Monday, July 22, 2019


Scientists Debate the Origin of Cell Types in the First Animals

Jordana Cepelewicz



From one came many. Some 700 million years ago, a single cell gave rise to the first animal, a multicellular organism that would eventually spawn the incredible complexity and diversity seen in animals today. New research is now offering scientists a fresh perspective on what that cell looked like, and how multicellularity could have emerged from it — a transition that marks one of the most pivotal events in the history of life on Earth.
For well over a century, it has been widely assumed that the ancestors from which the first animal evolved were simple blobs of identical cells. Only later, after the animals formed their own branch on the tree of life, did those cells start to differentiate into various cell types with specialized functions. But now, painstaking genomic analyses and comparisons between the most ancient animals alive today and their closest non-animal relatives are starting to overturn that theory.
The recent work paints a picture of ancestral single-celled organisms that were already amazingly complex. They possessed the plasticity and versatility to slip back and forth between several states — to differentiate as today’s stem cells do and then dedifferentiate back to a less specialized form. The research implies that mechanisms of cellular differentiation predated the gradual rise of multicellular animals.
Now, scientists are reporting the most compelling evidence yet for the new narrative. Their work, and the debate inspired by its publication inNature last month, also highlights how difficult it is to pin down definitive answers to these kinds of evolutionary questions — and how wide a net researchers have to cast in pursuit of those answers.
Looking for Close Relatives
In the 1860s, the biologists Henry James Clark and William Saville-Kent separately noted a striking resemblance between the cells of two organisms. Choanoflagellates are tiny spherical or egg-shaped cells crowned with a “collar” of fingerlike protrusions surrounding a single flagellum that whips back and forth. These protists stir up water currents with their flagella, sweeping their next meal (usually bacteria) into their collars to eat. Meanwhile, sponges are simple animals made up of many cell types, including choanocytes — collared, flagellated cells that line the chambers inside the sponge and capture its food. Choanocytes look and act remarkably like choanoflagellates, so much so that some scientists posited in the 1980s and ’90s that choanoflagellates might be animals that evolved from sponges and then simplified down to one cell.



The structural similarities prompted experts to think that the cells shared an ancestor, and that the single-celled choanoflagellates might be the key to understanding how the multicellular sponge came about. Building on this, the famed marine biologist Ernst Haeckel put forth a theory for the evolution of animal multicellularity in 1874, which researchers have since elaborated on: A choanoflagellate-like ancestral cell started it all. Many such cells came together to form a colony, a hollow ball of identical cells that, in turn, gradually differentiated into cell types and tissues with various functions. This eventually led to the first animal, the sponge — and the rest is history.
All the signs indicated that this was the right way to think about animal evolution. In the 2000s, more than a century after Haeckel proposed his theory, genomic evidence confirmed that choanoflagellates were animals’ closest living relatives. “Out of the many single-cell eukaryotes out there, 150 years ago choanoflagellates had been proposed as a close relative of animals,” said Pawel Burkhardt, a molecular biologist at the Sars International Center for Marine Molecular Biology in Norway. “Then the first genome was sequenced, and bam! It actually was really true.”

 “Scientists, including myself, have for a long time enjoyed this choanoflagellate-choanocyte connection,” said David Gold, a geobiologist at the University of California, Davis, “because it tells a clear and elegant story.”
Besides, said Douglas Erwin, a paleobiologist at the Smithsonian Institution’s National Museum of Natural History in Washington, D.C., “You’re going to question Haeckel? How do you question Haeckel? It’s almost like questioning Darwin.”  [[!!??!!]]
[[And in spite of all the signs confirming the theory, and its calirity and elegance – and acceptance in the scientific community – it is now seen to be wrong. Is the moral obvious for those contemporary theories that are supported by all the evidence and are clear and elegant and accepted?]]
The First Seeds of Doubt
But uncertainty about that clear and elegant story has been growing over the past decade. The idea that animals arose from a colony of choanoflagellate-like cells implies that cell differentiation evolved after multicellularity did. But “the data is demonstrating that it’s not like that,” said Iñaki Ruiz-Trillo, an evolutionary biologist at the Institute of Evolutionary Biology in Barcelona.
The first complication came in 2008, when a group of scientists, in an effort to more precisely map out the evolutionary relationships among animals on the tree of life, identified comb jellies rather than sponges as the earliest animals. [[Hmmm – what dating methods did they use first? And what methods second? And why did they not agree?]] The finding generated controversy. “It’s still very much a heated question,” Gold said, “but I think it forced the community to reappraise the classic narrative.”

Subsequent discoveries continued to fuel the debate over which animal group came first. And some studies uncovered overlooked differences  [[Hmm – overlooked differences – so they were there but no one paid attention….could that be happening again today?]]  between choanoflagellates and sponge choanocytes. The cells’ shared ancestry began to look less like a foregone conclusion.
Scientists also began to realize that choanoflagellates and two closely related unicellular groups all have complex life cycles that proceed through various cell states. These states essentially act as different cell types — but rather than all existing side by side as in a multicellular organism, they arise sequentially in a single cell. “They have temporal cell differentiation,” Burkhardt said.
And during those life cycles, all three of these protists spend part of their lives in a form that borders on something like primitive multicellularity. Choanoflagellates have a colonial form; the second protist group has amoeba-like cells that aggregate; the cells of the third group grow to have hundreds of nuclei.
This prompted a paper in 2009 that rejuvenated an old alternative to Haeckel’s hypothesis. Back in 1949, the Russian biologist Alexey Zakhvatkin had proposed that multicellular animals evolved when temporally differentiating cells formed colonies and began to commit to particular stages in their life cycles, allowing a few cell types to exist at once. Ruiz-Trillo and his colleagues provided further evidence for this so-called temporal-to-spatial transition. In a series of studies, they showed that certain families of regulatory proteins supposedly unique to animals, including those involved in cell differentiation, were actually already present in their far more ancient unicellular relatives.
Now, a team of researchers led by Sandie Degnan and Bernard Degnan, a married pair of marine biologists at the University of Queensland in Australia, have provided additional support for this view of animal evolution while also taking a swing at the traditional theory’s foundation: the evolutionary link between the choanoflagellates and the sponge choanocytes.
A More Flexible Ancestor
When the team started their project, they “really just wanted to put some meat on the bones of the [traditional] theory,” Bernard Degnan said. To do so, they examined the gene expression in choanocytes and other kinds of sponge cells, then compared those findings with published data on choanoflagellates and two other protists.

They expected to establish that sponge choanocytes had gene expression profiles most like those of choanoflagellates. Instead, they found that another type of sponge cell did.
That cell type, called an archaeocyte, acts like a stem cell for the sponge: It can differentiate into any other cell type the animal might need. Some of the gene expression patterns in archaeocytes are significantly similar to those of the protists during particular life cycle stages, according to Bernard Degnan. “They’re expressing genes that suggest that they have an ancestral regulatory system,” he said. “All animals are just variations on that theme that was created a long time ago.”
Moreover, the choanocytes seemed to be unexpectedly transient. “The choanocytes, which are supposed to be the bedrock of all animal origins … are almost ephemeral,” he said. “They don’t stay stably in that state, but kind of quickly dedifferentiate into these stem cells, the archaeocytes.”
To Gold, who was not involved in the study, this result is the strongest evidence yet that sponge choanocytes should not necessarily be used as “some sort of proxy for the origin of animals.”
Bernard Degnan thinks it’s possible that choanoflagellates and sponge choanocytes arrived independently at their collared, flagellated architecture. In the shared ancestry of choanoflagellates and sponges there could have been something like an archaeocyte or a pluripotent stem cell. “It transited between different cell types, and those cell types then became stable,” he said. “And essentially that’s what gave rise to true multicellularity.” Later, as animals got bigger and more complex, their cells had to become more precise, specialized and fixed in their identities, but they lost a lot of their versatility in the process.

In retrospect, this version of multicellularity’s origin makes a lot of sense. According to some experts, we can think of the single-celled organisms that came before animals as stem cells of sorts: They could go on dividing forever, and they could perform a variety of functions, including reproduction. Other early animals, such as jellyfish, show a great deal of that seemingly ancestral plasticity as well.
“Stem cells are something people have been working on for years” in studies of development, wound healing and cancer, Ruiz-Trillo said. Now, it’s becoming clear that they will be “interesting for understanding evolution as well,” for discovering how animals came to be.
A Path Toward Reconciliation
Not everyone agrees entirely with the Degnans’ conclusions. Drawing inferences from gene expression profiles isn’t so straightforward. “Dig into [it], and you could interpret some data completely differently,” Burkhardt said. Differences in gene expression don’t necessarily preclude two cell types from sharing ancestry.

This choanoflagellate, extracted from a colony, uses its signature collar and flagellum to trap food — much like choanocyte cells do in sponges.
Erwin agreed. Such data, he said, “is a snapshot [taken] at a particular point in time.” Given that choanoflagellates and sponge choanocytes have been evolving on their own for the past 700 million years, it makes sense that they express very different genes.
In any comparison of modern organisms, “you are looking at animals that have a history of loss and gain,” said Maja Adamska, an evolutionary developmental biologist at the Australian National University who did not participate in the Degnans’ study. “You risk that you will oversimplify your findings.” [[Hmm – could some of today’s accepted “findings” be oversimplified?]]
Other sponge species, she added, don’t have archaeocytes at all. Instead, their choanocytes perform those stem cell-like roles. “I suspect that if we did a comparison in [those choanocytes],” Adamska said, “we would have found higher similarity to choanoflagellates.”
Adamska thinks that the first animal could very well have been a pancake of stemlike cells that often shifted their identities. She also thinks that the gene expression comparison doesn’t rule out the evolutionary ties between choanoflagellates and the first multicellular animal cells. “In fact, I strongly believe that my ancestors did have choanocytes,” she said.
The two theories about the origins of animal multicellularity aren’t mutually exclusive. “I think there’s a place for both choanoflagellate-like features and [temporal differentiation] features in the last common ancestor we are trying to paint,” Adamska said. “I don’t see the contradiction there.” She and her colleagues are now working on profiling gene expression in sponges without archaeocytes to test this idea further.
Hints of a combined theory are already emerging from Burkhardt’s lab. In a preprint they posted on biorxiv.org in May, Burkhardt and his colleagues found that the cells in a choanoflagellate colony are not all identical: They differ in their morphology and in the ratio of their organelles. These observations, he said, suggest that spatial cell differentiation was already happening in the choanoflagellate lineage, and perhaps even earlier — a possibility that blends the new ideas (that the capacity for differentiation is ancient and the transition to animal multicellularity was gradual) with the old (that this could happen with choanoflagellate-like cells).
So while there’s still no definitive answer on what exactly the first animal looked like, the picture is getting clearer. “We are getting closer to understanding where we came from in the depths of time,” Adamska said. “And I think that is so cool.”


Thursday, July 18, 2019


From Chernobyl Disaster Site, a Boost for Intelligent Design 

July 11, 2019, 4:50
מה רבו מעשיך!
To evolutionists, radiation is like manna from heaven. It feeds the engine of Darwinian evolution — random mutation — providing variations that evolution’s Tinkerer, natural selection, can use to build new watches blindfolded. Well, the Chernobyl disaster of 1986 gave evolutionary biologists an unexpected natural lab to test their view, and this experiment has been going on for two years longer than Richard Lenski’s Long-Term Evolution Experiment with E. coli. 
The recent HBO miniseries Chernobyl brought back memories of the event that seems synonymous with “disaster.” Experts had predicted a high death toll on all life as a result of the radiation bath. People were quickly evacuated from a 3500-km area, and the cities closest to the nuclear plant quickly became ghost towns (see the video “Postcards from Pripyat”). A 30-km Chernobyl Exclusion Zone (CEZ) was enforced. To everyone’s surprise, though, life in the CEZ is thriving 33 years later. Therein is a story worth investigating: which view of biology scored, Darwin or intelligent design?

Some Considerations

Analyzing the situation requires some knowledge about nuclear radiation. Even though the CEZ will remain contaminated to some degree for thousands of years, not all the “hot” isotopes will last that long, and not all are equally dangerous. Toxicity depends on the emitted particles (alpha, beta, or gamma rays), the ratios emitted, and their respective energies. One of the most toxic radioisotopes of all, polonium-210, which was used to kill the former Russian spy Alexander Litvinenko in London in 2006, is only deadly when ingested; it is safe to hold in the hand. It also has a relatively short half-life, and its particles have such low energy they can be blocked by a sheet of paper. Inside the body, however, they make cells undergo apoptosis (cell suicide) as the hot particles are transported through the blood, tissues, and organs (Medical News Today).
The Chernobyl reactor released many radioisotopes into the atmosphere, some with relatively short half-lives. One of the biggest risks for humans from Chernobyl was radioactive iodine, which concentrates in the thyroid gland and can cause thyroid cancer. Its half-life is on the order of eight days, however, so within four years after the disaster, levels had dropped enough to make dairy products safe again for consumption. Cesium-137 and strontium-90 have half-lives of around thirty years, so they will remain a concern, but some of these can leach into the soil by rain and be transported by wind, and thus dissipate sooner. A United Nations report twenty years after the disaster says, “Although plutonium isotopes and americium 241 [half-life 432 years] will persist perhaps for thousands of years, their contribution to human exposure is low.” 
One other consideration is that the biosphere is bombarded with ionizing radiation all the time, from radon in the soil, carbon-14 in the air, gamma rays from space, and other sources. It’s the increment above what experts consider safe levels, therefore, that determines the risk, and that diminishes with distance from the source.
We should not think of the CEZ as glowing hot for 20,000 years, therefore. But without doubt, the area received a highly dangerous dose of radiation at first. A few dozen people died within the immediate aftermath of the explosion. Experts estimate that about 4,000 people “could” die from cancer, but as years go by, it’s increasingly hard to attribute the cause to Chernobyl as radiation levels decrease. Many more owe their lives to the heroes who died to entomb the reactor shortly after the accident. Pine trees died, and animals within the hot zone died — but not all of them. And now, to the experts’ surprise, the area is doing remarkably well. Stuart Thompson, a plant biochemist, writes for The Conversation:
Life is now thriving around Chernobyl. Populations of many plant and animal species are actually greater than they were before the disaster.
Given the tragic loss and shortening of human lives associated with Chernobyl, this resurgence of nature may surprise you. Radiation does have demonstrably harmful effects on plant life, and may shorten the lives of individual plants and animals. But if life-sustaining resources are in abundant enough supply and burdens are not fatal, then life will flourish. [Emphasis added.]

Why Life Is Resilient

The subject of his article is, “Why plants don’t die from cancer.” Unlike animals, he explains, plants can work around damaged tissue. They can also grow most tissues they need anywhere. “This is why a gardener can grow new plants from cuttings, with roots sprouting from what was once a stem or leaf.” Additionally, plant cell walls act as a barrier to metastasis, should tumors arise. Even though dying trees near the accident created a “Red Forest,” the local ecology did not collapse. 
Thompson retreats into Darwinism briefly, but he points out reasons why plants proved so resilient to the Chernobyl disaster. Are these not better explained by intelligent design?
Interestingly, in addition to this innate resilience to radiation, some plants in the Chernobyl exclusion zone seem to be using extra mechanisms to protect their DNA, changing its chemistry to make it more resistant to damage, and turning on systems to repair it if this doesn’t work. Levels of natural radiation on the Earth’s surface were much higher in the distant past when early plants were evolving, so plants in the exclusion zone may be drawing upon adaptations dating back to this time in order to survive.
Where did those extra mechanisms come from? Where did the “systems to repair” come from? Radiation has no power to bring forth complex systems. This is like saying a hail of bullets generates armor! No; if the systems were not already present, they could do nothing.

A Thriving Ecosystem

With plants rebounding (which presupposes the presence of worms, fungi and other ecological partners), mammals and birds quickly returned in force. Wolves, boars, and bears are now back in larger numbers than ever, and birds can be seen flying in and out of the sarcophagus built over the reactor, and even nesting in its cracks. Thompson shares another surprise: with the humans mostly gone, Chernobyl has become a thriving wildlife refuge!
Crucially, the burden brought by radiation at Chernobyl is less severe than the benefits reaped from humans leaving the area. Now essentially one of Europe’s largest nature preserves, the ecosystem supports more life than before, even if each individual cycle of that life lasts a little less.
Another surprise is that the people who refused to evacuate appear to be doing better than those who left. Forced resettlement wore evacuees down with anxiety, fear, and personal conflicts. The U.N. report says, “Surveys show that those who remained or returned to their homes coped better with the aftermath than those who were resettled.” 
For more astonishment, read “What Bikini Atoll Looks Like Today,” at Stanford Magazine. The spot where a hydrogen bomb exploded 62 years ago is once again a tropical paradise, complete with “big healthy coral communities” in the surrounding waters, and schools of fish swimming through the hulks of sunken warships. Despite 23 atomic bomb tests at the atoll, “Ironically, Bikini reefs look better than those in many places she’s dived,” writes Sam Scott about scuba diver Elora Lopez. “It didn’t look like this nightmare-scape that you might expect,” she says. “And that’s still something that’s weird to process.”

Designed Resilience

The lesson from Chernobyl is this: radiation kills, but life comes prepared to defend itself. No newly evolved organisms emerged at Chernobyl. Billions of mutations were not naturally selected to originate new species. The same organisms rebounded because DNA repair systems, involving exquisite machinery, were prepared to find mutations and fix them. The systems might be overwhelmed temporarily, but will rebound as soon as the threat diminishes. Machines do not make themselves in the presence of threats. They have to be prepared in advance. Think of it: the DNA code includes instructions on how to build machines that can repair DNA! 
The resilience of some life forms is truly remarkable. Common “water bears,” aka tardigrades, are some of the most durable animals known. These nearly microscopic arthropods might be found in your garden as well as in polar ice. They can survive the vacuum of space with no oxygen for days, endure temperatures from near absolute zero to boiling water, and survive radiation a thousand times stronger than levels at the surface of the earth. Some have been revived after a century in a dehydrated state! It wasn’t the conditions that produced these abilities; tardigrades had to already have these robust systems before the conditions arrived. Tardigrades never had to “evolve” in space; how did they pass that test? The answer is design.
Even some one-celled organisms are fantastically durable. A preprint at bioRxiv speaks of “Extreme tolerance of Paramecium to acute injury induced by γ rays,” due to “DNA protection and repair” genes. Some archaea and bacteria (thought to be the simplest life forms) can survive hot water above the boiling point in Yellowstone hot springs. Another ubiquitous microbe named Deinococcus radiodurans, “the world’s toughest bacterium,” is amazing. According to Genome News Network, “The microbe can survive drought conditions, lack of nutrients, and, most important, a thousand times more radiation than a person can.” It was discovered doing just fine in ground meat that had been irradiated for sterilization. How does it do it? 
An efficient system for repairing DNA is what makes the microbe so tough. High doses of radiation shatter the D. radiodurans genome, but the organism stitches the fragments back together, sometimes in just a few hours. The repaired genome appears to be as good as new.
“The organism can put its genome back together with absolute fidelity,” says Claire M. Fraser, of The Institute for Genome Research (TIGR) in Rockville, Maryland. She was the leader of the TIGR team that sequenced D. radiodurans in 1999.
The fantastic resilience of life to threats, whether from ionizing radiation, temperature, or deprivation, shouts design. As stated in a recent post about homeostasis, only intelligence builds machines that can maintain the state of other machines. The recovery of Chernobyl’s ecosystem offers powerful evidence for life’s pre-programmed resilience.

Monday, July 15, 2019


בס"ד
Parshas Hashavua Balak

Rav Nota Schiller, Rosh Yeshivat Ohr Somayach 
           וירא פנחס --ויקח רמח בידו



When immorality was involved, פנחס & לוי, risked their lives by being קנאים, (zealots) yet פנחס was praised for his קנאות  and לוי, on the other hand, was ostracized for his קנאות

The Netziv in שו"ת משיב דבר explains, that practicing קנאות should not be done even by Chasidim who are doing it for the sake and love of Hashem. It may only  be done by Talmidei Chachamim using their הגיון תורה (Torah logic- Hashkafah)

They are the only ones who know and understand the very minute and precise details as to when to be מקדש שם שמים by going out to fight for the cause and when to refrain from קנאות to avoid 'חילול ה.

According to the Netziv, perhaps, if in the future, there will be a need to be מקדש שם שמים by bringing traffic to a halt and the Egged buses to a standstill, etc., they should have the Ziknei Roshei Yeshiva be the ones who sit down on the pavement in the middle of the street instead of having14-year-old Bachurim doing it.

שו"ת משיב דבר חלק א סימן מד

והרי לוי ופנחס שניהם קנאו על הזנות ומסרו נפשם ע"ז, והנה פנחס עלה בשביל זה לגרם המעלות ולוי גער בו אביו וכיב"ז הרבה והוא משום שנדרש לזה דיוק רב לשקול הפעולה לפי הזמן והמקום וגם בכמה דברים נדרש לדעת כללי התורה שאינם מבוארים כ"כ, ע"כ א"א להיות חסיד בזה האופן אלא אחר הגיון תורה
….שו"ת משיב דבר חלק א סימן מד
ובכל אופני חסידות שנינו באבות (פרק ב' מ"ה) ולא עם הארץ חסיד:

Sunday, July 14, 2019


[[OOL part 2 - same author]]

Time Out

James Tour is a synthetic organic chemist at Rice University.
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IN 1952, Stanley Miller and Harold Urey derived a number of racemic amino acids from a handful of small molecules. These were electrifying results because they suggested that the methods of synthetic chemistry might finally explain the origins of life. The excitement was justified, but premature.1 Origins of life (OOL) research has, to be sure, become progressively more sophisticated, but its goal—to explain the origins of life—remains as distant today as it was in 1952. This is not surprising. The protocols in use have remained unchanged: buyhighly purified chemicals; mix them together in high concentrations and in a specific order under carefully devised laboratory conditions; derive a mixture of compounds; and publish a paper making bold claims about OOL. These protocols are as unrealistic as they are unimproved.
This essay comprises an argument, but it also contains an appeal to the OOL community. The history of science suggests that on occasion what is required for research to flourish is not further research—at least to the extent that further research involves doing the same thing. This is one of those times.
Needed for Life
FOUR MOLECULES are needed for life: nucleotides, carbohydrates, proteins, and lipids. Nucleotides are composed of a trimeric nucleobase-carbohydrate-phosphate combination, and once polymerized, constitute DNA and RNA. Five different nucleobases comprise the entire alphabet for DNA and RNA. The nucleotides and their subsequent DNA and RNA structures are homochiral, yielding one of two possible enantiomers. Amino acids are most often homochiral. When amino acids are polymerized, they form proteins and enzymes. Proteins and enzymes also display a tertiary homochirality. Lipids are dipolar molecules with a polar water-soluble head and a non-polar water-insoluble tail. They, too, are most often homochiral. Cells use carbohydrates for energy, and carbohydrates, along with proteins, are identification-receptors. Carbohydrates are also homochiral, and their polymeric forms take on tertiary homochiral shapes. OOL researchers have spent a great deal of time trying to make these four classes of molecules, but with scant success.
Constructing the molecules necessary for life from their prebiotic precursors represents one goal of OOL research; putting them together, another. Some of synthetic chemistry is pedestrian, and some ingenious. Fundamental questions remain unaddressed. Claims that these structures could be prepared under prebiotic conditions in high enantiomeric purity using inorganic templates, or any presumed templates, have never been realized. The carbohydrates, amino acids, lipids, and other compounds within each of these classes require specific methods in order to control their regiochemistry and stereochemistry. The differences in reaction rates often require chiral systems acting upon chiral molecules. If this were possible under prebiotic conditions, it is odd that it cannot be replicated by synthetic chemists.
They have, after all, had 67 years to try.
Synthetic Hyperbole
CONSIDER THE class of experiments that deal with the assembly of chemicals into what are referred to as protocells—“a self-organized, endogenously ordered, spherical collection of lipids proposed as a stepping-stone to the origin of life.”2 In 2017, a team from the Origins of Life Initiative at Harvard University performed a type of polymerization reaction in water known as the reversible addition–fragmentation chain transfer.3 This reaction type is not seen in nature, and neither are the monomers that figure in the experiment. Still, this is standard chemistry. Polymers are made by a controlled radical polymerization reaction, where two different monomer types are added sequentially to a chain bearing both a hydrophobic and a hydrophilic block. Researchers observed polymeric vesicles forming during polymerization—interesting, but not extraordinary. The vesicles grew to bursting as researchers kept the radical chain growing through ultraviolet light activation. There is, in this, nothing surprising: the forces between the growing vesicle and the surrounding water dictate a critical growth volume before the vesicle ruptures.
The claims should have ended there.
Here is how the work was portrayed in the published article:
The observed net oscillatory vesicle population grows in a manner that reminds one of some elementary modes of sustainable (while there is available “food”!) population growth seen among living systems. The data supports an interpretation in terms of a micron scale self-assembled molecular system capable of embodying and mimicking some aspects of “simple” extant life, including self-assembly from a homogenous but active chemical medium, membrane formation, metabolism, a primitive form of self-replication, and hints of elementary system selection due to a spontaneous light triggered Marangoni instability [provoked by surface tension gradients].4
These claims were then rephrased and presented to the public by the Harvard Gazette:
A Harvard researcher seeking a model for the earliest cells has created a system that self-assembles from a chemical soup into cell-like structures thatgrow, move in response to light, replicate, and exhibit signs of rudimentary evolutionary selection [emphasis added].5
This degree of hyperbole is excessive.6 Nothing in this experiment had growing cell-like structures with replication, or that exhibited aspects of evolutionary selection.
Teams from the University of California and the University of New South Wales recently conducted lipid bilayer assembly experiments, publishing a summary of their work in 2017.7 They combined nucleotides and lipids in water to form lamellae, with the nucleotides sandwiched between the layers. Nucleotides are trimers of nucleobase-carbohydrate-phosphate, and, in this case, both nucleotides and lipids were purchased in pure homochiral form. Both teams then demonstrated that a condensation polymerization of the nucleotides can take place within the lamella upon dehydration. Polymerization takes place by means of a reaction between pre-loaded phosphate and the purchased stereo-defined alcohol moiety found on a neighboring nucleotide. Similar reactions, they conjectured, may have occurred at the edge of hydrothermal fields, volcanic landmasses providing the necessary heat for reactions.
The chemistry that figures in these experiments is unremarkable. Bear in mind that derivatives were all pre-loaded. To provide the essential concentrations for the reactions, researchers removed the water, thus driving the intermolecular reactions to form oligomers that resembled nucleic acids. The problem with condensation polymerization is obvious: any alcohol can compete for the reactive electrophilic site. In the case under consideration, researchers added no other alcohols. They were scrupulous, but the system was stacked. Condensation polymerization reactions need to be very pure, free of competing nucleophilic and electrophilic components. Witness the Carothers equation, which defines degrees of polymerization based upon monomer purity.8 If there happened to be amino acids or carbohydrates mixed with the nucleotides, they would terminate or interrupt the growth of the oligonucleotides. What is more, the researchers did not confirm the integrity of the structures they claimed to have derived. If carefully analyzed, these structures would likely have shown attacks from unintended hydroxyl sites. Since their sequences are essentially random, short oligonucleotides are not realistic precursors to RNA. An alphabet soup is not a precursor to a poem. The authors go on to suggest that the lamella sandwiching oligonucleotides eventually break off to form lipid bilayer vesicles. These contain the oligonucleotide-within-vesicle constructs, which they call protocells. The conversion of planar lamella into multilamellar vesicles as they hydrate is well established, but shearing forces are generally required to form the requisite lipid bilayer vesicle. For this reason, yields were likely to be low.9 It is hard to imagine finding highly purified homochiral nucleotides trapped in a pure lipid lamella on the prebiotic earth.
But set all that aside. These vesicles bear almost no resemblance to cellular lipid bilayers. Lipid bilayer balls are not cellular lipid bilayers. One would never know this from reading the authors’ account. “Then, in the gel phase,” they write, “protocells pack together in a system called a progenote and exchange sets of polymers, selecting those that enhance survival during many cycles.”10 Chemicals, of course, are indifferent to their survival. No mechanism is described to demonstrate how protocells would bear different sets of polymers or exchange polymers among them. Terms from biology have generally been misappropriated in a way that makes no chemical sense. This is not an isolated or incidental defect. It reappears when the authors write that “[t]he best-adapted protocells spread to other pools or streams, moving by wind and water…”11 Best-adapted? Microbial communities apparently “evolve into a primitive metabolism required by the earliest forms of life.” Molecules do not evolve, and nothing is being metabolized. Condensation polymerization is a simple chemical reaction based upon the addition of nucleophiles to electrophiles with loss of water. Such a reaction is never referred to as a form of metabolism within synthetic chemistry.
Terminology is one thing, non-sequiturs quite another. “After much trial and error,” the authors write, “one protocell assembles the complicated molecular machinery that enables it to divide into daughter cells. This paves the way for the first living microbial community.” How is the molecular machinery made? They do not say. The mechanisms needed for cellular division are complex, requiring cascades of precisely functioning enzymes. There is nothing between what the authors demonstrate and what they claim to have established, and nothing they propose “paves the way for the first living microbial community.”
The Emerging Cell
A FUNCTIONING CELL contains a complex non-covalent interactive system. Nobody knows how a cell emerges from its molecular components. An interactome is the set of molecular interactions in a given cell.12 Interactions may be between proteins, genes, or molecules. Information is transferred within the cell through these molecular interactions. Electrostatic potentials permit information to flow through non-covalent molecular arrays, but these arrays require specific orientation.13 The interactome defines these intermolecular orientations, alignments that are unattainable through random mixing.
Peter Tompa and George Rose have calculated that if one considers only protein combinations in a single yeast cell, the result would be an estimated 1079,000,000,000 combinations.14 The authors understand that this is a very large number, one that precludes “formation of a functional interactome by trial and error complex formation within any meaningful span of time.” What Tompa and Rose call “a complicated cellular sorting/trafficking and assembly system” is required. Sophisticated scaffolding notwithstanding, “in the absence of energy even this well developed infrastructure would be insufficient to account for the generation of the interactome, which requires a continuous expenditure of energy to maintain steady state.” In their concluding paragraph, Tompa and Rose remark that
[t]he inability of the interactome to self-assemble de novo imposes limits on efforts to create artificial cells and organisms, that is, synthetic biology. In particular, the stunning experiment of “creating” a viable bacterial cell by transplanting a synthetic chromosome into a host stripped of its own genetic material has been heralded as the generation of a synthetic cell (although not by the paper’s authors). Such an interpretation is a misnomer, rather like stuffing a foreign engine into a Ford and declaring it to be a novel design. The success of the synthetic biology experiment relies on having a recipient interactome … that has high compatibility with donor genetic material. The ability to synthesize an actual artificial cell using designed components that can self-assemble spontaneously still remains a distant challenge.
The fact is that interactomes add a massive layer of complexity to all cellular structures. It is one that underscores the difference between a real cell and the protocells or extant cells made by OOL researchers.
In 2010, a team led by Craig Venter made a copy of a known bacterial genome and transplanted it into another cell.15 In 2016, they did something better, removing all but 473 genes from a natural genome and transplanting it into another cell.16 Venter and his team were circumspect; the press was enthusiastic. More recently, Henrike Niederholtmeyer, Cynthia Chaggan, and Neal Devaraj have made what they term, “mimics of eukaryotic cells.”17 Science declared them “the most lifelike artificial cells yet.”18 Microcapsules made of plastic and containing clay were prepared using microfluidics techniques. Clay has a high affinity for binding DNA. Thus when DNA was added to the solution, it diffused through the semi-porous plastic microcapsules and bound to the clay. The requisite RNA polymerases, together with the ribosomes, tRNA, amino acids, enzymatic cofactors, and energy sources were either purchased or extracted from living systems. The expected chemical reactions did result in protein synthesis. Newly formed proteins diffused from their microcapsules of origin to other microcapsules. The nearer the neighboring microcapsule, the greater the exchange of reagents between them. Diffusion between microcapsules the authors dubbed quorum sensing. The chemistry would work no matter the container, whether a test tube or a large-scale industrial production tank. If the experimental design is clever, the synthesis is unremarkable. Phys.org reported these modest results in markedly flamboyant terms, referring to “gene expression and communication rivaling that of living cells.”19 There is no rivalry here. All of the active chemical components were extracted from living systems. If these are “the most lifelike artificial cells yet,” this serves only to underscore the point that no one has ever come close to the real thing.20
Life as a Lucky Fluke
IN AN ARTICLE entitled “How Did Life Begin?” Jack Szostak asks whether the appearance of life on earth is “a lucky fluke or an inevitable consequence of the laws of nature.”21 It is a good, but premature question, a point obvious from his own appreciation of current research. Having vetted the usual suspects of asteroids, dust clouds, volcanoes, lightning, and time, Szostak appeals to “a concentrated stew of reactive chemicals”:
Life as we know it requires RNA. Some scientists believe that RNA emerged directly from these reactive chemicals, nudged along by dynamic forces in the environment. Nucleotides, the building blocks of RNA, eventually formed, then joined together to make strands of RNA. Some stages in this process are still not well understood. … Once RNA was made, some strands of it became enclosed within tiny vesicles formed by the spontaneous assembly of fatty acids (lipids) into membranes, creating the first protocells. As the membranes incorporated more fatty acids, they grew and divided; at the same time, internal chemical reactions drove replication of the encapsulated RNA.22
The thesis that “RNA emerged directly from these reactive chemicals, nudged along by dynamic forces [emphasis added]” is painful to a synthetic chemist. A complex pathway of reactions would have been needed incorporating purification, assembly, polymerization, and sequencing. Nothing emerged directly in Szostak’s scenario, let alone something as complex as RNA. Phrases such as “nudged along by dynamic forces” have no meaning in terms of synthetic chemistry. Nucleotides never form and join together to make strands of RNA without complex protection and deprotecting steps. It is perfectly true that “[s]ome stages in this process are still not well understood,” if only because we are clueless about the chemistry needed on a prebiotic earth.
In the diagram to which Szostak appeals, the compounds listed as simple sugars are, in fact, glycerol and ethylene glycol. There are known routes to convert them to simple sugars, but only in gross relative and absolute stereochemically mixed states, and as a mixture of several different polyols.23 Carbohydrate synthesis is a difficult prebiotic problem.24Szostak’s carbohydrates would be useless in their mixed states, and separations are hard. The diagram’s cyanide derivatives are unrecognizable as cyanide derivatives. In an act of grace, let us attribute these chemical structural errors to the faulty renderings of a staff artist. The chemical errors are Szostak’s own. There is simply no way that heat and light can directly make a nucleotide from simple sugars and cyanide derivatives. Such glossy presentations have become the standard of the OOL community when it tries to build upon the careful work of exacting synthetic chemistry.
I have discussed these issues with OOL researchers, and I am amazed that they fail to appreciate the magnitude of the problem in building molecules. They see little difficulty in accepting a chemical synthesis where a desired product is mixed with a large array of closely related yet undesired compounds. They seem unaware that separations would be enormously complex, and subsequent reactions unavailing. In a 2018 article for Progress in Biophysics and Molecular Biology, Edward Steele et al. concede the following.
The transformation of an ensemble of appropriately chosen biological monomers (e.g. amino acids, nucleotides) into a primitive living cell capable of further evolution appears to require overcoming an information hurdle of superastronomical proportions, an event that could not have happened within the time frame of the Earth except, we believe, as a miracle. All laboratory experiments attempting to simulate such an event have so far led to dismal failure.
“At this stage of our scientific understanding,” they write, “we need to place on hold the issue of life’s actual biochemical origins—where, when and how may be too difficult to solve on the current evidence [emphasis added].”25 All is not lost. If life on earth did not arise on earth, “[i]t would thus seem reasonable,” Steele et al. remark, “to go to the biggest available ‘venue’ in relation to space and time. A cosmological origin of life thus appears plausible and overwhelmingly likely.” Why chemical reactions that are unlikely on the earth should prove likely somewhere else, Steele et al. do not say.
Facing Facts
JOHN SUTHERLAND, one of OOL’s giants and the most skilled synthetic chemist to engage in OOL research, has recently proposed that “chemical determinism can no longer be relied on as a source of innovation, and further improvements have to be chanced upon instead.”26 Chanced upon? It appears that Sutherland has come to appreciate the depths of the problems facing OOL researchers. In 2017, Ramanarayanan Krishnamurthy et al. showed that diamidophosphate can phosphorylate nucleosides, nucleotides, and stereo-scrambled lipid precursors. These can further result in the formation of random oligonucleotides and oligopeptides. The fundamental challenges with respect to synthesis and assembly remain unaddressed. Krishnamurthy was rightly measured in writing about “the pitfalls of extrapolating extant biochemical pathways backwards all the way to prebiotic chemistry and vice versa.”27 In 2018, Clemens Richert argued that “the ideal experiment does not involve any human intervention.”28 This is a step in the right direction. So, too, is the fact that he scrupled at the pure chemicals used by the OOL community.
It is time for a temporary time out. Why not admit what we cannot yet explain: the mass transfer of starting materials to the molecules needed for life; the origin of life’s code; the combinatorial complexities present in any living system; and the precise non-regular assembly of cellular components?
It would be helpful if leading researchers, among them very sophisticated synthetic chemists, were to step back, pause, and join forces. If the origins of life remain a mystery, two goals are within reach: an agreement about the rational standards by which OOL research should be judged, and a candid acknowledgment of the problems that remain to be overcome. A statement of this sort would be reassuring in its candor.29
Wikipedia, “Miller–Urey Experiment”; Stanley Miller, “A Production of Amino Acids under Possible Primitive Earth Conditions,” Science 117, no. 3,046 (1953), doi:10.1126/science.117.3046.528; Stanley Miller and Harold Urey, “Organic Compound Synthes on the Primitive Earth,” Science 130, no. 3,370 (1959), doi:10.1126/science.130.3370.245. 
Wikipedia, “Protocell.” 
Anders Albertsen, Jan Szymański, and Juan Pérez-Mercader, “Emergent Properties of Giant Vesicles Formed by a Polymerization-Induced Self-Assembly (PISA) Reaction,” Nature Scientific Reports 7, no. 41,534 (2017), doi:10.1038/srep41534. 
Anders Albertsen, Jan Szymański, and Juan Pérez-Mercader, “Emergent Properties of Giant Vesicles Formed by a Polymerization-Induced Self-Assembly (PISA) Reaction,” Nature Scientific Reports 7, no. 41,534 (2017), doi:10.1038/srep41534. 
Alvin Powell, “Mimicking Life in a Chemical Soup,” The Harvard Gazette, March 31, 2017; Harvard University, “Researcher Creates Chemical System that Mimics Early Cell Behavior,” Phys.org, April 3, 2017; Ava Jones, “Harvard Scientist Discovers Phoenix Vesicles in Quest to Mimic Life,” University Herald, April 4, 2017; and “Researcher Creates Chemical Complement that Mimics Early Dungeon Behavior,” Health Medicine Network, n.d. 
See also James Tour, “An Open Letter to My Colleagues,” Inference: International Review of Science 3, no. 2 (2017). 
Martin Van Kranendonk, David Deamer, and Tara Djokic, “Life on Earth Came from a Hot Volcanic Pool, Not the Sea, New Evidence Suggests,” Scientific American 317, no. 2 (2017): doi:10.1038/scientificamerican0817-28. 
Wikipedia, “Carothers Equation.” 
See “Lipid Preparation,” Avanti Polar Lipids, Inc.; Barbara Gerbelli et al., “Multilamellar-to-Unilamellar Transition Induced by Diphenylalanine in Lipid Vesicles,” Langmuir 34, no. 5 (2018), doi:10.1021/acs.langmuir.7b03869. 
Martin Van Kranendonk, David Deamer, and Tara Djokic, “Life on Earth Came from a Hot Volcanic Pool, Not the Sea, New Evidence Suggests,” Scientific American 317, no. 2 (2017): 33. 
Martin Van Kranendonk, David Deamer, and Tara Djokic, “Life on Earth Came from a Hot Volcanic Pool, Not the Sea, New Evidence Suggests,” Scientific American 317, no. 2 (2017): 33. 
Wikipedia, “Interactome.” 
James Tour, Masatoshi Kozaki, and Jorge Seminario, “Molecular Scale Electronics: A Synthetic/Computational Approach to Digital Computing,” Journal of the American Chemical Society 120, no. 33 (1998), doi:10.1021/ja9808090. 
Peter Tompa and George Rose, “The Levinthal Paradox of the Interactome,” Protein Science 20 no. 12 (2011), doi:10.1002/pro.747. 
Daniel Gibson et al., “Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome,” Science 329, no. 5,987 (2010), doi:10.1126/science.1190719. 
Clyde Hutchison et al., “Design and Synthesis of a Minimal Bacterial Genome,” Science351, no. 6,280 (2016), doi:10.1126/science.aad6253. 
Henrike Niederholtmeyer, Cynthia Chaggan, and Neal Devaraj, “Communication and Quorum Sensing in Non-living Mimics of Eukaryotic Cells,” Nature Communications 9, no. 5,027 (2018), doi:10.1038/s41467-018-07473-7. 
Mitch Leslie, “Biologists Create the Most Lifelike Artificial Cells Yet,” Science, November 19, 2018, doi:10.1126/science.aaw1173. 
University of California, San Diego, “Copycat Cells Command New Powers of Communication,” Phys.org, December 7, 2018. 
Mitch Leslie, “Biologists Create the Most Lifelike Artificial Cells Yet,” Science, November 19, 2018, doi:10.1126/science.aaw1173. 
Jack Szostak, “How Did Life Begin? Untangling the Origins of Organisms Will Require Experiments at the Tiniest Scales and Observations at the Vastest,” Nature 557, no. S13–S15 (May 9, 2018), doi:10.1038/d41586-018-05098-w. 
See the caption for the diagram “Origins of Life” in Jack Szostak, “How Did Life Begin? Untangling the Origins of Organisms Will Require Experiments at the Tiniest Scales and Observations at the Vastest,” Nature 557, no. S13–S15 (May 9, 2018), doi:10.1038/d41586-018-05098-w. 
Dougal Ritson and John D. Sutherland, “Prebiotic Synthesis of Simple Sugars by Photoredox Systems Chemistry,” Nature Chemistry 4 (2012): 895–99, doi:10.1038/nchem.1467. 
James Tour, “Animadversions of a Synthetic Chemist,” Inference: International Review of Science 2, no. 2 (2016). 
Edward Steele et al., “Cause of Cambrian Explosion—Terrestrial or Cosmic?” Progress in Biophysics and Molecular Biology 136 (2018), doi:10.1016/j.pbiomolbio.2018.03.004. 
John Sutherland, “Opinion: Studies on the Origin of Life—The End of the Beginning,” Nature Reviews Chemistry 1, no. 0012 (2017), doi:10.1038/s41570-016-0012. 
Clémentine Gibard et al., “Phosphorylation, Oligomerization and Self-assembly in Water under Potential Prebiotic Conditions,” Nature Chemistry 10 (2018), doi:10.1038/nchem.2878. 
Clemens Richert, “Prebiotic Chemistry and Human Intervention,” Nature Communications 9 (2018). 
The author thanks Paul Nelson for helpful insights. Walt Shaw and Steve Burgess of Avanti Polar Lipids kindly provided information on lipid bilayer assemblies. 
Published on July 11, 2019 in Volume 4, Issue 4.