Origin of life

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Jeg har det seneste år haft nogle indlæg om livets oprindelse (Origin of life), som omhandler, hvordan det første liv kan være opstået. Astrobiologi er på en måde et fag uden noget sikkert at studere. Antagelsen om, at det første liv er lig det nuværende liv på Jorden er særdeles problematisk, som jeg tidligere har antydet. Jeg indsamlede derfor nogle artikler om emnet Origin of life på min Weblog. Da det vil kræve en hel del arbejde at at overføre artiklerne til AstroForum (og de er ikke længere nyheder), har jeg i stedet valgt at give dem mærket Origin of life. Man skal blot klikke på mærket for at få en liste med artiklerne. Her er den første artikel på min Weblog:

Første indlæg om Livets oprindelse

 

[nightskyDeltager Neutron star]

I tillæg.

 

Jeg kan anbefale “Astrobiology, A brief introduction”, Kevin Plaxco og Michael Gross. Kan fås til billige penge i Paperback udgaven.

[BjarneModerator Super Nova]

Tak. Den vil jeg undersøge. Problemet er stadig, hvad astrobiologien egentlig skal undersøge. Men der er nogle antydninger. Det er meget sigende, at livet på Jorden opstod inden for 500 millioner år efter Jordens dannelse. Kemiske eksperimenter med dannelsen af de nucleobaser, som indgår i den genetiske kode antyder også at det første liv kræver tilstande lige efter, at Jorden fik den første faste skorpe. Disse eksperimenter er beskrevet her:

Researchers may have solved origin-of-life conundrum

By Robert F. Service | Mar. 16, 2015 , 12:15 PM

The origin of life on Earth is a set of paradoxes. In order for life to have gotten started, there must have been a genetic molecule—something like DNA or RNA—capable of passing along blueprints for making proteins, the workhorse molecules of life. But modern cells can’t copy DNA and RNA without the help of proteins themselves. To make matters more vexing, none of these molecules can do their jobs without fatty lipids, which provide the membranes that cells need to hold their contents inside. And in yet another chicken-and-egg complication, protein-based enzymes (encoded by genetic molecules) are needed to synthesize lipids.

Now, researchers say they may have solved these paradoxes. Chemists report today that a pair of simple compounds, which would have been abundant on early Earth, can give rise to a network of simple reactions that produce the three major classes of biomolecules—nucleic acids, amino acids, and lipids—needed for the earliest form of life to get its start. Although the new work does not prove that this is how life started, it may eventually help explain one of the deepest mysteries in modern science.

“This is a very important paper,” says Jack Szostak, a molecular biologist and origin-of-life researcher at Massachusetts General Hospital in Boston, who was not affiliated with the current research. “It proposes for the first time a scenario by which almost all of the essential building blocks for life could be assembled in one geological setting.”

Scientists have long touted their own favorite scenarios for which set of biomolecules formed first. “RNA World” proponents, for example suggest RNA may have been the pioneer; not only is it able to carry genetic information, but it can also serve as a proteinlike chemical catalyst, speeding up certain reactions. Metabolism-first proponents, meanwhile, have argued that simple metal catalysts, as opposed to advanced protein-based enzymes, may have created a soup of organic building blocks that could have given rise to the other biomolecules.

The RNA World hypothesis got a big boost in 2009. Chemists led by John Sutherland at the University of Cambridge in the United Kingdom reported that they had discovered that relatively simple precursor compounds called acetylene and formaldehyde could undergo a sequence of reactions to produce two of RNA’s four nucleotide building blocks, showing a plausible route to how RNA could have formed on its own—without the need for enzymes—in the primordial soup. Critics, though, pointed out that acetylene and formaldehyde are still somewhat complex molecules themselves. That begged the question of where they came from.

For their current study, Sutherland and his colleagues set out to work backward from those chemicals to see if they could find a route to RNA from even simpler starting materials. They succeeded. In the current issue of Nature Chemistry, Sutherland’s team reports that it created nucleic acid precursors starting with just hydrogen cyanide (HCN), hydrogen sulfide (H2S), and ultraviolet (UV) light. What is more, Sutherland says, the conditions that produce nucleic acid precursors also create the starting materials needed to make natural amino acids and lipids. That suggests a single set of reactions could have given rise to most of life’s building blocks simultaneously.

Sutherland’s team argues that early Earth was a favorable setting for those reactions. HCN is abundant in comets, which rained down steadily for nearly the first several hundred million years of Earth’s history. The impacts would also have produced enough energy to synthesize HCN from hydrogen, carbon, and nitrogen. Likewise, Sutherland says, H2S was thought to have been common on early Earth, as was the UV radiation that could drive the reactions and metal-containing minerals that could have catalyzed them.

That said, Sutherland cautions that the reactions that would have made each of the sets of building blocks are different enough from one another—requiring different metal catalysts, for example—that they likely would not have all occurred in the same location. Rather, he says, slight variations in chemistry and energy could have favored the creation of one set of building blocks over another, such as amino acids or lipids, in different places. “Rainwater would then wash these compounds into a common pool,” says Dave Deamer, an origin-of-life researcher at the University of California, Santa Cruz, who wasn’t affiliated with the research.

Could life have kindled in that common pool? That detail is almost certainly forever lost to history. But the idea and the “plausible chemistry” behind it is worth careful thought, Deamer says. Szostak agrees. “This general scenario raises many questions,” he says, “and I am sure that it will be debated for some time to come.”

[BjarneModerator Super Nova]

At livet blev dannet på overfladen af en jord uden oceaner bliver bestyrket af denne spritnye artikel i Science:

Moon’s unusual bulge may indicate early Earth had no ocean

By Sid Perkins | Feb. 7, 2018 , 4:00 PM

It’s not just dads with beer bellies: Many objects in our solar system sport a bulge around their midsections, caused by fast rotations that tend to fling material outward at equatorial latitudes. But our moon’s rotational bulge—an equatorial diameter that would be, on average, about 200 meters longer than its diameter through the poles if the moon weren’t so cratered with huge basins—is about 20 times larger than expected, based on its current once-per-month rate of rotation. Now, researchers may have an explanation. A first-of-its-kind computer simulation suggests that the moon’s outer layers, and thus its rotational bulge, largely froze into their current shape to preserve the inordinately large rotational bulge about 4 billion years ago. Before that time, the moon’s spin rate was higher, the researchers report today in Geophysical Research Letters. The team’s model suggests that stems from a slower deceleration rate for Earth’s spin at the time, which affected the total amount of rotational momentum in the Earth-moon system and thus how rapidly the moon’s spin rate decelerates, among other things. And the fact that Earth’s spin rate wasn’t slowing down as quickly then as it is today hints that our planet had little or no ocean to slosh about and slow down our planet’s spin rate for its first 500 million years, the findings suggest. Or, the researchers propose, any ocean that did exist was largely frozen, possibly because of the sun’s 30% fainter output of radiation at the time.

De nødvendige organiske molekyler stammer fra nedfald af kometer og meteoritter, varmen kommer fra nedslagene, kulden kommer naturligt fra, at Solen var 27% svagere for 4 milliardet år siden og de nødvendige UV-stråler kommer fra Solen.

Hvis livet kan opstå på Jorden under sådanne betingelser, er det naturligt, at noget tilsvarende er sket på Mars for 4 milliarder år siden. Det giver derfor mening at søge efter tegn på gammelt liv på Mars.

 

[BjarneModerator Super Nova]

Problemet med livets oprindelse ses tydeligt i denne Nature artikel fra 2006:

Smallest genome clocks in at 182 genes

How much can you remove from a bacterium before it stops working?

Philip Ball

How small can a genome get and still run a living organism? Researchers now say that a symbiotic bacterium called Carsonella ruddii, which lives off sap-feeding insects, has taken the record for smallest genome with just 159,662 ‘letters’ (or base pairs) of DNA and 182 protein-coding genes. At one-third the size of previously found ‘minimal’ organisms, it is smaller than researchers thought they would find.

At the same time, a second group reports another bacterium, Buchnera aphidicola, also with a surprisingly small genome — at just over 400,000 base pairs of DNA it’s little more than twice the size of C. ruddii’s, but again smaller than anything seen previously. The human genome, by comparison, has 3 billion base pairs.

The discoveries, reported today in Science, suggest that only a remarkably small collection of molecular parts is needed to make up a viable life form. It’s rather as if a computer can be put together from just a handful of transistors.

This is encouraging news for synthetic biologists who are hoping to make designer bacteria from scratch, which could perform useful functions such as synthesizing pharmaceuticals or fuels.

Amparo Latorre of the University of Valencia, Spain, who co-authored the B. aphidicola work, says the genomes of both these symbionts are small enough to be made by today’s DNA-synthesis technology.

But researchers warn that the natural streamlined bacteria are both symbionts, dependent on their host organisms for certain functions or nutrients that they can’t provide themselves. “They can’t be grown on their own,” says Latorre.

Do-it-yourself

Geneticist Craig Venter, head of the J. Craig Venter Institute in Rockville, Maryland, is hoping that small-genome organisms will point the way to a minimal genome: the smallest possible set of genetic parts needed to generate life, from which an organism might then be designed and built. One of Venter’s goals is a synthetic bacterium that makes fuels such as hydrogen from renewable raw materials.
When Venter announced plans to synthesize a working genome from scratch in 2002, his team estimated that one well-studied bacterium needed at least 300 or so of its genes to survive.

But estimates have been getting smaller. A review published in Nature Molecular Systems Biology this year3 posited a hypothetical minimal genome of 113,000 base pairs and 151 genes — rather close to the new find.

Bare necessities

It is generally thought that a minimal genome will need to include genes for replication and for protein synthesis, and probably also for making the enzymes needed to construct basic building blocks, such as amino acids, from chemicals available in the immediate environment.

B. aphidicola challenges that idea, because it lacks the genes needed to make the essential amino acid tryptophan. Since the aphid hosts can’t make this amino acid either, where does it come from? Latorre and her colleagues think it is supplied by a secondary symbiotic bacterium, showing just how interdependent these groups of organisms may become.

“The work shows that all discussions of minimal genomes have to think about the environment in which the organism will live,” says Siv Andersson, an evolutionary molecular biologist at the University of Uppsala in Sweden.

C. ruddii seems even more extreme. “Its gene inventory seems insufficient for most biological processes that appear to be essential for bacterial life,” write Atsushi Nakabachi at the University of Arizona in Tucson, Masahira Hattori at the University of Tokyo, Japan, and their colleagues. At the moment, the researchers are not sure how C. ruddii copes, although they speculate that some of the necessary genes may have been transferred over evolutionary time to the genomes of the host.

That is precisely what is thought to have happened during the evolution of the compartments called mitochondria in our own cells, which are responsible for energy production. These are believed to have once been symbionts that lost all autonomy by relinquishing most of their genes to the host (mitochondria still have their own DNA).

Andersson says that C. ruddii might be analogues of mitochondria, caught in the process of changing from separate but dependent organisms into structures that will be engulfed and incorporated into the host cells.

Kun 3 gener kan kopieres uden en fejlkorrektionsmekanisme, som kræver ekstra gener. Problemet er springet fra 3 til 182 gener. Man har endnu ikke, såvidt jeg ved, nogen ide om, hvordan det er foregået.

 

[BjarneModerator Super Nova]

Denne artikel fra oktober 2017 finder, at nukleobaser blev dannet nogle få år efter nedfaldet af meteoritter. Dannelsen af RNA molekyler sker efter nogle få perioder med et skiftende vådt og tørt miljø:

The Fate of Nucleobases in Warm Little Ponds

Prior to the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favourable environments on the early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet-dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA. We couple Earth’s early evolution with complex prebiotic chemistry in these environments. We find that RNA polymers must have emerged very quickly after the deposition of meteorites (< a few years). Their constituent nucleobases were primarily meteoritic in origin and not from interplanetary dust particles. Ponds appeared as continents rose out of the early global ocean but this increasing availability of “targets” for meteorites was offset by declining meteorite bombardment rates. Moreover, the rapid losses of nucleobases to pond seepage during wet periods, and to UV photodissociation during dry periods means that the synthesis of nucleotides and their polymerization into RNA occurred in just one to a few wet-dry cycles. Under these conditions, RNA polymers likely appeared prior to 4.17 billion years ago.
Significance: There are two competing hypotheses for the site at which an RNA world emerged: hydrothermal vents in the deep ocean and warm little ponds. Because the former lacks wet and dry cycles, which are well known to promote polymerization (in this case, of nucleotides into RNA), we construct a comprehensive model for the origin of RNA in the latter sites. Our model advances the story and timeline of the RNA world by constraining the source of biomolecules, the environmental conditions, the timescales of reaction, and the emergence of first RNA polymers.

 

[BjarneModerator Super Nova]

‘Astrobiology – A Brief Introduction’ by Kevin W. Plaxco & Michael Gross

Jeg får den sidste på lager hos Amazon UK. Anmeldelsen er jo ret god, så jeg ser frem til, om

The authors, biochemists Kevin Plaxco and Michael Gross, have produced a well structured and clearly written book that aims to convince the reader that ‘astrobiology has a subject matter to study’.

astrobiologien nu også har et emne at studere, i den forstand, at man ikke springer over, hvor gærdet er lavest.

 

[nightskyDeltager Neutron star]

Og her er en god side om emnet, dog 10 år gammelt. Jack Szostak m.fl. står bag, hvilket vel siger ok for ens kildekritik.

The goal of this project is to use molecular illustration and animation to help describe origins of life research and theories to broad audiences. Illustrations and animations may be downloaded in the Resources for Educators section.

This website is part of a multimedia exhibit at the Museum of Science that includes live presentations on the Current Science & Technology stage and a touch-screen kiosk.

http://exploringorigins.org/index.html

 

 

[BjarneModerator Super Nova]

Ja. Molekylær biologi bliver hurtigt enormt kompliceret. Problemet er at kunne se de simplest mulige linier, da livet nødvendigvis må være startet relativt simpelt for at udvikle sig mod større og større kompleksitet. Hvilket Museum of Science er der tale om?

Science Park, Boston

 

 

[BjarneModerator Super Nova]

Jeg har modtaget bogen Astrobiology. Selvom det er A brief introduction, er bogen på 300 sider, så det vil tage lidt tid.

 

[BjarneModerator Super Nova]

Jeg vil kommentere bogen løbende for ikke at glemme detaljerne. Freeman Dyson påstår, at amerikanske bøger om livet aldrig inkluderer stofskiftet i definitionen af liv. Både Dyson og denne bog starter med Schrodingers berømte bog What is life? fra 1943. Schrødingers svar er (1) genetik og (2) stofskifte. Men han anvender mere fysiske termer: (1) order from order og (2) order from disorder. Bogen uddyber (2) på side 1: Schrodinger clarified that organisms can create ordered arrangements of molecules within themselves by creating even greater disorder in the environtment. Dette er netop, hvad en organismes stofskifte gør. Schrodinger forsøgte på ingen måde at forklare livets oprindelse, kun at forklare dets funktion i fysiske termer. Aligevel fortsætter bogen uden nærmere forklaring: Thus the evolution of highly complex organisms from a chaotic pool of simple, lifeless chemicals was kept in line with the immutable laws of thermodynamics. Dette er historieforfalskning. Det er selvfølgelig korrekt, at livets oprindelse skal opfylde termodynamikkens love. Men Dyson har ret. Det ligner en bortforklaring af Schrodingers klare henvisning til en organismes stofskifte.

Hvis stofskifte ikke er en del af livets definition, han man ikke som Dyson spørge: Hvad kom først? Genetik eller stofskifte?

 

[BjarneModerator Super Nova]

Situationen afklares på side 18 under Energy of Life, hvor man kan læse:

… , llife also requires energy to drive reactions that underlie its metabolism (stofskifte) and replication (genetik) machinery. This is obvious to a chemist, as living organisms create an implausible amount of order out of disorder, …

Dette var netop, hvad Schroedinger skrev, så hvorfor den forvirrende sætning på side 1?

Så kommer jeg til kapitlet om astrofysik. På side 22 står: “the Hungarian-born George Gamow”. Han var altså russer. “the British astronomer Edwin Hubble”. Hubble var altså amerikaner, selvom han var anglofil. “Moreover, when, in 1929, he measured the spectral lines”. Hubble var ikke i stand til at bruge en spektrograf. Det var V.M. Slipher, som startende i 1912, målte radialhastighederne for Hubbles galakser. Fodnoten nederst på side 23 er vildledende. Det er forkert at tro, at udtrykket Big Bang blot blev skabt for at latterliggøre Gamow. Hoyle var den første, som forstod, at skabelse af stof kun kan ske via et felt med et negativt tryk, som medfører en eksponentiel acceleration. Dette er også tilfældet for skabelse af stof og energi i Gamows univers. Big Bang hentyder til, at stoffet skabes i løbet af meget kort tid, hvorimod Hoyles steady state skaber stoffet løbende. Hoyles ide blev genopfundet i 1980’erne som et inflationsfelt, med en vigtig tilføjelse af kvantefluktuationer i inflationsfeltet. Det negative tryk sørger for, at ekspansionen forløber på en fantastisk ordnet måde. Universet bliver flad som en pandekage, og ekspansionen bliver ens i alle retninger. En sådan orden er tegn på en ekstrem lav entropi, idet entropi er et udtryk for uorden. Universets entropi bliver dog ikke helt nul på grund af feltets kvantefluktuationer. Levende organismer er kemiske systemer med meget høj grad af organisering, dvs lav entropi. At Universet (eller Multiverset?) startede på denne måde sikrer, at livet kan opstå. Der kræves selvfølgelig også kemi, som er bogens hjemmebane.

 

[BjarneModerator Super Nova]

Jeg fortsætter med at finde mærkelige bemærkninger i kapitel 1. Om James Jeans kan jeg læse: who calculated the relationship between gravity and the pressure within a protostellar nebula … Dette er korrekt, men bogen påstår at dette fandt sted … in the 1940s … Det fandt sted langt tidligere, men hvornår? Jeg har slået det op. Jeans lange artikel blev offentliggjort i 1902!

Den moderne kosmologis resultater bliver beskrevet i teksten uden en omtale af inflationsfeltet. Der er dog en sidebar 2.2 på side 39, som introducerer det Antropiske Princip med ordene: In astrobiology, however, the Copernican principle itself must be held suspect, for the very fact of our existence has profound consequences, … This idea is called the “antropic principle”. Det kopernikanske princip blev tidligere anvendt som argument for, at universet måtte være homogent og isotropt. Det er mere en antagelse end en fysisk begrundelse. Det store problem ved antagelsen er, at gravitationen tenderer til at gøre universet mere og mere kaotisk. Hvad er den fysiske forklaring på Universets homogenitet? Hvordan er Universets indhold af stof og energi skabt? Svaret på disse spørgsmål er et inflationsfelt, som jeg tidligere har omtalt. Det kopernikanske princip er ikke blevet anvendt i de seneste 35 år. Sidebar 2.2 slutter med at omtale inflationsuniverset. I denne sammenhæng introduceres Multiverset som en speciel variant af inflation, hvor forskellig dele af rummet har forskellige naturkonstanter. Vi kan selvfølgelig kun observere den del af Multiverset, hvor konstanterne har værdier, som tillader at liv kan opstå.

Inflationen nævnes altså, men nærmest som en undskyldning til sidst. Der er desuden en direkte fejl i venstre side af figur 2.6. Det er altså en planetarisk tåge, ikke en nova, som vises.

Jeg er lidt træt af at læse korrektur, så jeg vil springe frem til kapitel 4 om kemi. Jeg formoder, at forfatterne føler sig bedre hjemme i kemi end i asytrofysik. Jeg ved til gengæld meget mindre om kemi, så jeg opdager ikke enentuelle fejl.

 

[BjarneModerator Super Nova]

Jeg har nu læst kapitel 5 The Spark of Life. Dyson har ret. Plaxco når som biokemiker til slut frem til, at livet startede med RNA molekylet. Han gennemgår dog først forskellige geologiske/geokemiske forløbere, som han dog finder helt uden evidens. Han mener, at et netværk af katalysatorer ikke kan udvikle sig. Den eneste mulighed er eksistensen af et molekyle, som kan katalysere sin egen kopiering. Man opdagede for 35 år siden, at et foldet RNA molekyle kan kopiere et andet ufoldet RNA molekyle, men det viste sig enormt vanskeligt at finde et stykke RNA, som bare kunne kopiere 14 monomere enheder. En foldning kræver desuden, at de monomere enheder alle har samme chirality (venstre- eller højrehåndet). Plaxco viser, at en tilfældig polymerisering af et sådant RNA molekyle er astronomisk usandsynlig. Der skal 40000 solmasser RNA molekyler til, før man rammer det rigtige.

But does this render the RNA-world hypothesis invalid? It does not. … the anthropic principle says that even super-astronomically improbable mechanisms may lie at the heart of the origins of life … the probability of life arising in our Universe is not zero, but it could be infinitesimally close to zero.

Dette er ikke mine ord. Det er bogens argument for, at livet startede med et selvkopierende RNA molekyle. Jeg gad vide, hvad der skal til for at gøre hypotesen falsk? Vi kan ikke forvente at finde liv i Mælkevejen, hvis dette er sandt. Sandheden er, at man intet ved om forløberne for de levende organismer på Jorden. Man bør efter min mening holde alle muligheder åbne. Det er dumt på forhånd at antage, at generne kom før et stofskifte i form af et enzymnetværk. Det ville være interessant at læse, hvad geologerne og geokemikerne mener om denne sag.

 

[nightskyDeltager Neutron star]

Den er svær at gøre falsk. Hvis vi er er liv og sandsynligheden for selvkopierende RNA er tæt på nul, men dog ikke nul, så kan man vende den rundt og med god grund sige at hvor usandsynligt det end er, er det sket. Indtil vi har en teori om at det kan være foregået på en anden måde, kan vi ikke dømme denne hypotese ude.

Hvis sandsynligheden for liv er tæt på nul ud fra denne hypotese, skal vi så acceptere vi er alene i universet?

Jack Szostaks forskning er spændende i denne sammenhæng.

Se bla. her http://molbio.mgh.harvard.edu/szostakweb/publications/Szostak_pdfs/Szostak_2016_MedicinaB.pdf

 

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