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How did scientists establish the reactions that occur in metabolism?


How did scientists establish that macromolecules like proteins, carbohydrates and lipids are synthesized from other molecules with intermediate products by living cells. Did they observe this under microscope. I want to know this because I am studying bioenergetics and while studying photosynthesis and cellular respiration I have doubt that whether this all stuff is correct or not. I hope that you will help me to clear this doubt.


In addition to biochemical methods, a lot of this was figured out using radioactive tracers. Cells would be fed a radioactive substrate and as they convert the substrate to other molecules through metabolic reactions, the radioactivity can be detected in the products and intermediates.

Calvin's 1940s-50s experiments to establish carbon flow during photosynthesis (i.e. the Calvin-Benson Cycle) using $^{14}CO_2$ remain some of the most elegant work along these lines. You can actually read some of his reports here, though maybe someone else has a good link to a less technical overview.

Similar methods are still used today, though stable isotopes instead of radioactive ones are more commonly used.


The short answer is no, you do not study metabolism under the microscope. (Modern high resolution microscopes can visualize macromolecular processes like transcription and translation, but that is not how they were studied originally.)

In brief, biochemical pathways were studied in broken cells by studying individual reactions or in whole tissues or animals studying chains of reactions. In broken cells chemical methods (often colorimetric, but historically by measuring the evolution of gases) were used to identify products of reactions when particular chemicals are added, and enzymes purified from tissues to find out what reactions they catalyse. Centrifugation methods were used to different organelles from cells (mitochondria, nuclei, ribosomes). In whole cells radioactive precursors are added and one separates and identifies the compounds in the cell to find out which compounds have acquired radioactivity, i.e. what the original compound has been converted to.

In bioenergetics the methods are/were more specialized using spectrometry to identify the oxygenation state of different cytochromes, and the oxygen electrode to measure the utilization of oxygen. In animal cells isolated mitochondria were often used.

This is a very wide area, although because it is not currently very active it is difficult to find an internet source to recommend you. Perhaps someone else knows of one.


How did scientists establish the reactions that occur in metabolism? - Biology

Energy production within a cell involves many coordinated chemical pathways. Most of these pathways are combinations of oxidation and reduction reactions. Oxidation and reduction occur in tandem. An oxidation reaction strips an electron from an atom in a compound, and the addition of this electron to another compound is a reduction reaction. Because oxidation and reduction usually occur together, these pairs of reactions are called oxidation reduction reactions, or redox reactions.

Learning Objectives

  • Relate the movement of electrons to oxidation-reduction (redox) reactions
  • Describe how cells store and transfer free energy using ATP

Sandwalk

There are several competing hypotheses about the origin of life. Most people know about the Primordial Soup scenario that's the one where complex organic molecules are created by spontaneous chemical reactions. Over time these complex molecules, such as amino acids and nucleotides, accumulate in a warm little pond and eventually they come together to form proteins and nucleic acids.

The RNA World scenario is similar except that nucleic acids (RNA) are thought to form before proteins. For a while, RNA molecules are the main catalysts in the primordial soup. Later on, proteins take over some of the catalytic roles. One of the problems with the RNA world hypothesis is that you have to have a reasonable concentration of nucleotides before the process can begin.

The third hypothesis is called Metabolism First. In this scheme, the first reactions involve spontaneous formation of simple molecules such as acetate, a two-carbon compound formed from carbon dioxide and water. Pathways leading to the synthesis of simple organic molecules might be promoted by natural catalysts such as minerals and porous surfaces in rocks. The point is that the origin of life is triggered by the accumulation of very simple organic molecules in thermodynamically favorable circumstances.

Simple organic molecules can then be combined in various ways that result in simple amino acids, lipids, etc. These, in turn, could act as catalysts for the formation of more organic molecules. This is the beginning of metabolism.

Eventually simple peptides will be formed and this could lead to better catalysts. Nucleic acids and complex amino acids will only form near the end of this process.

One of the advantages of the metabolism first scenario is that it offers a simple "solution" to the chirality/racemization problem by explaining why all naturally occurring amino acids are left-handed [see Can watery asteroids explain why life is 'left-handed'?]. Another advantage is that it doesn't require spontaneous formation of nucleotides&mdasha major limitation of the RNA world scenario since spontaneous formation of such molecules is very improbable. 1

James Trefil, Harold Morowitz, and Eric Smith have written up a very nice summary of the Metabolism First hypothesis for American Scientist: The Origin of Life. The subtitle, "A case is made for the descent of electrons," is a clever play on words. It illustrates the point that synthesis of simple organic molecules such as acetate are thermodynamically favorable. This is science writing at its best. 2

The authors have reconstructed the simplest, most fundamental, biochemical pathways concluding that a reductive citric acid cycle is probably the best example of the first metabolic pathway. In this pathway, the two-carbon acetate molecule is made from carbon dioxide and water in the reverse of the common citric acid pathway found in eukaryotes.

In fact, the reductive pathway occurs in many bacteria. They can still use it to fix carbon. The authors use the figure on the left to illustrate the basic pathway.

Almost all of the common molecules of life are synthesized from acetate or the molecules of the citric acid cycle. The simple amino acids, for example, are formed in one step. More complex amino acids are derived from the simple amino acids, etc. Similarly, simple fatty acids can be formed from acetate and more complex ones come later once the simple ones accumulate.

The central role of citric acid cycle metabolism in biochemistry has been known for decades. It's involvement in biosynthesis pathways is often ignored in introductory biochemistry courses because they are heavily focused on fuel metabolism in mammals and biosynthetic pathways get short shrift in such courses.

The essence of Metabolism First is that the various complex molecules of life came after the spontaneous formation of very simple molecules. Pathways leading to the complex molecules evolved and their evolution was assisted by the evolution of various catalysts, some of which were biological in nature.

1. In spite of the claims surrounding a recent paper in Nature: RNA world easier to make.

2. Probably good science editing as well. My friend Morgan Ryan is managing editor and he is very good.

[Photo Credit: American Scientist, courtesy of Scripps Institution of Oceanography, University of California, San Diego.]

31 comments:

I don't see a conflict between RNA World and Metabolism First. To me, RNA World says that RNA came before DNA, specifically sequenced proteins and any other complex biopolymers.

But of course those polymers developed in a suitable environment of precursors and favorable energetics. But I don't think of those as life, and most certainly not life as we know it. That would be like calling the phosphorus and nitrogen fertilizer I spread on my lawn life. They are the background, the environment.

The NYTimes article on this:
Chemist Shows How RNA Can Be the Starting Point for Life
Dr. Sutherland’s proposal has not convinced everyone. Dr. Robert Shapiro, a chemist at New York University, said the recipe “definitely does not meet my criteria for a plausible pathway to the RNA world.” He said that cyano-acetylene, one of Dr. Sutherland’s assumed starting materials, is quickly destroyed by other chemicals and its appearance in pure form on the early earth “could be considered a fantasy.”
Dr. Sutherland replied that the chemical is consumed fastest in the reaction he proposes, and that since it has been detected on Titan there is no reason it should not have been present on the early earth.

I think Shapiro has simply become too accustomed to saying no.

Shapiro has a nickname Dr No he is very proud of

I don't see a conflict between RNA World and Metabolism First.

Me neither. I thought the recent paper in Nature on how nucleotides may form spontaneously is great and, in essence, illustrates a possible pathway of transition from one to another.

V. interesting This supplements what I have already heard about "Metabolism first".

Tell me Larry when you delve into these rather unfossilferous speculative areas on the origin of life, do you ever get doubts? No, of course not: I get doubts, but you just react with a "bah humbug!"

Timothy V Reeves writes: ". unfossiliferous speculative areas on the origin of life. "

As I read it, the post concerns simple(r) chemistry being a more probable starting point for life than more complex chemistry. Speculative in the sense that we don't have a record of events as they unfolded, yes but not so in the sense that the chemistry involved is familiar and well-understood.

Late to this, but love the subject and wonder if you are familiar with the Morris/Russell treatment of the subject? here and here? I loved the American Science article focussing on the movement of electrons through the metabolic cycles, while Martin and Russell focus on the pumping of protons through the same cycles. An interesting suggestion is that since archaebacteria and eubacteria share DNA/RNA and various metabolic pathways, but have utterly different ways to form cell membranes, their shared history includes a period of development within naturally occurring "cell-type" spaces, but diverges prior to the independent membrane-bounded emergence of each to the external environment.

There is a third possibility, which I am afraid, you have overlooked. Life has three fundamental characteristics. 1. replication, 2. metabolism and 3. consciousness (or irritability). I think the last one is the most essential feature for life to form. So I propose "Consciousness First Theory". Consciousness has originated from primordial cell membrane in the form of membrane potentials. I have proposed that primordial membranes have formed from "Hydrocarbon Mass" in the Earth's crust 3.7 billion years ago. Organic molecules have formed due to erosion of hydrocarbon chains by the electrical (membrane) potentials.

I have written a book on this subject "The Role of Cell Membrane in the Origin of Life and in Cell Biology", which explains this theory in detail.

Any takers of this theory?

THIS ARTICLE SUCKS HOW AM IM SUPPOSED TO CHEAT FOR MY HOMEWORK BY THE WAY MY NAME IS KENDALL EDISON.

There is only 2 articles on the origins of life? I wonder why?

In this question I don´t think you have got the right answer. I see no possibility of life without replication, and the most primitive replicator we know of is RNA. As RNA can also catalyze reactions, I see it as evident that there was an RNA world. There is still a problem to be solved: how the first RNA molecules were created. But I am sure this question will be solved.

"But I am sure this question will be solved."

It is solved by postulating that basic metabolism arose before there was RNA. The beginnings of life required ways to make sugars and nucleotides and confine them to small volumes. The catalysts for those reactions were inorganic molecules (e.g. metals) and small peptides.

Of course you need replicators and of course RNA is the most logical choice. But you just can't get to RNA from carbon dioxide without metabolism first.

While metabolism first is an idea, there had to be more to it than that I think. There had to be some kind of a shield from harsh environment for life to continue. A protective membrane of some kind before metabolism.

I'm also puzzled as to how even the simplest lifeforms developed without information for their development. They need it now how come they didn't need it early on?

"But you just can't get to RNA from carbon dioxide without metabolism first."

You are right that synthesis of nucleotides is not a simple process. And there were other sources than carbon dioxide, which probably was the main component of the atmosphere. Atmosphere may at an early stage also have contained ammoniac, methane and even some free hydrogen. There may also have been some free chlorine, as there may not have been enough sodium to bind all of it. This chlorine may have been crucial for many reactions by activating molecules.

If the only possibility was creation of life in the oceans, then I would choose an active site like a hydrothermal vents. But I do not think there is a choice only between "soupers" and "smokers", even if these two theories are the most popular today. I have seen no proof that the early Earth was totally covered with water. On the contrary, the processes that created life must have started once there was liquid water, and in the beginning most of the surface would have been land. Although there would have been dramatic greenhouse effect, there would have been a clear difference between daytime and nighttime temperatures. And I am not convinced that the lack of an ozone layer would have let through so much UV light that primitive life was impossible, at least not in areas shadowed by local stones or by clouds.

I don’t think oceans ever have been "sweet". There would simply not have been enough carbon for that. But there could locally have been sweet spots. Areas around hydrothermal vents would have had high concentrations of minerals, but not organic molecules, and probably not either much phosphate.

If we look at the basics of life, nucleotides, proteins and fatty acids, then we see that all the elements that they consist of are gaseous, except phosphor and sulphur. We can easily imagine that the first proteins did not contain methionine or cysteine, but nucleotides without phosphate is not possible unless there was initially another backbone. Leslie Orgel was convinced that there was a change of backbone, but I find such a change difficult. I have instead speculated how phosphate could have been incorporated directly.

As Miller-Urey showed with their famous experiment, molecules like amino acids are synthesized from gaseous molecules if there is something triggering reactions and there is good contact between an aqueous phase and the gaseous phase. I imagine that good contact will be present on a changing surface like the one that is formed when dew drops form on a solid surface, i.e. on a mineral. An extra effect of the mineral could be to catalyze reactions, and substances in the surface could even take place in the reactions.

If the surface was apatite, then it could work as a source of phosphate. The ribose may have been synthesized on another mineral. Different surfaces could be connected e.g. through rain drops, and various substances could be purified during the day, when heating dried up the dew.

Slower drying processes combined with drops e.g. in caves could purify sugars and other easily crystallizable substances. Different minerals would sort out specific molecules due to their catalytic effect.

With the right positioning of different mineral surfaces and maybe also surfaces that created shadow at the right periods during the day, there could be factories suited especially for connecting ribose or other sugars to phosphate. The source of sugars could be a cave that e.g. during the nights had extra supply of water and therefore washed out some crystalized sugar. Further there could also have been purine/pyrimidine factories that could also supply the RNA bases. In apatite, the phosphate groups are perfectly aligned in parallel lines with a distance that gives the required space for sugar and bases.

Ad RNA world starting on mineral surfaces: Dew drops may have been the first encapsulations. Large fatty molecules that did not dissolve in water would have migrated to the drop boundary, and eventually, a beehive structure of a tar-like substance would be built between the drops. Thereby drops would form at the same places every day. With higher humidity the drops would have fused across this boundary, and larger drops would have formed. It is therefore likely that beehive structures would have formed in a hierarchical system. This would have given room for fusion during moisture increase and fission during drying up. This could have been the first reproduction.

Fatty acids would migrate to the surface of the drops, and before they dried up completely, they could sometimes be completely covered by a single layer membrane. We can also imagine that an extra layer formed if these drops crossed a fluid surface that was covered by a fatty acid surface. Fusion and fission processes between these cells could have been the first cellular reproduction.

I am not saying that there were no proteins in the RNA world, but they had no simple coding, and therefore they had to be built in quite complex ways. I am not either saying that there were no DNA in the RNA world. DNA was probably soon invented as a substitute for RNA for long term storage of information.

I have not performed any experiment to support this theory, and I do not know of any others that have similar theories. I would however be very pleased if somebody knows about any similar. I would especially appreciate if somebody could design and maybe also perform experiments that could support origin of life on mineral surfaces.

Phosphate has been crucial not only for replication, i.e. in the synthesis of RNA, but also for metabolism. The general energy carrier, ATP, is just a nucleotide that has been extra phosphorylated two times. Another variant, based on the G base instead of A is also in use. The energy lies in the phosphate group. But also other molecules take up one or two phosphate groups, probably from a mineral source. These phosphate groups can be transferred to ADP, thereby producing ATP. Two of the phosphorylated molecules are 1,3-bisphosphoglycerate and phosphoenolpyruvate. They are part of the most important reaction chains of life, glycolysis and gluconeogenesis. These reaction chains involve electron transport, which is also performed by an RNA-like molecule: NAD+/NADH.

Different reaction chains established to take care of the released electron pair. One of them produced succinate as end product via fumarate. But also another reaction chain with succinate as end product established, this one via citrate. This chain was used more for anabolic purposes, but it could only be used in limited amount because it produced free electrons. A bridge established between the start point of these two chains, and the anabolic chain could run the reaction in the opposite direction. Thereby a cycle was established, which we can call the reverse Krebs cycle. It could effectively consume free electrons when there was enough carbon dioxide available. It was binding carbon dioxide, and it could serve the anabolic purpose when there were enough free electrons.

At a later stage, membranous release of electrons also established, first by something quite similar to hydrogenosomes. As earth was oxidized, more and more efficient electron acceptors became available: sulfur, iron ions, and eventually oxygen. An electron transport chain established in the membrane of organelles, that eventually resulted in the mitochondrion. Membrane processes could help the Krebs cycle run in the succinate - fumarate direction, and thereby this cycle could be used as a supply of electrons instead of consumption. Instead of using carbon dioxide as an energy source (by reacting with hydrogen, producing methane), it was now an end product, and Krebs cycle was now mainly used for breaking down the end product of glycolysis. Thereby it was producing electrons to drive the electron transport chain in the membrane.

James Trefil, Harold Morowitz, and Eric Smith came to the conclusion that the reverse Krebs cycle established before the version that we see today. I have come to the same conclusion, but I have seen it as an extension of the glycolysis pathway. Both these authors and later
Bill Martin and Nick Lane saw the consumption of electrons in this cycle as primary to life. But the source of electrons was not the glycolysis pathway, as in my scenario, but membrane processes. My theory is based on RNA first, and I see that RNA components are used in electron carriers and in energy carriers like NAD+/NADH. They assume that some metabolism established before RNA was in place, and the problem that this should solve in this way is the creation of nucleotides. But can anybody tell me how they explain the existence of nucleotides in the electron and energy carriers?

Or do they see it as Bayesian Bouffant does: "I don't see a conflict between RNA World and Metabolism First. To me, RNA World says that RNA came before DNA, specifically sequenced proteins and any other complex biopolymers." He then argues that everything based on RNA, without reproductive proteins, were not life, because there was no metabolism. Thereby he can combine the two theories. Even though metabolism was the last component to establish, according to common definitions of life the occurrence of metabolism was tantamount to occurrence of life. But I am sure there was metabolism also in the RNA world, even though none of the ribozymes we have today are engaged in metabolism.

There are different definitions of "RNA world". Some see it as the world that existed before DNA. But I see no need for a separate "DNA world". The transition from RNA to DNA is quite simple, and I assume DNA was used quite early as a more reliable long term storage of genetic information. But RNA was still the building block of catalysts. Translation is a complex process, and it was probably not invented before a lot of metabolic pathways built on ribozymes were in place. That does not mean proteins were not in use. They were probably parts of many ribozymes. We see that even today in some of the remaining ribozymes, e.g. the ribosomes. They may even have played more active roles than what we see in the ribosomes. But as there was no translation, the synthesis of proteins must have been based on a lot of special mechanisms, in much the same way as sugar chains are produced even today.

Velhovsky writes: "There had to be some kind of a shield from harsh environment for life to continue. A protective membrane of some kind before metabolism."

A membrane, yes, but not to protect the organism from the environment. The membrane *is* the organism, and the role of metabolism is to make the membrane grow, and ultimately reproduce by fission. Only later in life's history did the membrane assume the role of a fence, separating the soluble molecules 'owned' by the organism from those belonging to the environment, and preventing the former from diffusing away.

Velhovsky: "I'm also puzzled as to how even the simplest lifeforms developed without information for their development. They need it now how come they didn't need it early on?"

Oh, they needed information. The information just took a different physical form. For example, one gene, or bit of information, might have been "This organism contains much more D-Glyceraldehyde than L-Glyceraldehyde." Another might be "This organism contains acetyl CoA". A third: "This organism does not contain pyruval CoA".

It should be obvious that this kind of 'gene' is automatically inherited when the organism reproduces by fission. The gene is passed from parent to child. The tricky thing is to establish that it is preserved by growth - the gene remains unchanged as the child becomes the parent of the next generation.

The conceptual gulf that separates the 'metabolism first' and 'replication first' mechanisms for the emergence of life continues to cloud the origin of life debate. In the present paper we analyze this aspect of the origin of life problem and offer arguments in favor of the 'replication first' school. Utilizing Wicken's two-tier approach to causation we argue that a causal connection between replication and metabolism can only be demonstrated if replication would have preceded metabolism. Source 1 There are also several metabolism foods which helps to burn fat.

Jim Menegay writes: "The membrane *is* the organism, and the role of metabolism is to make the membrane grow, and ultimately reproduce by fission."

Membrane metabolism is among the most complex of life. The heart of it is membraneous ATPase. Do you anticipate that such systems have occurred from scratch? And if so, how could they have been produced repeatably? I suppose you know about Eigen’s theories about self-regulatory systems consisting of a few molecule types. We could compare such systems with "non-intelligent" electronic regulatory systems. It is obvious that such systems are much more limited than computer controlled systems. It is quite evident that the intelligent electronic systems do not have the same limitations. And with nature’s systems we are talking about systems that are immensely more complex than the most complex systems that humans have built.

The original membrane anabolism could have been quite simple, consuming CO or HCN and yielding (disproportionating to) CO2 and straight chain hydrocarbons with a hydrophilic end group. Think Fischer-Tropsch. No additional energy source required.

Later, a switch could be made to a pathway more like modern biological ones, like reductive TCA or the Wood-Ljungdahl.

As for the ATPase, that arose much later in evolution. However, if you look at the mechanism of, say, joining two phosphorylated lipid heads into a high-energy anhydride, you will see that bringing in a proton or two from across the membrane can make it easy to extract a hydroxyl from one phosphate and neutralize the negative charge on the other.

Modern metabolism is complicated. Primitive metabolism need not have been. In fact, the metabolism-first idea insists that almost all biological complexity arose gradually over time under the direction of natural selection.

I wrote: ". almost all biological complexity arose gradually over time under the direction of natural selection." Hmmm. Since Larry has recently been promoting the work of Michael Lynch on the origin of genome complexity, I suppose I should back away from this a little.

As Lynch points out, complexity in the genome often arises from an accumulation of almost-neutral changes. Natural selection's role in this is nothing like that of the director of a stage-play. Instead it is the looser kind of guidance provided by a referee in a sporting match.

As is the case with the complexity of the modern genome, many aspects of the complexity of modern metabolism are best understood as the result of a co-evolutionary modus vivendi, rather than as a Panglossian optimization of a unified objective function.

This paper from my lab entitled "Metals Promote Sequences of the Reverse Krebs Cycle" might add to the discussion.

Also this blog entry: https://natureecoevocommunity.nature.com/users/62052-joseph-moran/posts/20558-metabolism-before-enzymes

Thanks a lot for your posting!
I just wonder why nothing of the pioneering work from Marcello Guzman (or Scott Martin's group before) has been mentioned in your remarkable new paper in this regard.
cf.:
https://doi.org/10.1089/ast.2009.0356
http://www.guzmanlab.com/publications/Guzman_Chem_Comm_2010.pdf
http://link.springer.com/chapter/10.1007/978-3-642-21625-1_4

Thanks! We did in fact cite the pioneering work of Scot Martin in ref. 32 of our paper. I also cited Guzman's independent work (he was a postdoc in Martin's group), which is essentially studying the same reactions as Martin in further detail, in earlier drafts of the manuscript but it had to be cut due to a 50 reference limit for that journal. Glad you enjoyed the paper!

To those of you who still are concerned about any possibilities for precursory forms of proto-life without replication, here is some pertinent input from the Loren Williams group in pointing out the potentially deceptive idolizing of tentative “privileged functions” in various conventional models in Origins of Life (OoL) research “The Origin of Life: Models and Data”:
[https://link.springer.com/article/10.1007/s00239-017-9783-y]
“A privileged function is an extant biological function that is excised from its biological context, elevated in importance over other functions, and transported back in time to a primitive chemical or geological environment [… but] the simplicity of these models is seen to be an illusion on the realization that the models require fluidity in principles of evolution”.
Most notably, ‘replication’ is one of these illusively simple ‘privileged functions’.

Contrary to the opinion expressed in that paper, however, I do not consider ‘metabolism’ to rank at the very same level in this regard. Metabolism is the “sum total of the chemical processes that occur in living organisms”. By this token, metabolism is more inclusive than the faithful replication of certain molecules, such as RNA or DNA. As far as science can tell and evaluate, life (the living state) is strictly coupled to the physical coherence, chemical functionality and unbroken historical continuity of certain material entities. Strictly following the arrow of time, it is the sum total of chemical reactions that is evolving together with the physical cohesion as material entities, which thus qualify as coherent and historically connected “systems”. To my views (as well as of others), therefore, molecular replication is a subsystem of metabolism but not the other way round.

Shortly after I first read the Lanier & Williams article, I also hit upon another one from the same group, “Frozen in Time: The History of Proteins”:
[https://academic.oup.com/mbe/article/2996746]
Yet, the following passage in the abstract appeared strangely provocative to me:
“Coded proteins originated as oligomers and polymers created by the ribosome, on the ribosome and for the ribosome. […] Protein catalysis appears to be a late byproduct of selection for sophisticated and finely controlled assembly”. These statements, in fact, happen to isolate ‘ribosomal protein synthesis’ as yet another ‘privileged function’, deceptively “transported back in time” before the posited later beginnings of metabolism as a protein-catalyzed phenomenon.

To my views, these statements postulate a partisan selfishness for emerging ribosomes that seems strangely detached from their pivotal system-supporting role at later stages, when the vast majority of proteins made by ribosomes are NOT incorporated in the ribosomal particles themselves. This caveat, in fact, is calling for alternative interpretations about the transition from uncoded to coded protein synthesis when the stochastic variation of peptide chain elongation was strongly reduced. First of all, ribosomes are not acting alone in making proteins they heavily depend on the presence of aminoacylated tRNAs. Arguably, tRNAs are substantially older than ribosomes and may originally have functioned as genuine peptidyl transferases for uncoded peptide/protein synthesis. See:
[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0072225]
From a general systems continuity perspective, therefore, a significant share of early uncoded peptides supposedly began to participate in similar functions to those of coded proteins later on, and main progress resulting from the ribosomal assistance of tRNAs was a matter of vastly increased overall efficiency rather than a qualitative change in the most basic systems properties.

Richard, I can't help but ask what you (or anyone else) would add to the water and if necessary gasses to form RNA from common household items, in this home/classroom experiment of mine:


Introduction

Metabolism can be studied at a systems level using genome-scale metabolic networks that describe the total collection of metabolic reactions required for the generation of biomass and energy, and the general maintenance of homeostasis (O'Brien et al, 2015 Angione, 2019 ). A systems-level understanding of metabolism in complex multicellular organisms requires the reconstruction of metabolic networks at the level of different tissues and, ultimately, individual cells. To understand the function of metabolic networks at the level of individual cells or tissues, it is important to know which parts of the whole network are active in each cell or tissue and which parts are inactive. Single-cell or tissue-level protein expression and enzyme activity data are often not available. However, we and others have shown that mRNA levels provide a powerful proxy to construct context-relevant metabolic network models (Machado & Herrgard, 2014 Robaina Estevez & Nikoloski, 2014 Yilmaz & Walhout, 2016 ).

The nematode Caenorhabditis elegans is a hermaphrodite that develops from embryos through four larval stages to adults via a deterministic lineage. Adult C. elegans are comprised of 959 somatic nuclei that form the major tissues, such as muscle, intestine, and hypodermis (skin). Caenorhabditis elegans is a bacterivore that can be fed individual bacterial strains. Caenorhabditis elegans tissues and metabolism share many functions with mammals. Therefore, it provides a relatively simple model for understanding animal metabolism at a systems level. We have previously reconstructed a C. elegans genome-scale metabolic network model (Yilmaz & Walhout, 2016 ), which we validated using flux balance analysis (FBA) (Raman & Chandra, 2009 ).

Metabolic network models and gene expression data can be integrated at the network level qualitatively, semi-quantitatively, or quantitatively. Qualitative methods typically define context-specific networks by excluding reactions that are not associated with highly expressed genes (Jerby et al, 2010 Agren et al, 2012 Wang et al, 2012 Vlassis et al, 2014 ). Semi-quantitative approaches predict the metabolic state in the form of a flux distribution that avoids flux in reactions associated with lowly expressed genes and may divert flux to reactions associated with highly expressed genes (Becker & Palsson, 2008 Zur et al, 2010 ). Quantitative integration methods that can model tissue metabolism have also been developed (Brandes et al, 2012 Navid & Almaas, 2012 Pandey et al, 2019 ). Such methods fit flux distributions to expression data in a continuous fashion. However, these methods typically depend on a selected objective function such as biomass production, and it is not feasible to capture all metabolic functions with a single objective function.

Here, we developed a new computational pipeline we name MERGE (MEtabolic models Reconciled with Gene Expression), a combined approach (Fig 1A) that starts with a semi-quantitative, network-level integration, evaluates the variability of the resulting flux distribution to obtain tissue-specific metabolic networks, and finally uses these networks to quantitatively integrate local gene expression data at the pathway level to provide relative flux predictions at the reaction and metabolite levels. We used MERGE to study tissue metabolism in the nematode C. elegans based on scRNA-sequencing data obtained at the second larval stage (L2) (Cao et al, 2017 ). We derived functional metabolic network models of seven major tissues for which transcriptomes were generated in the reference study (Cao et al, 2017 ) by aggregating scRNA-seq data from thousands of individual cells that originate from the same tissue in a population of animals. Our results recapitulate known tissue functions, reveal metabolic properties that are shared with similar tissues in human, and predict numerous novel metabolic functions. MERGE provides a versatile tool for the integration of high-quality gene expression data with genome-scale metabolic network models that provides an important step toward the quantitative modeling of metabolism at the level of individual cells.

Figure 1. Overview of the updated Caenorhabditis elegans metabolic network model and gene expression dataset used to derive tissue-relevant functions

  1. Computational pipeline to predict tissue function using tissue-level gene expression data.
  2. Cartoon outlining the update of the C. elegans metabolic network model. GPR, gene-protein-reaction association.
  3. Conceptual overview of integration of iCEL1314 with four categories of genes: highly, moderately, lowly, and rarely expressed. The predicted flux state in a tissue is a flux distribution that trails reactions associated with highly expressed genes in that tissue, while avoiding those associated with lowly expressed and rarely expressed genes. Circles and arrows indicate metabolites and reactions, respectively. Black arrows show flux, with thicker arrows indicating higher flux. Boxes depict enzymes encoded by genes that have expression levels indicated by color. Dashed arrows indicate reactions with no flux in the preliminary flux distribution stage according to Fig 2B but are then detected as latent reactions and are forced to carry flux when possible (see text for details).
  4. To derive tissue-relevant metabolic network functions, a gene expression dataset obtained with single-cell RNA-seq of L2 animals was used (Cao et al, 2017 ). Single-cell data were combined by the authors to provide high-quality gene expression data for the seven tissues shown.
  5. Distribution of metabolic genes in iCEL1314 in different expression categories in each individual tissue and in all tissues combined, with colors as in (B). For the combination of data, the union set of highly expressed genes and the intersection set of rarely and lowly expressed genes are illustrated with corresponding colors. One gene which was lowly expressed in some tissues and rarely expressed in others is not shown in the combined data.

Biology GP2

The L-D reactions need CO2 and light energy, and the L-IND reactions needs water and O2.

The L-D reactions require light energy and water, and the L-IND reactions require ATP, NADPH and CO2.

The L-D reactions can only occur during daylight, and the L-IND reactions can only occur during the night.

They produce ATP and NADPH.

They release oxygen as waste.

ATP and NADPH are produced in both reactions.

ATP and NADPH are used in both reactions.

ATP and NADPH are produced in the light-dependent reactions and used in the light-independent reactions.

During the citric acid cycle, what happens to acetyl-CoA?
It enters the citric acid cycle and gains carbon dioxide to form citric acid, and gains more carbon dioxide through redox reactions to form a 4-carbon molecule.

It enters the citric acid cycle and associates with a 4-carbon molecule, forming citric acid, and then through redox reactions regenerates the 4-carbon molecule.

It enters glycolysis and associates with a 5-carbon molecule through redox reactions, forming another acetyl-CoA molecule.

Which statement could be categorized only in the anaerobic section of the Venn diagram?

is performed by eukaryotes

Which process occurs in the structures that are labeled X?
lactic acid fermentation

Both require light energy.

Both start with glycolysis.

Glycolysis produces ATP by oxidizing water.

Glycolysis produces ATP and pyruvate by oxidizing glucose and NAD+.

Glycolysis produces pyruvate, ATP, and NADH by oxidizing glucose.

What is the net ATP production at this stage of cellular respiration?
2 ATP


Beyond the two cultures: rethinking science and the humanities

Cross-disciplinary cooperation is needed to save civilization.

  • There is a great disconnect between the sciences and the humanities.
  • Solutions to most of our real-world problems need both ways of knowing.
  • Moving beyond the two-culture divide is an essential step to ensure our project of civilization.

For the past five years, I ran the Institute for Cross-Disciplinary Engagement at Dartmouth, an initiative sponsored by the John Templeton Foundation. Our mission has been to find ways to bring scientists and humanists together, often in public venues or — after Covid-19 — online, to discuss questions that transcend the narrow confines of a single discipline.

It turns out that these questions are at the very center of the much needed and urgent conversation about our collective future. While the complexity of the problems we face asks for a multi-cultural integration of different ways of knowing, the tools at hand are scarce and mostly ineffective. We need to rethink and learn how to collaborate productively across disciplinary cultures.


The processes of Catabolism and Anabolism

All anabolic processes are constructive, using basic molecules within an organism, which then create compounds that are more specialized and complex. Anabolism is also known as ‘biosynthesis’, whereby an end product is created from a number of components. The process requires ATP as a form of energy, converting kinetic energy into potential energy. It is considered an endergonic process, meaning it is a nonspontaneous reaction, that requires energy 2 . The process uses up energy to create the end product, such as tissues and organs. These complex molecules are required by the organism, as a means of growth, development and cell differentiation 3 . Anabolic processes do not use oxygen.

Catabolic processes on the other hand are destructive, where more complex compounds are broken down and energy is released in the form of ATP or heat – instead of consuming energy as in anabolism. Potential energy is converted into kinetic energy from stores in the body. This results in the formation of the metabolic cycle, whereby catabolism breaks down the molecules that are created through anabolism. An organism then often uses many of these molecules, which are used again in a variety of processes. Catabolic processes do utilize oxygen.

At a cellular level, anabolism uses monomers to form polymers, resulting in the formation of more complex molecules. A common example is the synthesis of amino acids (the monomer) into larger and more complex proteins (the polymer). One of the most common catabolic processes is digestion, where ingested nutrients are converted into more simple molecules, that an organism can then use for other processes.

Catabolic processes act to break down many different polysaccharides, such as glycogen, starches and cellulose. These are converted into monosaccharides, which include glucose, fructose and ribose, used by organisms as a form of energy. Proteins that are created by anabolism, are converted to amino acids through catabolism, for further anabolic processes. Any nucleic acids in DNA or RNA, become catabolized into smaller nucleotides, that are a component of the natural process of healing as well as used for energetic needs.

Organisms are classified on the basis of type of Catabolism they use 4 :

  • Organotroph An organism that acquires its energy from organic sources
  • Lithotroph → An organism that acquires its energy from inorganic substrates
  • Phototroph → An organism that acquires its energy from sunlight

Additional data files

The following additional data files are available with the online version of this paper: supplemental material in terms of results, discussion and methods and supplementary figures S1-S7 (Additional data file 1) a table listing the complete and partial genomes used in this study (Additional data file 2) a table listing the conservation of individual enzymes (Additional data file 3) a table listing enzymes restricted to either bacteria or eukaryotes (Additional data file 4) a table showing the conservation of 118 metabolic pathways analyzed in this study (Additional data file 5) a table listing the modularity of 166 metabolic pathways analyzed in this study (Additional data file 6) a table listing the conservation of 25 regulatory pathways defined by KEGG (Additional data file 7).


Ω-Amidase: an underappreciated, but important enzyme in l -glutamine and l -asparagine metabolism relevance to sulfur and nitrogen metabolism, tumor biology and hyperammonemic diseases

In mammals, two major routes exist for the metabolic conversion of l -glutamine to α-ketoglutarate. The most widely studied pathway involves the hydrolysis of l -glutamine to l -glutamate catalyzed by glutaminases, followed by the conversion of l -glutamate to α-ketoglutarate by the action of an l -glutamate-linked aminotransferase or via the glutamate dehydrogenase reaction. However, another major pathway exists in mammals for the conversion of l -glutamine to α-ketoglutarate (the glutaminase II pathway) in which l -glutamine is first transaminated to α-ketoglutaramate (KGM) followed by hydrolysis of KGM to α-ketoglutarate and ammonia catalyzed by an amidase known as ω-amidase. In mammals, the glutaminase II pathway is present in both cytosolic and mitochondrial compartments and is most prominent in liver and kidney. Similarly, two routes exist for the conversion of l -asparagine to oxaloacetate. In the most extensively studied pathway, l -asparagine is hydrolyzed to l -aspartate by the action of asparaginase, followed by transamination of l -aspartate to oxaloacetate. However, another pathway also exists for the conversion of l -asparagine to oxaloacetate (the asparaginase II pathway). In this pathway, l -asparagine is first transaminated to α-ketosuccinamate (KSM), followed by hydrolysis of KSM to oxaloacetate by the action of ω-amidase. One advantage of both the glutaminase II and the asparaginase II pathways is that they are irreversible, and thus are important in anaplerosis by shuttling 5-C (α-ketoglutarate) and 4-C (oxaloacetate) units into the TCA cycle. In this review, we briefly mention the importance of the glutaminase II and asparaginase II pathways in microorganisms and plants. However, the major emphasis of the review is related to the importance of these pathways (especially the common enzyme component of both pathways—ω-amidase) in nitrogen and sulfur metabolism in mammals and as a source of anaplerotic carbon moieties in rapidly dividing cells. The review also discusses a potential dichotomous function of ω-amidase as having a role in tumor progression. Finally, the possible role of KGM as a biomarker for hyperammonemic diseases is discussed.

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The Denialist Playbook

Once upon a time, in a land not far away, there was a horrible virus that instilled terror in every town and home. Although most people who became infected showed no symptoms or recovered within a week, in a small fraction of cases the illness progressed, causing loss of reflexes and muscle control, paralysis and, sometimes, death.

Children were especially vulnerable, so parents watched anxiously for any sign of infection, often keeping them away from swimming pools, movie theaters, bowling alleys, anywhere where there were crowds and the dreaded microbe might lurk. Travel and business were sometimes curtailed between places with outbreaks, and public health authorities imposed quarantines on healthy people who may have been exposed, in order to halt the spread of the disease. In the first half of the 1950s, with no cure and no vaccine, more than 200,000 Americans were disabled by the poliovirus. The virus was second only to the atomic bomb as to what Americans feared most.

Then, on April 12, 1955, public health officials at the University of Michigan announced that a &ldquosafe, effective, and potent&rdquo vaccine had been found. This set off a national celebration that recalled the end of World War II. Church bells rang, car horns honked, people wept with relief. President Eisenhower invited the vaccine&rsquos inventor, Jonas Salk, to the White House. In a Rose Garden ceremony, the former Supreme Allied Commander told the scientist in a trembling voice, &ldquoI should like to say to you that when I think of the countless thousands of American parents and grandparents who are hereafter to be spared the agonizing fears of the annual epidemic of poliomyelitis, when I think of all the agony that these people will be spared seeing their loved ones suffering in bed, I must say to you I have no words in which adequately to express the thanks of myself and all the people I know&mdashall 164 million Americans, to say nothing of all the people in the world that will profit from your discovery.&rdquo

But, alas, not everyone joined the party and expressed such gratitude. One group in particular did not welcome the vaccine as a breakthrough. Chiropractors actively opposed the vaccination campaign that followed Salk&rsquos triumph. Many practitioners dismissed the role of contagious pathogens and adhered to the founding principle of chiropractic that all disease originated in the spine. Just a few years after the introduction of the vaccine, as the number of polio cases was declining rapidly, an article in the Journal of the National Chiropractic Association asked, &ldquoHas the Test Tube Fight Against Polio Failed?&rdquo It recommended that, rather than take the vaccine, once stricken, &ldquoChiropractic adjustments should be given of the entire spine during the first three days of polio.&rdquo

Opposition to the polio vaccine and to vaccination in general continued in the ranks such that even four decades later, long after polio had been eradicated from the United States, as many as one third of chiropractors still believed that there was no scientific proof that vaccination prevents any disease, including polio. That belief and resistance continues to this day, with some chiropractors campaigning against state vaccination mandates.

I was shocked when I first learned about chiropractors&rsquo opposition to the polio vaccine. The vaccine is widely viewed as one of medicine&rsquos greatest success stories: Why would anyone have opposed it? My shock turned into excitement, however, when I began to recognize the chiropractors&rsquo pattern of arguments was uncannily similar to those I was familiar with from creationists who deny evolutionary science. And once I perceived those parallels, my excitement became an epiphany when I realized that the same general pattern of arguments&mdasha denialist playbook&mdashhas been deployed to reject other scientific consensuses from the health effects of tobacco to the existence and causes of climate change. The same playbook is now being used to deny facts concerning the COVID-19 pandemic.

In brief, the six principal plays in the denialist playbook are:

  1. Doubt the Science
  2. Question Scientists&rsquo Motives and Integrity
  3. Magnify Disagreements among Scientists and Cite Gadflies as Authorities
  4. Exaggerate Potential Harm
  5. Appeal to Personal Freedom
  6. Reject Whatever Would Repudiate A Key Philosophy

The purpose of the denialism playbook is to advance rhetorical arguments that give the appearance of legitimate debate when there is none. My purpose here is to penetrate that rhetorical fog, and to show that these are the predictable tactics of those clinging to an untenable position. If we hope to find any cure for (or vaccine against) science denialism, scientists, journalists and the public need to be able recognize, understand and anticipate these plays.

To illustrate how the playbook works&mdashand sadly, it is very effective &ndashI will break down the chiropractor and creationist versions, which have endured for many decades in spite of overwhelming evidence, and point out parallels to the coronavirus rhetoric.

THE PLAYBOOK

1. Doubt the Science

The first tactic of denialism is to raise objections to scientific evidence or interpretations. This may take the form of seemingly legitimate specific arguments against a scientific claim. For example, chiropractors sought other explanations besides vaccine efficacy to account for the decline of infectious diseases: &ldquoThe Center for Disease Control statistics make it clear that the majority of diseases that are now routinely vaccinated against were disappearing before either the cause was discovered or the vaccine developed,&rdquo stated a 1995 letter to the editor of Dynamic Chiropractic magazine. In polio&rsquos case, this argument does not hold up against the facts that: (a) the disease was surging in the 1950s (b) the vaccine was proven effective in a massive double-blind, placebo-controlled trial and (c) infections declined precipitously after the introduction of the vaccine.

Alternatively, some statements are blanket arguments against an entire scientific discipline. For example, Henry Morris, whose 1961 book The Genesis Flood is credited with reviving the creationism movement, alleged: &ldquoSince there is no real scientific evidence that evolution is occurring at present or ever occurred in the past, it is reasonable to conclude that evolution is not a fact of science, as many claim. In fact, it is not even science at all, but an arbitrary system built upon faith in universal naturalism.&rdquo

2. Question Scientists&rsquo Motives and Integrity

As a growing body of consistent evidence can be hard to explain away, one fallback is to impugn the source. In the vaccination arena, this often takes the form of alleging financial conflicts of interest on the part of scientists, greed on the part of manufacturers, and complicity of government officials. &ldquoIt appears that the scientific foundation on which these vaccines have been erected is fragile enough that only compulsory laws, expensive public relations efforts, outrageous propaganda, and expensive advertising must ensue for compliance to be maintained,&rdquo wrote one author in American Chiropractor. Salk, by the way, filed no patent.

In the evolution arena, scientists are often accused of being part of a conspiracy to undermine religion through educational systems. Kenneth Cumming, of the Institute for Creation Research, objected to a PBS series on evolution by drawing a parallel to the 9/11 attackers: &ldquoAmerica is being attacked from within through its public schools by a militant religious movement of philosophical naturalists (i.e., atheists) under the guise of secular Darwinism. Both desire to alter the life and thinking of our nation.&rdquo One noteworthy counter to such assertions is the Clergy Letter Project, which has gained the support of more than 15,000 Christian clergy for the teaching of evolution.

3. Magnify Disagreements among Scientists and Cite Gadflies as Authorities

In all scientific arenas, there is honest disagreement about the interpretation of evidence. However, these differences are deliberately inflated by denialists to imply a lack of consensus on more fundamental points, while often propounding the contradictory views of a few unqualified outliers. An example of the latter is how some chiropractors have seized on the anti-vaccination stance of one critic, Viera Scheibner. Her claim that there is no evidence for vaccine efficacy or safety is cited repeatedly, while overlooking the fact that her training and expertise is in geology, not medicine.

In the evolution arena, differences of interpretation among scientists are relished by antievolution voices. For example, the initial discovery of a new fossil hominid usually elicits some different interpretations and expressions of uncertainty in the scientific community. Creationists often mischaracterize these normal dynamics of scientific discourse as &ldquoskepticism&rdquo over the significance of such finds so as to discount them. By overblowing legitimate disagreements and propounding &ldquoalternatives&rdquo to evolution, denialists often make appeals to &ldquoteach the controversy,&rdquo when no such controversy exists in the scientific community. Different interpretations of a fossil do not negate the discomfiting evidence for the antiquity of human ancestors.

Antievolution leaders in the U.S. also include a small number of scholars whose credentials are in other disciplines. For example, the abovementioned Henry Morris was an engineer, not a biologist. Phillip E. Johnson, whose book Darwin on Trial inspired many adherents to the intelligent design movement, was a law professor with no formal training in biology.

A lack of credentials or status within the scientific community is often seen not as a liability but as a virtue. Scientists Pascal Diethelm and Martin McKee note, &ldquoDenialists are usually not deterred by the extreme isolation of their theories, but rather see it as the indication of their intellectual courage against the dominant orthodoxy and the accompanying political correctness, often comparing themselves to Galileo.&rdquo

4. Exaggerate Potential Harm

When the evidence contradicts a position, another recourse is to try to incite fear. No vaccine or medicine is 100 percent safe, without any risk of side effects. Chiropractors have long emphasized the potential side effects of vaccines, for example in a statement in Dynamic Chiropractic offering a litant of possible effects: &ldquodeath, encephalopathy, demyelinating diseases, brachial neuritis, Guillain-Barré syndrome, infections generated by vaccine agents, anaphylaxis, subacute sclerosing panencephalitis, seizure disorder, optic neuritis, arthritis,&rdquo and so on. However, they generally fail to acknowledge the serious consequences of infections that would be prevented by vaccination.

But what harm could arise from knowing a bit about evolution? Well, Hitler, of course! &ldquoOf the many factors that produced the Nazi Holocaust and World War II,&rdquo wrote one critic in the Journal of Creation, &ldquoone of the most important was Darwin&rsquos notion that evolutionary progress occurs mainly as a result of the elimination of the weak in the struggle for survival.&rdquo It is an oft-repeated argument that has no bearing of course on the veracity of Darwin&rsquos theory.

Vaccination foes have lobbed similar accusations, likening physicians who administer vaccines to Nazi doctors and alleging that vaccines violate the 1947 Nuremberg Code of medical ethics.

5. Appeal to Personal Freedom

If fear is not persuasive, there is another fallback position that resonates strongly with Americans: the freedom of choice. The American Chiropractic Association leaned on this cherished notion when it established its official vaccination policy:

&ldquoSince the scientific community acknowledges that the use of vaccines is not without risk, the American Chiropractic Association supports each individual&rsquos right to freedom of choice in his/her own health care based on an informed awareness of the benefits and possible adverse effects of vaccination. The ACA is supportive of a conscience clause or waiver in compulsory vaccination laws&hellip providing an elective course of action regarding vaccination.&rdquo

Likewise, the International Chiropractic Association &ldquoquestions the wisdom of mass vaccination programs&rdquo and views compulsory programs as an infringement of &ldquothe individual&rsquos right to freedom of choice.&rdquo

Similarly, the teaching of evolution in public schools is viewed as an assault upon the religious freedom of those who oppose it. Those holding this view advocate for disclaimers on textbooks (&ldquojust a theory&rdquo), the teaching of &ldquoalternative&rdquo views of the history of life (Genesis or intelligent design), or the freedom to opt out of the evolution curriculum of biology classes.

Notably, the U.S. Supreme Court has rejected challenges to compulsory vaccination partly on the grounds that individual belief cannot subordinate the safety of an entire community. And U.S. courts have repeatedly struck down attempts to subvert the teaching of evolution as religiously motivated and violations of the establishment clause of the First Amendment of the U.S. Constitution.

6. Reject Whatever Would Repudiate a Key Philosophy

Once the courts have spoken, and the scientific evidence grows to be overwhelming, one might think that denialists would be out of plays. But there is one last line of defense that reveals the nucleus of denial: It is not that some scientific claim is untrue it is that it is unacceptable in light of some philosophical commitment. The science must be summarily rejected.

Chiropractic was founded in the early 20th century on the assertion that all disease has its origins in misalignments of the spine. &ldquoChiropractors have found in every disease that is supposed to be contagious, a cause in the spine,&rdquo claimed Bartlett Joshua Palmer, the son of chiropractic founder Daniel David Palmer. Acceptance of germ theory and vaccination would repudiate the founding premise of the profession that all disease stems from vertebral misalignments. Therefore, that premise cannot be questioned.

With respect to evolution, Henry Morris made it plain: &ldquoWhen science and the Bible differ, science has obviously misinterpreted its data.&rdquo

Any credence granted to evolutionary science is a threat to a worldview based on interpretation of the Bible David Cloud, a publisher of Bible study materials argues: &ldquoIf the Bible does not mean what it says, there is no way to know what it does mean.

Historian of science and author Naomi Oreskes has coined a term for this stance: &ldquoimplicatory denial&rdquo&mdashthe rejection of scientific findings because we don&rsquot like their implications.

As these positions are reinforced by family or community, they harden into part of one&rsquos identity. &ldquoIn this way, cultural identity starts to override facts,&rdquo Norwegian climate psychologist Per Espen Stoknes has said. &ldquoAnd my identity trumps truth any day.&rdquo

Psychologists Elliot Aronson and Carol Tavris write in the Atlantic: &ldquo[W]hen people feel a strong connection to a political party, leader, ideology, or belief, they are more likely to let that allegiance do their thinking for them and distort or ignore the evidence that challenges those loyalties.&rdquo

The denialist playbook is now erupting around the coronavirus. Although COVID-19 is new, the reactions to public health measures, scientific claims, and expert advice are not. Attitudes and behaviors concerning the threat posed by the coronavirus (doubting the science), the efficacy of lockdowns and mask wearing (freedoms being eroded) and alternative treatments (gadflies over experts) are being driven as much or more by rhetoric than by evidence.

Polls indicate that despite the devastating health and economic impacts of the pandemic, with respect to a potential vaccine we are nowhere near as united as Americans were in 1955. But as epidemiologist Michael Osterholm noted in June, &ldquoEventually there won't be any blue states or red states. There won't be any blue cities or red rural areas. It'll all be COVID colored.&rdquo

Now, sadly, there is no denying that.

ABOUT THE AUTHOR(S)

Sean B. Carroll is Distinguished University Professor of Biology at the University of Maryland and vice president for science education at the Howard Hughes Medical Institute. His latest book is A Series of Fortunate Events: Chance the Making of the Planet Life (Princeton University Press).


Sandwalk

There are many ideas about the origin of life but the only ones that concern me are the scientific ones. The 21st century debate mostly involves smokers vs. soupers [Changing Ideas About The Origin Of Life].

Soupers are people who believe in some version of the primordial soup. They believe that life originated in a solution of organic molecules and the most primitive way of getting energy was by oxidizing these molecules. For them, the first biochemical pathways were like glycolysis. Most of them think that complex organic molecules were delivered to Earth by asteroids [see NASA Confusion About the Origin of Life].

Smokers, on the other hand, promote an origin of life scenario that relies on the chemistry surrounding hydrothermal vents on the ocean floor. These environments favor reactions that build up organic molecules from inorganic substrates like hydrogen and carbon dioxide. In this case, the most primitive reactions are simple oxidation-reduction reactions and the most primitive pathways are biosynthesis pathways, not catabolism. This view is often referred to as "metabolism first" [Metabolism First and the Origin of Life].

I'm a big fan of metabolism first and especially the versions promoted by Bill Martin and Nick Lane. I think it's the only reasonable model for the origin of life.

A reader alerted me to a paper published last year by all the big names in metabolism first [Sousa et al., 2013]. It's an excellent paper. You should read this paper if you really want to learn about modern thinking on the origin of life problem. The biochemistry is complicated but well worth the effort.

I don't have time to explain it all. Here's a teaser .

At first sight, the idea that chemiosmosis is a very ancient means of energy transduction might seem counterintuitive. More familiar to many is the old (and popular) doctrine that the most ancient pathway of energy metabolism is a fermentation such as glycolysis [77], an idea that goes back at least to Haldane [2] and hence arose long before anyone had a clue that biological energy can be harnessed in a manner that does not involve substrate-level phosphorylations and ‘high-energy’ bonds [149,150]. In modern life, all biological energy in the form of ATP comes ultimately from chemiosmotic coupling [151], the process of charge separation from the inside of the cell to the outside, and the harnessing of that electrochemical gradient via a coupling factor, an ATPase of the rotor–stator-type. It was not until the 1970s that it became generally apparent that Mitchell [152] was right, his Nobel prize coming in 1978, and it is hard to say when it became clear to microbiologists that all fermentative organisms are derived from chemiosmotic ancestors. We also note that Mitchell's consideration of the problem of the origin of life introduced key concepts of his later chemiosmotic hypothesis, including a definition of life as process, and the idea of vectorial catalysis across a membrane boundary that is inseparable either from the environment or from the organism itself [153].

The maxim that glycolysis is ancient might be an artefact of experience, since it was the first pathway both to be discovered and that we learned in college in that sense, it really is the oldest. When one suggests that chemiosmotic coupling in methanogens or acetogens might be ancient, many listeners and readers shy away, mainly because the pathways are unfamiliar and often entail dreaded cofactor names.

31 comments:

Hi Larry, Thank you for this block quote. If you ever decide to write a *metabolism first for biochemical dummies* essay, then I would check that out. Peace, Jim

You should mention that the paper is free.

There's more being published on this alkaline hydrothermal vent idea, recently, Larry. These should be right up your alley too:

Membrane bioenergetics are universal, yet the phospholipid membranes of archaea and bacteria—the deepest branches in the tree of life—are fundamentally different. This deep divergence in membrane chemistry is reflected in other stark differences between the two domains, including ion pumping and DNA replication. We resolve this paradox by considering the energy requirements of the last universal common ancestor (LUCA). We develop a mathematical model based on the premise that LUCA depended on natural proton gradients. Our analysis shows that such gradients can power carbon and energy metabolism, but only in leaky cells with a proton permeability equivalent to fatty acid vesicles. Membranes with lower permeability (equivalent to modern phospholipids) collapse free-energy availability, precluding exploitation of natural gradients. Pumping protons across leaky membranes offers no advantage, even when permeability is decreased 1,000-fold. We hypothesize that a sodium-proton antiporter (SPAP) provided the first step towards modern membranes. SPAP increases the free energy available from natural proton gradients by

60%, enabling survival in 50-fold lower gradients, thereby facilitating ecological spread and divergence. Critically, SPAP also provides a steadily amplifying advantage to proton pumping as membrane permeability falls, for the first time favoring the evolution of ion-tight phospholipid membranes. The phospholipids of archaea and bacteria incorporate different stereoisomers of glycerol phosphate. We conclude that the enzymes involved took these alternatives by chance in independent populations that had already evolved distinct ion pumps. Our model offers a quantitatively robust explanation for why membrane bioenergetics are universal, yet ion pumps and phospholipid membranes arose later and independently in separate populations. Our findings elucidate the paradox that archaea and bacteria share DNA transcription, ribosomal translation, and ATP synthase, yet differ in equally fundamental traits that depend on the membrane, including DNA replication.

The Drive to Life on Wet and Icy Worlds
Russell Michael J., Barge Laura M., Bhartia Rohit, Bocanegra Dylan, Bracher Paul J., Branscomb Elbert, Kidd Richard, McGlynn Shawn, Meier David H., Nitschke Wolfgang, Shibuya Takazo, Vance Steve, White Lauren, and Kanik Isik.
ABSTRACT

This paper presents a reformulation of the submarine alkaline hydrothermal theory for the emergence of life in response to recent experimental findings. The theory views life, like other self-organizing systems in the Universe, as an inevitable outcome of particular disequilibria. In this case, the disequilibria were two: (1) in redox potential, between hydrogen plus methane with the circuit-completing electron acceptors such as nitrite, nitrate, ferric iron, and carbon dioxide, and (2) in pH gradient between an acidulous external ocean and an alkaline hydrothermal fluid. Both CO2 and CH4 were equally the ultimate sources of organic carbon, and the metal sulfides and oxyhydroxides acted as protoenzymatic catalysts. The realization, now 50 years old, that membrane-spanning gradients, rather than organic intermediates, play a vital role in life's operations calls into question the idea of “prebiotic chemistry.” It informs our own suggestion that experimentation should look to the kind of nanoengines that must have been the precursors to molecular motors—such as pyrophosphate synthetase and the like driven by these gradients—that make life work. It is these putative free energy or disequilibria converters, presumably constructed from minerals comprising the earliest inorganic membranes, that, as obstacles to vectorial ionic flows, present themselves as the candidates for future experiments.

This alkaline hydrothermal vent theory seems to be gaining quite a lot of support recently. It is also interesting to see how the theory can help shed light on some long-standing questions regarding the split between bacteria and archaea.

I've read lots of recent papers but I hadn't seen the massive review that I mentioned in my post.

What puzzles me is that these ideas have been around for a long time but most scientists are still soupers and most biochemistry teachers still teach the old primordial soup nonsense.

I certainly like the idea that chemiosmotic coupling is more ancient than 'solution biochemistry'. A physical entity of fixed location and reasonably consistent conditions to either side seems more plausible than free-floating reactions, which would rapidly descend into thermodynamic wells, and lose products to diffusion. I'm less convinced of the early involvement of polypeptides (as opposed to the incorporation of amino acids into pre-protein biosynthetic pathways).

Larry said:
What puzzles me is that these ideas have been around for a long time but most scientists are still soupers and most biochemistry teachers still teach the old primordial soup nonsense.

I believe there is a certain sluggishness in the scientific 'system' how long before the Big Bang theory really took hold?

Maybe my 'position' as an interested but irresponsible layman has made me less reluctant to latch on to new and surprising ideas? Or maybe scientists feel they have to hedge their bets until the new horse has proven itself beyond reasonable doubt? I'v been a stacker for a long time now and have been waiting for news like this.

I remember reading an essay on how scientific progress is influenced by resistance to new ideas, and how that resistance eventually may help to avoid selling the pelt before the bear has been shot. So I guess that's more or less how it is and probably better than any alternative.

Not my best, I am forever in a struggle with the English language.

The most interesting thing to me is the centrality of ATP. There doesn't appear to be a strong chemical or energetic reason for that purine, as opposed to another, or a non-purine, to be at the end of ATP, NAD, FAD, CoA etc. But of course it has the special property that, chained polymerically through ribose-phosphate linkages, it can bind a chain of polyuridine running antiparallel, likewise mixed random monomers of those two bases can bind a complementary sequence. This preferentially increases the half-life of these molecules over bases and chain configurations (eg mixed L and D ribose) lacking a complement. So the first nucleic acids worth the name may have actually been formed from hybridisation of short complementary (and probably cyclic) sequences, possibly initially restricted to two bases, and fixing chirality at the outset even before replication was achieved.

In this scenario, it's the 'informatic' role that fixes adenosine, not the energetic one. When the authors talk of the 'acetyl CoA' pathway, for example, it would not seem to be favoured unless there was a role for that specific purine already in place - ie, in the post-RNA world.

Of course you need amino acids to make purines, and this may be, as the authors suggest, a 'fossil' of primordial biochemistry. But the polymerisation of those amino acids into catalysts, I think, awaited a means of specification, which the nucleic acids provided, and which their competitive replication allowed to be tuned.

I love this website's animations about the self-assembly of fatty acids and micelles then membranes and protocells. http://exploringorigins.org/protocell.html I'd love to hear what you think of this. It certainly seems more smoker than souper to me.

I know genetic connectivity and population studies are being done at deep sea vents and seeps. I'm truly excited to learn how this information might inform knowledge of LUCA and likely locations of the origin of life. Here's some info about research on cold seeps http://www.charlotteobserver.com/2014/07/13/5031223/nc-state-duke-university-team.html#.VDAjDWddWSo The NCSU researchers I know (Eggleston and McVeigh) are mostly working on larval movement and the Duke researchers are doing more of the genetic work in these deep sea environments.

Larry,
We’ve been over this many times…
How does your view metabolism first, differ from “the primordial soup sense”…or the pathetic vent worshipers like Rumraket…? I don’t get it…Neither theory has any merit and has nothing to do with real science…What I mean by that is that no experiment has even shown that any of these theories can be considered scientific…Calling them such is like Chris B believing that “the flagellum evolved from a type III secretion complex, common among bacteria. This is based on DNA/protein sequence and functional similarities among type III secretion systems and their corresponding proteins in the flagellum”… This theory may seem pretty good to a moron who either knows nothing about the theme or like many morons here want it to be true… it is pretty clear to most people that an automobile has roots or “has evolved” from a bicycle… however… nobody believes that the more complex parts in an automobile somehow self-improved and excelled in complexity froin m a simple bike…
Please tell me why you chose to believe this pile of crap…

Quest makes a good point. It would be simpler if we just went back to saying god did it.

Yeah, but then we would just argue about which god. :)

Hey Quest, please tell us the details of your alternative, scientific hypothesis of how, when, and where life originated on Earth.

That much is obvious. You should have just left it at that.

Please tell me why you chose to believe this pile of crap

Been there. Done that. Time wasted.

nobody believes that the more complex parts in an automobile somehow self-improved and excelled in complexity froin m a simple bike…

What does this tell you about its relevance to biology?

Actually Quest, there is a good body of peer reviewed scientific literature showing the similarities between bacterial type II secretion systems and the flagellum. Literature you are completely unaware of. You never even attempt to engage in a scientific and rational manner. You pretend to understand things you know nothing about, and leave comments strewn with ad hominem attacks and declarations that you are right- with zero evidence to support yourself.

You belittle and ridicule the homology between Type III secretion systems and the flagellum not because of some alternative scientific hypothesis for which you have any evidence, but because the flagellum is a favorite place for you to hide your invisible magical spook.

That is also why you so predictably jumped on this post. Dr. Moran went clickety-clack across your bridge again by talking about plausible origins of lfe, another favorite gap to put your invisible magical spook. So you had to submit another one of your content-free "refutations" of science.

Pest:" This theory may seem pretty good to a moron"

Why, no, apparently not. After all, Quest doesn't believe it.

Pest: "nobody believes that the more complex parts in an automobile somehow self-improved and excelled in complexity froin m a simple bike…"

Pest, have you ever noticed that automobiles don't have sex organs? (Hint: truck nuts are not real, they're made of plastic.) Since they don't have sex organs, they can't reproduce, right? Since they don't produce offspring, their offspring can't have mutations, right? Since they don't reproduce, there can't be natural selection, that is, differential reproduction rates for different mutants, right? Since their offspring that don't exist can't have mutations, there are no mutations for biologists to study, right?

Could it be that perhaps the fact that automobiles can't have offspring with mutations, but organisms do have offspring with mutations, might perhaps explain why biologists think the first did not evolve, but the second did?

Chris B, Dinogene and the rest,

I personally think it is pretty hilarious that you believe that life originated by some accident which neither of you or anybody else considering himself intelligent can't replicate. I think this is rather embarrassing not to be able to replicate it and still believe that damn luck did what you can't.

If there was a Nobel Prize for stupidity. you would be the front runners. lol

Quest, once again you demonstrate how ill-equipped you are for rational discourse.

"I personally think it is pretty hilarious that you believe that life originated by some accident"

Nobody but youmade this claim.

"which neither of you or anybody else considering himself intelligent can't replicate. "

Whether or not a human being can create new life in the lab has no relevance whatsoever as to the validity of evolution. Where do you get these irrational ideas?

Been there. Done that. Time wasted."
Actually. this is the first time you responded to my demands for evidence for your beliefs on the theme..I didn't expect anything scientific. because there is no such thing and you know it. and that is why you never did respond. What a pity.

"I didn't expect anything scientific"

In response to an entry discussing a summary paper about metabolism-first origin of life.
Fucking classic.
You just can't make this stuff up.

Not sure if this went through so putting in again Part 1 of 2.
Many microbes are found in extreme environments, especially Archaea which tend to like toxic conditions. These types of Bacteria and Archaea are the ones that probably were the earliest ones when Earth was toxic. When comets were bringing in toxic organic molecules like formaldehyde, although I am not much of a fan of such "Act of God' theories for how life started here.

The type of protocells which must have developed on the early Earth must have found a way to utilise the toxic compounds available, just like organisms find ways to survive now. Thus I think that if people are looking for methanogens such as on Mars where the production of methane was sought as evidence of life, they may have it the wrong way around. What is needed is an organism that can somehow utilise toxic conditions and/or a toxic atmosphere, not ones that can produce it! Such organisms that may have existed for the first billion years of toxic Earth, surviving and feeding off what was available! The organisms I suggest may have been involved were anaerobic methanotrophs as there was no oxygen but a lot of methane in the early toxic Earth. Wikipedia describes these ((https://en.wikipedia.org/wiki/Anaerobic_oxidation_of_methane). Anaerobic oxidation of methane occurs in anoxic marine and freshwater sediments. During AOM methane is oxidized with different terminal electron acceptors such as sulfate, nitrate, nitrite and metals. And they produce CO2 which became the next major component of the early atmosphere to be utilised by unicellular organisms. Sadly not much is known about them.

The pursuit of ET might best be investigated, given our knowledge of life on Earth, in terms of the production of oxygen for an advanced evolutionary atmosphere, or the production of carbon dioxide from methane by methanotrophs for an earlier, toxic one. All that is needed for the production of proteins is apparently a puddle undergoing drying and wetting. However I am a skeptic about the prospects of there being life on any other planet!

References given by Wikipedia worth following up:
Ettwig, K. F. Butler, M. K. Le Paslier, D. Pelletier, E. Mangenot, S. Kuypers, M. M. M. Schreiber, F. Dutilh, B. E. Zedelius, J. De Beer, D. Gloerich, J. Wessels, H. J. C. T. Van Alen, T. Luesken, F. Wu, M. L. Van De Pas-Schoonen, K. T. Op Den Camp, H. J. M. Janssen-Megens, E. M. Francoijs, K. J. Stunnenberg, H. Weissenbach, J. Jetten, M. S. M. Strous, M. (2010). “Nitrite-driven anaerobic methane oxidation by oxygenic bacteria”. Nature 464 (7288): 543�. doi:10.1038/nature08883.
Hanson, R. S. and Hanson, T. E. (1996). “Methanotrophic bacteria”. Microbiological reviews 60 (2): 439�.
Haroon, M.F., Hu, S., Shi, Y., Imelfort, M., Keller, J., Hugenholtz, P., et al. (2013) Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage. Nature 500: 567�.

Part 2
Recent research has just changed the ball-game for how life developed on Earth. Forsythe et al. (described in Science Daily as “Finding the origins of life in a drying puddle http://www.sciencedaily.com/releases/2015/07/150720094522.htm July 20, 2015 link to 2015 paper below) produced polypeptides in wetting and drying conditions at 65 deg. C., with the likelihood being that proteins evolved on terrestrial Earth and not in the oceans as previously envisaged. This confirmed to me the importance of the role evaporation in life’s evolution. Given that water is the most fundamental molecule to life, the absence of it due to evaporation must play some role.

Although it is very interesting that a puddle containing the necessary ingredients may have been available for evaporative and hydrating processes to work on, creating polypeptides and later complex proteins in terrestrial zones, that does not per se mean that life itself i.e. the initial protocell, arose terrestrially. Life may still have arisen in the oceans, but this would necessitate the “puddles” being nearby to an ocean, so that coastal inundation could have swept the new proteins into the ocean. There they then would have to have replicated to become abundant enough to reach locations where life formed, e.g. deepsea vents, indicating that RNA may have preceded life. If however the process of polypeptide formation leading to proteins led to life on land, then RNA may have arisen at an early stage after life arose.


What I do think though is that there is now a conundrum in which it appears proteins may have evolved on land, but life possibly in the sea, so it is the question of getting a to b, and where does RNA then fit in? For example if you have a few complex protein molecules sitting in an evaporating pool, even close to the sea such as on a coast, with the tides washing them into the ocean, how do they multiply to spread to vents without RNA? As much as I admire Nick Lane, I think this new information has thrown something of a spanner into the works.

I think that there is a further possibility for membranes. Where previously I thought that membranes were water or water-metallic membranes that stretched between rocks eventually forming an enclosure around protein complexes, it seems something else is now possible. Given the desire to prevent evaporation in a drying pond, or alternatively to drown, could the nascent proteins have worked with proteins to form a hydrophobic layer? To me that seems to fall into place so that evolution of proteins was followed by membrane-bound proteins which may have learnt to replicate using RNA, and these then spread to the oceans, where the true protocells began. Fossil bacteria seem to indicate life began in the oceans.

Forsythe, Jay G. et al. (2015): “Ester-Mediated Amide Bond Formation Driven by Wet-Dry Cycles: A Possible Path to Polypeptides on the Prebiotic Earth” Angewandte Chemie International Edition (early version online: http://onlinelibrary.wiley.com/doi/10.1002/anie.201503792/abstract) .

@ccatctc: You seem to like the expression "toxic" a lot, while not defining it so we can understand its use. If it has any: obviously the first populations would thrive in their environment (or life wouldn't survived), so it wasn't 'toxic' for them. Rather, anoxic chemotrophs prefer the same redox conditions that the "smoker" theories are based on. It is a strength of these theories by the way.

Re the many pot non-reactor soup theory vs a smoker one pot reactor theory, the likelihood is apriori greatest for the latter one. Now there were many impactors that could have partaken in the soup pathway, but there were many vents as well. If impactors and dry/wet cycle on early continents (which we now know were present from 4.4 billion years ago on, see the Jack Hill zircon results) contributed it may have been useful. But it isn't crucial for the "smoker" theories. (Which by the way now have their necessary oceans observed by the JH zircons from before 4.3 billion years, so are much as good time wise.)

More problematic for the "soup" theories is the recent demonstration by Lane et al that universal chemiosmosis _had_ to evolve near the surface of alkaline hydrothermal vents, only their can the evolutionary pathway proceed. (And it is also only promoted by such an environment.) Now you can possibly have earlier cells establish themselves on a vent, evolve chemiosmosis and then compete all other lineages into extinction. But it seems far fetched. Much easier to believe that chemiosmosis was necessary to free cells from their constrained environment.

The earlier commentary started out intending to be a simple "I don't think so" response. =D But as it swelled, I may as well put in my remaining 2c on the interesting and valuable series of Larry's abiogenesis posts.

I agree with the distinction between the two soup and vent theories up to a point. But I think the separation is artificially made too severe. Keller et al showed recently that glycolysis (and so gluconeogenesis, by way of product separation) has a non-enzymatic pathway in an anoxic FeII solute Hadean ocean. [ http://msb.embopress.org/content/10/4/725 and see the accompanying editorial on the gluconeogenesis pathway.] Now that fits more convenient in a vent environment, since the temperature - a 70+/70- degC differential for gluconeogenesis - does, and since it was recently shown in experiments that alkaline vent greigite minerals catalyze the production of the necessary pyruvate substrate from CO2/H2 in the alkaline vent redox environment.

Keller et al pathway is by the way to my knowledge the first demonstrated non-enzymatic metabolism-like (sufficient lossless, same efficiency as cellular metabolism) pathway before the many-pot one you point to. They make away with the notions of Woese (IIRC), that claimed a chicken-and-egg problem for metabolism vs enzymes. There were 5 such major stumbling blocks a year ago, including how chirality interacted with RNA replication (cross-chirality is actually helpful), but they have now all fallen! [So, a lot of references from here on. In the interest of saving time, I'll produce them if asked to.]

An environmental glycolysis/gluconeogenesis makes away with Larry's aldolase/separate evolution constraint I think, but his post on those may explain why gluconeogenesis may appear phylogenetically older. Vent and cellular leakage/production variations should have made an enzymatic takeover of the glucose/pentose production a series of fitness promoting events.

Finally, I don't see today's vent theorists try to explain why substrate level ATP production evolved if chemiosmosis ATP production is both more efficient (

20 ATPs vs 2) and evolved first. Yes, they regulate the controlling steps, the irreversible committed steps, of glycolysis. But why there, if not to balance gluconeogenesis ATP demands? You can argue that such balance is useful. But evolution is contingent so it appears as a lucky coincident. Instead I think it could have been enforced by substrate level ATP production evolved as the only - and simpler - game in town at the time.

Net production of ATP by catalysis can only be productive in an environment where there's lot of "high-energy" organic compounds available for degradation ( e.g. glucose). We are used to thinking about animals where such food is readily available and, unfortunately, much of metabolism is taught from this perspective.

Think about bacteria and algae living in the oceans. This is a more appropriate analogy to the primitive cells that first evolved on Earth. They could not make ATP or its more simple equivalent by substrate level phosphorylation because there's no substrate available. That's why the bottom up approach of metabolim first is so much more reasonable.

Production of ATP at the substrate level by glycolysis is much simpler than the membranous production by ATPases. The latter does not only use a very complex molecular machine, but it is also dependent on generation of membrane potential. The idea that membraneous processes established before substrate level processes is associated with the "Metabolism first" idea. In my view the only possible solution is that RNA established before controlled metabolism could take place. I have given my thoughts on how RNA could have been synthesized on another "Metabolism First and the Origin of Life", first published on Sandwalk in 2009.