https://phys.org/news/2021-01-salmonella-metabolite-reprogram-krebs-survival.html

"A team of researchers affiliated with several institutions in Israel has discovered the means by which salmonella bacteria use a metabolite to reprogram the Krebs cycle to promote their own survival. In their paper published in the journal Science, the group describes their study of the reaction of salmonella to the presence of succinate and what it revealed about the role succinate might play in bacterial infections in general.

***

"When bacteria enter the body, the immune system carries out a response aimed at killing them to prevent harm. Part of that response involves the activation of macrophages—phagocytic cells that attack and kill pathogens. Prior research has shown that they also produce chemicals that set off an inflammatory response to slow the spread of the pathogen. In this new effort, the researchers took a closer look at that process to better understand why this inflammatory response does not always occur during an infection.

"The researchers chose the bacteria salmonella as a pathogen because it is well understood. Their work involved watching what happened when salmonella entered the macrophages that were intent on killing it. They discovered that once inside the cell, the bacteria made their way to the parts involved in the Krebs cycle—the series of reactions inside certain cells that result in generation of cell energy during aerobic respiration.

"The researchers discovered that the bacteria reprogramed the Krebs cycle to make it behave in ways that enhanced its own chances of survival (such as increasing oxygen in intestinal epithelial cells, making it easier for the bacteria to replicate.) The researchers also discovered via RNA sequencing of both the macrophages and the bacteria that the bacteria activated this process when it sensed the presence of succinate, one of the metabolites produced by the macrophage to instigate an inflammatory response. The researchers suggest that other pathogens also likely sense the presence of succinate and use it to initiate their own survival mechanisms."

Comment: In this case the salmonella reprogram the Krebs cycle by altering DNA in the invaded cells!!! Not their own DNA, which Shapiro studied, but to me editing is editing..

https://www.sciencedaily.com/releases/2018/02/180207102751.htm

"In the study, Erives analyzed the genome of a virus family called Marseilleviridae and found it shares a similar set of genes, called core histones, with eukaryotes.

"That places Marseilleviridae, and perhaps its viral relatives, somewhere along eukaryotes' evolutionary journey.

"'We now know that eukaryotes are more closely related to viruses," says Erives, "and the reason is because they share core histones, which are fundamental to eukaryotes."

"Core histones are packagers, like professional gift-wrappers. They're proteins that, in humans, coil DNA in the chromosomes so vital genetic information is compact and protected. Prokaryotes don't have core histones, so somehow, somewhere, eukaryotes picked them up.

"Viruses like Marseilleviridae may have been the source. (An alternative and equally fascinating explanation is that an ancestor of the Marseilleviridae picked up this gene from a proto-eukaryotic organism, an intermediate between prokaryotes and eukaryotes.)

***

"As he analyzed Marseilleviridae's genomes in data provided by the National Institutes of Health, Erives noticed the giant virus family encodes the eukaryotic core histones H2B-H2A and H3-H4. Unlike eukaryotes, however, these Marseilleviridae core histones are primitively fused as dimer proteins.

"'So, when I saw this, it was wild," Erives says. "No one has ever seen a virus with histones."

"Moreover, he realized Marseilleviridae "did not get these genes from any one eukaryotic lineage living, but rather from some ancestor who was proto-eukaryotic -- that is, on its way to becoming a eukaryote. Until now, no 'organism' was known to have core histone genes besides eukaryotic cells," he says.

"The discovery begs a larger question about the role giant viruses have played in the evolution of all life on Earth. Erives likens giant viruses to vines spreading out into the cellular tree of life -- sampling here, borrowing there, and sharing genetic material among the branches of archaea, bacteria, and eukaryotes.

"'Giant viruses have genes that no one has seen before," he says. "They're conserved. They've been using them for something, and for a very long time. Why not use them now to peer into the past?'"

Comment: There is a theory that viruses have helped direct evolution. Is horizontal gene transfer a mechanism here? See this entry from our past:

https://www.agnosticweb.com/index.php?id=20373

dhw: In my original post I asked what part of his thesis you were talking about: “Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount?” So you are indeed back to flogging the dead horse of gradualism.

DAVID: What is it you think is missing from my discussion? The only thing that Darwin proposed that is without question for me is common descent with modification. How modification occurred is still up for grabs. Remember, for all we know God could be doing the genetic modification.

dhw:So Darwin’s thesis of common descent in fact IS supported by genetic modification. But how it happened is still up for grabs, though you and I agree that however it happened, it would not have been random or gradual. Shake hands on this one?

No gradualism and we do shake hands on evolution by common descent as Darwin's only real contribution.

In my original post I asked what part of his thesis you were talking about: “Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount?” So you are indeed back to flogging the dead horse of gradualism.

DAVID: What is it you think is missing from my discussion? The only thing that Darwin proposed that is without question for me is common descent with modification. How modification occurred is still up for grabs. Remember, for all we know God could be doing the genetic modification.

So Darwin’s thesis of common descent in fact IS supported by genetic modification. But how it happened is still up for grabs, though you and I agree that however it happened, it would not have been random or gradual. Shake hands on this one?

DAVID’S comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

DHW: So which part of Darwin’s thesis is not supported by genetic modification?

DAVID: Darwin did not know about genetics! Neo-Darwinism incorporated genetics much later on, and we are still studying how genetic change results in new species.

dhw: So...once more...which part of Darwin’s thesis is not supported by genetic modification?

Darwin proposed itty bitty changes like breeders used. That was his thesis! No more. What is it you think is missing from my discussion? The only thing that Darwin proposed that is without question for me is common descent with modification. How modification occurred is still up for grabs. Remember, for all we know God could be doing the genetic modification

DHW: So which part of Darwin’s thesis is not supported by genetic modification?

DAVID: Darwin did not know about genetics! Neo-Darwinism incorporated genetics much later on, and we are still studying how genetic change results in new species.

So...once more...which part of Darwin’s thesis is not supported by genetic modification?

DAVID: I accept common descent, but I remain doubtful about the importance of natural selection. It becomes active only when presented with alternative organisms, so it is basically passive in advancing evolution. Survival of the fittest is a tautology, and worthless.

dhw:So which part of Darwin’s thesis is not supported by genetic modification?

Darwin did not know about genetics! Neo-Darwinism incorporated genetics much later on, and we are still studying how genetic change results in new species.

dhw: There are three points here that we have discussed over and over again. Firstly, NOBODY knows how speciation occurred, and that is why we theorize. Secondly, what part of Darwin’s original thesis are you talking about? Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount?

DAVID: I accept common descent, but I remain doubtful about the importance of natural selection. It becomes active only when presented with alternative organisms, so it is basically passive in advancing evolution. Survival of the fittest is a tautology, and worthless.

So which part of Darwin’s thesis is not supported by genetic modification?

dhw: Thirdly, it is not only such modifications that Shapiro has championed, but also the all-important factor of cellular intelligence, which means that “Where’s there a will there’s a way” is to be taken literally. Please give us your “theological explanation” for Prochlorococcus’s amazing talent.
DAVID: I think God gave unicellular organisms the ability to edit their DNA for adaptations to changes in environment, but not to the degree of actual speciation, in agreement with what Shapiro presents.

Yes, if Shapiro subscribed to the theistic version, he might say God gave cells the INTELLIGENCE to edit their DNA. (Remember, he believes in cellular intelligence.) We do not know whether that intelligence extends so far as to create the multicellular innovations that cause speciation. That is why it is a hypothesis.

David's comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

dhw: There are three points here that we have discussed over and over again. Firstly, NOBODY knows how speciation occurred, and that is why we theorize. Secondly, what part of Darwin’s original thesis are you talking about? Common descent? Natural selection?

I accept common descent, but I remain doubtful about the importance of natural selection. It becomes active only when presented with alternative organisms, so it is basically passive in advancing evolution. Survival of the fittest is a tautology, and worthless. Survival is not dog eat dog, but is the environment friendly enough for survival, the 'bad luck' theory? Is nature balanced or not?

dhw: Or the same old random mutations plus gradualism that you and I have long since agreed to discount? Thirdly, it is not only such modifications that Shapiro has championed, but also the all-important factor of cellular intelligence, which means that “Where’s there a will there’s a way” is to be taken literally. Please give us your “theological explanation” for Prochlorococcus’s amazing talent.

I think God gave unicellular organisms the ability to edit their DNA for adaptations to changes in environment, but not to the degree of actual speciation, in agreement with what Shapiro presents.

QUOTE: 'The dramatic and widespread change in the metabolic network is really a shock," said Casey. "However, we're seeing that these changes provide a substantial growth advantage for this ubiquitous microbe in phosphorus-limited regions of the ocean, so it seems that where there's a will there's a way."

David's comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

There are three points here that we have discussed over and over again. Firstly, NOBODY knows how speciation occurred, and that is why we theorize. Secondly, what part of Darwin’s original thesis are you talking about? Common descent? Natural selection? Or the same old random mutations plus gradualism that you and I have long since agreed to discount? Thirdly, it is not only such modifications that Shapiro has championed, but also the all-important factor of cellular intelligence, which means that “Where’s there a will there’s a way” is to be taken literally. Please give us your “theological explanation” for Prochlorococcus’s amazing talent.

https://www.sciencedaily.com/releases/2016/11/161115150109.htm

"Researchers from David Karl's laboratory at the University of Hawai'i at Mānoa (UHM) and from Professor Jens Nielsen's laboratory at Chalmers University of Technology in Göteborg, Sweden, developed a computer model which takes into account hundreds of genes, chemical reactions, and compounds required for the survival of Prochlorococcus, the most abundant photosynthetic microbe on the planet. They found that Prochlorococcus has made extensive alterations to its metabolism as a way to reduce its dependence on phosphorus, an element that is essential and often growth-limiting in the ocean.

***

"Microbes are known to employ three basic strategies to compete for limiting elemental resources: cell quotas may be adjusted, stressed cells may synthesize molecules to make more efficient use of available resources, and cells may access alternatives or more costly sources of the nutrient.

"In the case of phosphorus, a limiting resource in vast oceanic regions, the cosmopolitan Prochlorococcus thrives by adopting all three strategies and a fourth, previously unknown strategy.

"'By generating the first detailed model of metabolism for an ecologically important marine microbe, we found that Prochlorococcus has evolved a way to reduce its dependence on phosphate by minimizing the number of enzymes involved in phosphate transformations, thus relieving intracellular demands"

***

"Prochlorococcus has an extremely minimal genome. If it were to lose the function of any one metabolic gene, its survival would be nearly a coin toss. To their surprise, Casey and co-authors discovered that the world's most abundant microbe has performed, through a process called "genome streamlining" -- the concerted loss of frivolous genes over evolutionary time -- a comprehensive re-design of the core metabolic pathways in response to the persistent limitation of phosphorus.

"'The dramatic and widespread change in the metabolic network is really a shock," said Casey. "However, we're seeing that these changes provide a substantial growth advantage for this ubiquitous microbe in phosphorus-limited regions of the ocean, so it seems that where there's a will there's a way."

***

"'We're interested in the underlying principles guiding metabolism and physiology in marine microbes, and that is going to require a deep understanding of not only the 1-dimensional genetic code, but also the 4-dimensional product it codes for," said Casey. "So we're looking to a systems-level approach to incorporate a great variety of physiological and 'omics studies all in one computational structure, with the hope that we can start to learn from the design and interactions of these complex systems.'"

Comment: This modification is just what Shapiro has championed. A dramatic editing of DNA removing the metabolic stress of producing enzymes by finding a simpler way of manufacturing photosynthesis products. Still the same species! Doesn't show how speciation occurs and is no support for Darwin's original thesis.

dhw: The great question is the degree of its autonomy. I do not think it IS lots; I think it MAY BE lots. If you put your cowboy six-shooter to my head, I will certainly opt for lots rather than your all-inclusive preprogramming of all innovations and complex lifestyles 3.7 billion years ago, but that is not the point. The limits for invention are unknown, so how can you as a scientist champion one theistic hypothesis and reject the other (remember, I have allowed for your God designing the IM), believing that your dilemma has been solved when this directly relevant and enormously important area of research remains so incomplete?-My response is simple as previously stated. How do you know the limits of God's ability to program in the beginning? I don't. Early life was complex to begin with. My dabbling problem has to do exactly with my estimate of his powers. Could He do it all from the first or did He have to dabble? With our discussion of an IM as a definite possibility and the Tony's step-wise pattern programming, I am of the opinion that God more than likely did it from the beginning with rare intervention, thereafter. If He was extremely purposeful evolution might have been more direct than it was to arrive at us. Therefore, that any intervention was minimal seems reasonable to me..

dhw: Your own hypothesis is that from the very beginning God preprogrammed all the innovations and complex lifestyles that have punctuated evolution from bacteria to humans. THAT is our subject. So please find me a reference in Talbott that supports your preprogramming hypothesis as opposed to my intelligent mechanism hypothesis. Bet you can't. See also my post under “Evidence for pattern development; mulling”, and mull some more.-I've said that I am not going to quote Talbott. His writing is verbose, but some of his opinionated quotes fall in line with my thinking and some with yours. He discusses beautifully the problems with the atheistic approach to Darwinism and he ascribes an inventive mechanism to evolved organisms, but it is a nebulous description. They seem to do it be he can't describe how. And that is because none of us know how it is done, or the limits in capability to do the job. Our debate is over the degree of modification. You thinks it is lots, and I think it is much more limited. I'm afraid we have to agree to disagree. There is no doubt epigenetic changes play a role in furthering evolution, but that is as far as Shapiro, the champion of epigenetics, can go. We are forced to wait for further research to clear up the issue if it can. To be precise: an epigenetic IM exists, its limits for invention are unknown.