precursors of RNA and proteins naturally self-assemble.

            https://en.wikipedia.org/wiki/Laboratory_of_Molecular_Biology

            https://en.wikipedia.org/wiki/John_Sutherland_(chemist)

            Still others study prebiotic interactions among nucleotides and amino acids:

            https://www.sciencedaily.com/releases/2019/08/190801093310.htm

            Their pure research is akin to applied sciences such as genetic engineering, directed evolution and synthetic biology now used in medicine and industry.

            Searching the Internet, you’ll find numerous recent papers on advances in origin of life research. If the molecular biologists and biochemists who know the most about the subject thought it was impossible to make a simple living thing from scratch, they wouldn’t waste their time and ability trying. Yet they do, to include Nobel Prize winners who could get funded to study just about anything else.

          • Thanks for the information. I will check that out. I am always open to new ideas. I do not think that Dr. Tour should be discounted because he disagrees with what others are saying. But isn’t that what science is? The trick is when doing science to set aside our biases and worldviews and let the data speak for itself. But that is not always easy to do, especially when the data is unclear and we are all human.

            Given that, I am a Christian and follow more or less what you would find at Reasons to Believe (reasons.org).

            Thanks for the conversation.

          • Mike,

            You’re very welcome.

            Tour however has no valid scientific objections to the fact of evolution. No one does. It’s an observation of nature, like the fact that earth goes around the sun, which was formerly only an hypothesis, contrary to the consensus. Dangerously so.

            Objections to the scientific fact of evolution thus are only religious.

            There are many good reasons for being a Christian, but, as noted, the vast majority of Christians belong to denominations which recognize the reality of evolution. Some Catholic theologians have speculated as to when in human evolution our ancestors acquired souls. Homo habilis? Probably not. H. erectus? Possibly. Later Homo species and subspecies? Probably.

            Three duplication mutations in the SRGAP2 gene, which codes for a protein important in brain development, occurred in the human lineage at about 3.4, 2.4 and 1.0 million years ago. If our bodies became fitting repositories for a soul around the time of the first mutation, then even late members of genus Australopithecus might have qualified. If all three were required, then H. antecessor or H. heidelbergensis.

            https://en.wikipedia.org/wiki/SRGAP2

          • I was just a lowly Microbiologist and much of the biochemistry and genetics are difficult for me to get hold of. I can understand it eventually. What I do know is that random mutations and natural selection do not have enough creative power by their selves to produce the diversity we see today. Something else is going on and further study is warranted. I am currently reading Michael Behe’s new book. This link lists 10 problem areas of Neo-Darwinism. (https://evolutionnews.org/2012/07/what_are_the_to_1/). I have not researched these too much but I do know the Cambrian explosion is still a problem for Darwin’s theory, even one he recognized as a problem. Isn’t science fun!!
            Concerning souls. The uncaused first cause (i.e. “God”) created mass/energy space/time out of nothing. Given that, it is not unreasonable that “God” could intervene into his creation. It is my belief that Homo sapiens-sapiens is a “special” creation. We are separate from all other primates with our ability to communicate and our ability to use symbolism, even being biochemically similar. Dr. Gary Habermas is a philosopher and his main area of expertise is on the Resurrection but another area he is interested is in near death experiences. He is a reviewer for the only peer-reviewed journal of Near Death Studies. He has a YouTube video on that and part of it is actually funny. They only review data that can be confirmed, no angels or vistas of Heaven or Hell.
            Of course, all of this pales into insignificance, when I heard on the news tonight that in October you will be able to get Pumpkin Spice Spam!!! Beam me up Scotty……
            Been nice talking to you and there is much to think about.

          • Mike,

            Thanks likewise.

            In the Dover trial, Behe was forced to admit that evolution is a fact. Just throwing up your hands and calling the thousands of different bacterial flagella irreducibly complex is the opposite of practicing science. His goal should have been to discover how each flagellum evovled, or at least some of them. Instead he left that useful work, which offers opportunities to attack bacterial pathogens, to others interested in practicing science rather than promoting a false religious belief.

            As others here have pointed out, that abiogenesis and evolution include elements of randomness, that is no argument against their reality. When and where a sugar-eating microbe’s genome is struck by a passing cosmic ray is more or less random, but that such a mutation will arise sooner or later is certain, given the large number of bacteria. The simple point mutation which turns sugar-consumers into nylon-eaters must have occurred many times in the past, but was always lethal until nylon entered the environment.

            We know that nucleotides and amino acids form without human aid, and now even how they do so. Short chains of them also form spontaneously. The trick is getting them to polymerize without a biological enzyme. There is no magic involved. It’s just chemical engineering.

            On the early earth nucleotides and amino acids were concentrated in various locales with energy sources and other organic compounds and minerals. Possible abiotic enzymes and substrates are being investigated. Nature had at least one hundred millions years with trillions of reactions per second among these precursor compounds in order to form the first nucleic acid chain capable of replicating itself.

            The odds so favor the formation of life that it’s probably inevitable wherever the conditions exist. It solves energy flow problems in these cases, so its origin is driven by physics as well as chemistry.

            Whether life exists elsewhere in the solar system or not, it’s highly likely to be out there in our galaxy.

          • Mike,

            All the normal people have already moved on to other threads, so it’s just down to you and me, my brother.

            The last word is thus yours.

    • Science is all about “might”. It’s not about religious certitude. But evolution is a fact. Catastrophic anthropogenic climate change is not a fact, or even a well supported hypothesis. Indeed, it was born falsified.

      Biology is the opposite of “climate science”. It’s based upon observation and the testing of predictions via experiment, not politically driven GIGO computer gaming.

  19. Simple question. I see a lot of comments from people educated in evolutionary biology, so please forgive my ignorance.
    What is the point of DNA without DNA polymerase ? Did DNA and DNA polymerase spontaneously co-evolve, and if so where did the code for DNA polymerase come from?
    The reason I ask is that DNA polymerase seems to be a fairly complicated protein and it seems essential to any sort of DNA based life. However, in order for an organism to build DNA polymerase it has to have the blueprint in the DNA itself, so did DNA polymerase exist first, or did the code to build DNA polymerase slowly evolve over time, and if it evolved how in the world did any organism actually reproduce without DNA polymerase ?
    I have no background in evolutionary biology, so I find this chicken-egg problem to be a bit intractable.

    • I was privileged to know Arthur Kornberg, discoverer of DNA polymerase, and his recombinant DNA colleague, Joshua Lederberg, the smartest person I’ve ever met, who got a Nobel for his PhD. thesis, typed by his wife.

      Various versions of DNA and RNA polymerase have evolved. It appears that the RNA egg evolved before the DNA polymerase chicken. RNA is both a genetic information storehouse and enzyme capable of catalyzing its own replication. Scientists are investigating how replicated RNA strands might separate without a biological enzyme. The first polymerase might have been a peptide coded for by an early RNA strand.

      • I get that, but somehow RNA morphed into DNA which is only useful if DNA polymerase exists. What I was asking about was not the RNA side, but the DNA side. Were molecules of DNA polymerase floating around before RNA morphed into DNA, or did the DNA polymerase form only after a need arose? This doesn’t make any sense to me at all. Infact, it is confusing enough that I am fully aware I am having trouble forming a coherent question. Even so I will try because I really am interested. (In order to provide a little clarity I will use “DNA polymerase” as a generic term even though there are several forms, and I mean it as distinct from RNA polymerase. I will also use the term “organism” to refer to anything capable of reproducing whether or not it has organelles and a cell wall) It seems like there are a few options
        a) An instruction set for forming DNA polymerase evolved on early strands of RNA. This seems ridiculous because instructions for DNA polymerase can serve no function to an RNA based organism.
        b) An RNA organism evolved an ability to build DNA based off of the RNA molecule. DNA polymerase then later evolved. This seems even more absurd since the DNA would be non-functioning until the later DNA polymerase evolved
        c) An RNA organism evolved a DNA polymerase like molecule that was able to both form DNA and also read it back. That molecule later evolved into DNA polymerase. While this seems feasible it assumes the first evolutionary step was the most complicated – resulting in a molecule that is even more complicated than current DNA polymerase. That would go in the exact opposite direction that evolution is supposed to run (gradual process of small changes accumulating over time).
        I’m not seeing an option d, and a, b, and c all appear to fundamentally disagree with the tenets of random mutation and natural selection. What is the valid option d, or must we swallow that the process of RNA to DNA involved forming DNA polymerase in a single evolutionary step?

        • Lots of papers have been written on the origin of polymerases and their subsequent evolution in viruses and the three domains of cellular life.

          Since RNA appears to have preceded double-stranded DNA as an informational macromolecule, RNA polymerase is the place to start. It is hypothesized to have been among the first proteins to evolve. For over 30 years, scientists have suggested that an important vestige of the original enzyme is found in the contemporary bacterial beta’ subunit of DNA-dependent RNA polymerase and its homologues among archaean and eukaryotic enzymes.

          https://www.ncbi.nlm.nih.gov/pubmed/3146647

          When DNA started replacing RNA as the informational macromolecule, it might have gotten by with a version of RNA polymerase until natural selection improved upon its function, leading to the complex situation today, with RNA-dependent RNA polymerases, RNA-dependent DNA polymerases, DNA-dependent RNA polymerases and DNA-dependent DNA polymerases in bewildering abundance. Variants look to have been transmitted horizontally across domains and from viruses as well as inherited with mutations.

          Reverse transcriptases could shed light on the origin of DNA polymerases. While RTs are enzymes of various uses, their main function is as RNA-directed DNA polymerases in first-strand complementary DNA synthesis.

          https://www.ncbi.nlm.nih.gov/pubmed/18972389

          I hope this helps.

        • DNA developed in the RNA world, in which RNA polymerases already existed. They would have worked well enough for DNA still to have supplanted RNA in the bioinformation role.

          Then natural selection would have worked its wonders to improve RNA-dependent DNA polymerases into the bewildering variety now on offer, to include DNA-dependent RNA and DNA polymerases.

  20. Excellent and illuminating article, thanks!

    Endosymbiosis between different domains!
    No wonder it happened only once.

    So we’re all archaeans…

    • So it seems.

      You’re welcome, and many thanks to you and all commenters.

      I’m glad we managed to keep the discussion civil.

  21. Rather than count galaxies to guess at the chance that life can arise elsewhere, I wonder if it might be easier to look to its development here.

    Life appeared almost as soon as the planet cooled enough for life to exist.

    That suggests, but does not prove, that the appearance of life on other planets is likely.

Leave a Reply

Your email address will not be published. Required fields are marked *