Researchers search for the “last bacterial common ancestor” in a world of horizontal gene transfer

_{Denyse O'Leary

April 3, 2021

Evolution, Genomics, horizontal gene transfer, Intelligent Design}

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They admit the difficulty of finding LBCA:

Higher life forms pass on their genetic code from parent to offspring via vertical gene transfer. As a result, the genome provides information on phylogenetic history. But bacteria are masters in another form of gene transfer, namely lateral gene transfer (LGT). This allows bacteria to exchange genetic information across different strains. This posed a major challenge in reconstructing the LBCA genome, as it renders the traditional phylogenetic methods incapable of inferring the root in the bacterial evolutionary tree.
For this reason, the researchers in Duesseldorf used biochemical networks together with thousands of individual trees. They investigated 1,089 anaerobic genomes and identified 146 protein families conserved in all bacteria. These proteins make up a nearly complete core metabolic network …
“We can infer with confidence that LBCA was most likely rod-shaped,” says Xavier. “If it was similar to Clostridia, it is possible that LBCA was able to sporulate.” This hypothesis was recently laid out by other researchers “and is highly compatible with our results,” says Xavier. Forming spores would allow early cells to survive the inhospitable environment of the early Earth.
Heinrich-Heine University Duesseldorf, “In search of the first bacterium” at ScienceDaily

One senses that the reconstruction will be subject to considerable revision. It’s not entirely clear what “ancestry” means in a world of rampant horizontal gene transfer.

The paper is open access.

See also: Horizontal gene transfer: Sorry, Darwin, it’s not your evolution any more

Comments

They are the bastard offspring of materialistic thought. It isn't reasonable to think that an intelligent designer intelligently designed a universe, planetary system(s) and living organisms only to leave the rest to contingent serendipity. Meaning in light of the universe, planetary systems and living organisms being intelligently designed, we would infer something like Lee Spetner's "built-n responses to environmental cues" to be the main driver of variation.ET_{April 4, 2021
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So you are saying that all those words imply materialism - true?Viola Lee_{April 4, 2021
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Call it Darwinism, Neo-Darwinism/ modern synthesis or the extended evolutionary synthesis. All of those posit evolution by means of blind and mindless processes. Darwin was the first to give it a good narrative. So he's the number 1 evolutionary story-teller. It's cool how he made pure BS seem so sciencey.ET_{April 4, 2021
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As News said, universal common descent was all about ancestor-descendent relationships. It was never about ancestor-(descendent + some other discarded genes that just happened to find their way into the genome) relationships.ET_{April 4, 2021
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Viola Lee, yes, I remember those exercises in high school as well. But when I went to university they expanded on this exponentially. We were taught HGT, inversions, neutral theory and lots of other details that we were not taught in high school. I don’t think this is different than any other subject. High school just gives you the foundational elements of everything from physics to history. When you go to college for the subject you are interested in, you are exposed to a far greater expanse of information specific to that subject.count of crisco_{April 4, 2021
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Yes, CC, all those different things that can happen are fascinating: a far cry from the simple dominant/recessive genes, X and Y chromosomes, simple mutations, etc. that I learned about in high school biology many years ago. Scientists have learned so much, and keep learning the more we investigate.Viola Lee_{April 4, 2021
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What I’m interested in here are the fascinatingly complex ways genes change and are passed on to new organisms.
Genes change all the time. What is rare if almost nonexistent is the origination of a genetic sequence that leads to a new functional protein. So one’s worldview should include how did all these functional genetic sequences arise. The only logical explanation on the table that makes sense is an entity of massive intelligence made it happen.
There is no doubt that natural selection is an important driving force in evolution.
Trivial at best. Might explain a polar bear vs a grizzly bear but not the bears themselves.jerry_{April 4, 2021
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Viola Lee, yes, I am interested in this as well. There is no doubt that natural selection is an important driving force in evolution. And it only acts on the phenotype. But how the phenotype changes throughout the lineage of a species is complicated. For bacteria, they generally make exact copies of themselves, with a few point mutations thrown in for fun. Then there is the bacterial version of sex, the transfer of plasmids from other cells of the same type. Then there is the transfer of DNA from one cell to another of a different type. It really starts to get interesting with protozoans. As with bacteria, their most common form of reproduction is fission, where the two daughter cells are identical to the parent, barring any point mutations. But they also reproduce sexually, where two cells get together, undergo meiosis, and then make a transfer to each other. At this point, both cells are different genetically than they were before, increasing the variation of the population. There are some that can even undergo meiosis without swapping spit with another cell. This changes the genetic makeup of the cell. And then we get into metazoans, where the sex games become really strange. For example, cladocerans are born pregnant. And we haven’t really talked about another source of genetic transfer, although I guess it can be classified as HGT. It has been estimated that as much as 8% of the human genome is made up of viral DNA.count of crisco_{April 4, 2021
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Thank you, Count of Crisco, for paying attention to what I've written, and for your understanding. To be clear, because the distinctions interest me a lot, I am not a materialist but I am an atheist in that I don't believe any of the gods as described by human religions exist. Furthermore, my speculative metaphysical leanings are that whatever non-material creative power or principle does exist is not a personal one that is involved in the lives of human beings in the way Western theistic religions assume is the case. All of this is off-topic for the conversation in this thread, however. But on-topic is Steve's comment: in other threads I've seen Darwinism and Darwinist used in a pejorative way that seems to imply an adherence to materialism. However, it seems to me that the discussion about whether HGT should be included as part of Darwinism doesn't bring that issue into play. What I'm interested in here are the fascinatingly complex ways genes change and are passed on to new organisms.Viola Lee_{April 4, 2021
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SA2
Some ID proponents use this term much in the way that some people use Creationist when referring to an ID proponent. Technically, neither term is incorrect but they are used in a pejorative sense rather than a technical one.
I have seen both used as an insult, but I think this is a minority. However, the motivation of the person using the term comes clear when the person is corrected and continues to use the term. I have seen this when Viola Lee repeatedly corrects a couple commenters that she is not an atheist or a materialist, and they continue to use these terms to refer to her. In my mind, that is just a lazy and cheap debate tactic.count of crisco_{April 4, 2021
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Jerry “ Most who profess a belief in a natural mechanism for evolution would not call themselves Darwinists.” In the strictest sense, I agree with this. Darwin was important because he caused a paradigm shift in how we look at life. But the science has progressed far beyond Darwin’s understanding in his day. but the foundation still conforms, in the broadest sense, with Darwin’s framework. Some ID proponents use this term much in the way that some people use Creationist when referring to an ID proponent. Technically, neither term is incorrect but they are used in a pejorative sense rather than a technical one.Steve Alten2_{April 4, 2021
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Steve used the phrases “neo-Darwinism” and “modern synthesis.” Do those phrases include HGT?
Probably but those terms are a hundred years old. They keep getting updated and then abandoned and then accepted again by some. They are irrelevant to the evolution debate but feel free to pursue it. Most who profess a belief in a natural mechanism for evolution would not call themselves Darwinists.jerry_{April 4, 2021
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Jerry writes, "So whether HGT is part of Darwinism or not is beside the point." Well, it's not beside the point that I am interested in, and the points you made are not what I am interested in. So in the context of this discussion, I am still interested in the correct terminology. Steve used the phrases "neo-Darwinism" and "modern synthesis." Do those phrases include HGT?Viola Lee_{April 4, 2021
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A layperson’s understanding
All this is well known and irrelevant to the evolution debate. Whether one includes HGT in the engines of variation or not, none explains major changes in life forms over time. That is what Darwin and his current adherents want to explain - non trivial change by a natural mechanism. Their desperation is to find any natural mechanism. That there isn’t any is their embarrassment. That they pretend there is, is their hypocrisy. To use a famous expression. Not the survival of the fittest but the arrival of the fittest. So whether HGT is part of Darwinism or not is beside the point. As far as the tree of life it just means that two branches got intertwined. But in reality there is no tree of life by any natural mechanism known to man. .jerry_{April 4, 2021
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Hmmm. If Darwinism is being used to describe vertical gene transfer (to use a term for genes being transferred through reproduction = VGT), as opposed to HGT, and since reproduction is certainly a widespread form of gene transfer, it doesn't make sense to say Darwinism "is nothing". It seems to me that HGT extends our understanding of how genes get passed on to new organisms, but it doesn't negate the role of genes being passed on by reproduction. That would be my understanding. Also, as Steve pointed out, if HGT is then followed by VGT (such as a bacteria incorporating some new genes, and then passing them on through asexual reproduction), then descent has come into play: the results of the HGT are then passed on to succeeding generations. It seems to me both methods can be involved, at times, in the creation of descendents. I do understand, also, that we don't have a nice tidy tree of descendents, like when I trace myself back to my great-grandfather. The picture I have is at the level at which HGT takes place, there can be more of mesh or network, so you couldn't point to a clearcut line of descent. All a layperson's understandings, FWIW.Viola Lee_{April 3, 2021
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News “ Whatever Darwin knew or didn’t know, horizontal gene transfer makes merry hell out of traditional views of natural selection (as in “leaving more *descendants*”)” How so? An organism that acquired a new trait through HGT, and it improved fitness, it will leave more descendants and the HGT trait will increase in frequency in the population. Where it originally came from is irrelevant.Steve Alten2_{April 3, 2021
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Hi Viola Lee, neo-Darwinism and the modern synthesis are essentially the same thing. It combined Darwin’s theory with genetics. I think it is fair to say that it was far too restrictive when it started as things like HGT, meiosis, gene duplication, etc were not yet well understood. The modern synthesis postulated that all variation was the result of mutation. Although this is, ultimately, still the case, there is far more known about means of “gene shuffling” that effectively increase genetic variation within a population.Steve Alten2_{April 3, 2021
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Whatever Darwin knew or didn't know, horizontal gene transfer makes merry hell out of traditional views of natural selection (as in "leaving more *descendants*"). If Darwinism is everything and anything to do with evolution, it is nothing.News_{April 3, 2021
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That's a good explanation, Steve. I have heard the phrase "neo-Darwinism", although I don't know whether that is widely accepted or just colloquial, but would that be a term that would include both "vertical gene transfer" via reproduction and horizontal gene transfer also? And, as you point out, Darwin knew nothing about genes, so the term Darwinism, it would seem to me, would mean more than Darwin's theory itself, as he described it more than 150 years ago, as we've learned so much that he didn't know since then.Viola Lee_{April 3, 2021
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News “ At one time, no one seriously considered horizontal gene transfer.“ But also at one time, in Darwin’s day, no one seriously considered DNA and genes. Darwin’s theory was just about selection working on natural heritable variation. He did not know where the variation came from and even considered the inheritance of acquired characteristics as a source of this variation. HGT, a means of increasing variation, is heritable and therefore consistent with Darwinism.Steve Alten2_{April 3, 2021
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I guess my next question is what is a word or phrase that incorporates both HGT and reproductive descent as means of genes being changed as the generations of organisms go by? That is, what is a broader term that includes both Darwinism and HGT?Viola Lee_{April 3, 2021
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Thanks. That's very clear, and agrees with what I said.Viola Lee_{April 3, 2021
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Viola Lee at 1, Darwinism is about descent. At one time, no one seriously considered horizontal gene transfer. The sea slug that grabs chloroplasts from plants is not their descendant in any meaningful sense.News_{April 3, 2021
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Hi News. I asked this question in another thread, but not directly to you: Is HGT more than Darwinism because it doesn't depend on direct inheritance of genes through reproduction? In your article you wrote, "Bacteria just do not play by Darwin’s rules." Is reproduction from a parent or parents, then, a defining feature of Darwinism? Is this what you mean?Viola Lee_{April 3, 2021
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