Book Review: ‘The Genesis Quest’ by Michael Marshall.

One of the most fundamental questions waiting to be answered by science is “How did Life on Earth Begin?” For most of human history this question was answered by a story from myth or legend rather than by science. Our local chief god created the universe and all living things in some way. The first chapter of Genesis is not only a typical example of this but even gave us the word that we use to describe the whole process, genesis.

Why is it that all of the legends and myths about the beginnings of life always make our creation the climax of the story? (Credit: Wikipedia)

Basically our ancestors thought that ‘who’, created life was more important than ‘how’ it was done. After all we poor humans could never understand the mystery of how life was created. That was god’s greatest secret and it was enough for us to know that he did it. It’s only been since the start of the scientific revolution and Darwin’s demonstration that all modern living creatures have evolved from earlier forms of life that scientists first began to wonder how the first living thing, the ancestor of all life on Earth ever became alive.

Darwin’s Theory of Evolution by Natural Selection is really about what happened after the first living thing came into being. Darwin was very cautious about how that first living thing originated. (Credit: AZ Quotes)

The search for a answer to that question is the thesis behind Michael Marshall’s new book ‘The Genesis Quest’. Starting at the very beginning Marshall discusses not only the mythology but also several reasoned although not scientific hypothesis such as the èlan vital and spontaneous generation. It’s once the actual chemists and biologists begin working on the problem however that ‘Genesis Quest’ really gets good.

Cover of ‘The Genesis Quest’ by Michael Marshall. (Credit: Amazon)
Author Michael Marshall is a Science Writer for several magazines who has published several books on science. (Credit: Goodreads)

Reviewing the early advances on just what life is and where living things come from Marshall has certainly done his homework. From Robert Hooke’s discovery of cells, Antonie van Leeuwenhoek’s descriptions of microscopic ‘animalcules’ and Friedrich Wőhler’s first synthesis of an organic chemical to Darwin himself we see how science was forced, almost against itself to consider the question of how the first living thing came into existence.

Antonie van Leeuwenhoek using his microscope to observe the ‘animalcules’ in a drop of pond water. (Credit: Vox)

By the way I just illustrated one of the key elements of ‘Genesis Quest’, you will be reading about a lot of discoveries made by a lot of different scientists. Some of the scientists will be famous, like Louie Pasteur but there will also be some not so famous ones like botanist Matthias Schleiden who was the first to definitely assert that all living things were made of cells. In Marshall’s telling each of these discoveries becomes a tale in itself and the whole becomes woven together for a grand story, the ‘Genesis Quest’.

Louis Pasteur is generally given credit with finally putting an end to ideas about ‘Spontaneous Generation’ of living things. But it must have happened once billions of years ago. (Credit: ThoughtCo)

In fact the cast of characters in ‘Genesis Quest’ is so large that it’s difficult to keep track of everyone without a scorecard. For example the physicist George Gamow, best know as an early proponent of the Big Bang theory is given a brief mention because he was the first to suggest that a group of three DNA bases could provide the code for the 20 amino acids used in the proteins of living cells. Gamow’s steady-state rival, astronomer Fred Hoyle is also mentioned because late in life he became an adherent of life on Earth originally coming from outer space, a theory known as Panspermia. (I mention Gamow and Hoyle because I just ordered a new book “Flashes of Creation” about the beginnings of the Big Bang theory in which Gamow and Hoyle are the two main characters. I can’t wait to read it!)

Physicist George Gamow (l) and Astronomer Fred Hoyle (r) fought for decades over not just the origin of life but the origin of the Universe itself. (Credit: Hacker News)

Much progress was made during the 20th century as Alexander Oparin and J. B. S. Haldane first developed the ‘primordial soup’ model of the beginning of life. This model saw its greatest success with the Miller-Urey experiment in 1953, which even today is still touted as evidence that simple chemical reactions on the early Earth could produce complex organic compounds.

British geneticist J. B. S. Haldane helped popularize the ‘Primordial Soup’ model of life’s origin. (Credit: The Economist)
The Miller Urey experiment was so simple yet the results so profound that it made the ‘Primordial Soup’ model dominate for decades. (Credit: Research Gate)

But 1953 was also the year that Watson and Crick first described the shape of the DNA molecule and in the years thereafter the very intricate and complex mechanism by which DNA builds proteins, DNA to Messenger RNA to Transfer RNA to Ribosome to Protein was discovered bit by bit. Such a complex chain of very delicate chemical reactions could never have arisen spontaneously in a primordial soup. So a new model of RNA first for the beginnings of life arose to challenge the protein based primordial soup model.

It’s actually a lot more complicated than this. How the Primordial Soup could generate such complex chemical reactions was difficult to understand so new models for life’s origins had to be developed. (Credit: Expii)

However both proteins and nuclides don’t last long in nature, so another model; a cell wall first model was also developed. From the 1970s throughout the 1990s these three models fought fiercely over who was right with none of them able to gain the upper hand.

All of the structures inside a cell are rather delicate needing a ‘Cell Wall’ for protection. How did the pre-biotic chemicals protect them selves. (Credit: Science Facts)

Finally, in the last chapters Marshall discusses the modern synthesis that has developed since about 2000. A self-replicating molecule contained inside a lipid shell, something that has already been achieved by the chemist Jack Szostak. Marshall also asks the question, just how complex do ‘protocells’ like Szostak’s have to be in order to be considered ‘alive’. Have we in fact already created life in the labouratory?

Current leader in the race to develop synthetic life is Nobel laureate Jack Szostak at Harvard. (Credit: Ciencia del Sur)
Doctor Szostak has already developed a ‘species’ of protocell that meets several of the criteria of life, including replication! (Credit: Church and State)

Throughout ‘Genesis Quest’ Marshall manages to keep his descriptions of the, sometimes very sophisticated experiments and theories both simple and understandable. At the same time however he also includes footnotes with more technical information as well as sources for further reading. A well regarded science writer whose has worked for both New Scientist and the BBC Marshall knows just how much detail is needed in order to tell the story he wants to tell. ‘Genesis Quest’ is in fact a fast paced, very enjoyable overview of one of the most important scientific endeavors of all time. I cannot recommend it enough to anyone who is interested in how science and scientists work.   

Paleontologists are making progress in unlocking the secrets of two of the most events in the history of life here on Earth.

There have been many events in the long history of Earth that have shaped the course of the evolution of life for millions of years. Whether it be the rise of multi-cellular organisms or the asteroid that ended the reign of the dinosaurs, life today would be very different if those events hadn’t happened, certainly we wouldn’t be here. 

The history of life is a combination of gradual change and Earth-Shattering events. (Credit: www.seeker.com)

In today’s post I’ll be talking about recent progress that is being made in understanding two of these events. One of those events was the first time that an animal with an internal skeleton, a vertebrate left the ocean to walk on land but I’m going to start by discussing new revelations concerning the very origin of life itself.

Timeline of the history of our Planet. (Credit: Slideplayer.com)

Scientific speculation about the origin of life began even before Darwin published his ‘On the Origin of Species’ but for about a hundred years it was little more than speculation. Then in the 1950s the Miller-Urey experiment was performed showing how easily the gasses that made up our planet’s early atmosphere could be converted into complex organic molecules like amino acids. (For more information on the Miller-Urey experiment see my post of 9 March 2019.)

Setup of the Miller _ Urey experiment. (Credit: Big Picture)

For the last fifty years however real progress in determining the chemical path that led to the first living things ran into a roadblock, the chemical phosphorus. You see phosphorus is critical in many of the chemicals processes in living cells; Adenosine triphosphate is often referred to as the match that lights the chemical engine of cell metabolism while phospholipids make cell membranes stronger and more watertight. Perhaps most importantly phosphorus is an essential element in the formation of both the DNA and RNA molecules that form the genetic code of life.

The Chemical Structure of Adenosine triphosphate. The phosphorus atom on the far left contains a lot of easily usable energy. (Credit: Wikipedia)

Problem is that phosphorus doesn’t usually combine well with organic chemicals, combining more easily with calcium, an element that is abundant in the oceans. This leaves very little free phosphorus around with which to create the first living things. Biochemists were stumped, to build the first living creatures you need phosphorus, where did those, not yet living, complex organic compounds get it.

Jonathan D. Toner and David C. Catling of the Department of Earth and Space Sciences at the University of Washington have recently suggested a solution to this problem. In their paper published in the ‘Proceedings of the National Academy of Science’ they have suggested that carbonate rich lakes might be the locations where phosphorus was incorporated into organic chemistry. You see carbon bonds with calcium even more strongly than phosphorus does. So lakes that are rich in carbonates will use up all of the calcium leaving whatever phosphorus there is free to get incorporated into organic compounds.

Mono Lake in California. It may not look hospitable but there is plenty of primitive life here. (Credit: News Deeply)

The kind of lakes we’re talking about here is not the sort commonly considered hospitable to life. Lakes with little or no outlets where salts and other chemicals can build up. Mono Lake in California and Lake Magadi in Kenya would be a good examples. Although such environments are hostile to advanced forms of life they are often rich in primitive bacteria and algae.

Lake Magadi in Kenya is famous for the huge number of Flamingos that feed on the small crustaceans there. (Credit: Africa Dream Safaris)

Doctors Toner and Catling have even measured high levels of free phosphorus in many such lakes, see chart below, demonstrating that the more inorganic carbon in the water, the more free phosphorus there is as well. Other scientists will have to critique and challenge Toner and Catling’s theory before it’s accepted but it certainly looks as if they may have found the solution to a longstanding problem.

Phosphorus levels versus free carbonates in lakes examined by Toner and Catling. (Credit: SciTech Daily)

Another crucial event in the history of life occurred when the first vertebrate crawled out of the water and onto the land. From the paleontological record we know that this transition occurred during the late Devonian period some 3755 million years ago. While the actual species of fish that first succeeded in wiggling out of the water is a subject of debate one possibility is Tiktaalik rosa, see image below, discovered by Neil Shubin of the University of Chicago and Edward Daeschler of the Academy of Natural Science here in Philadelphia.

Artists impression of Tiktaalik roseae. (Credit: Paleocast)
Proposed family tree of the fish who crawled out of the ocean. (Credit: Pinterest)

Looking at Tiktaalik it is immediately obvious that this animal is not a streamlined swimmer. In fact Doctors Shubin and Daeschler think that Tiktaalik crawled along the bottom of shallow, muddy lakes and ponds using its four fins more like legs than fins. Such an anatomy and lifestyle seems perfect for the first land walker but it also raises the question of how did the fins of a fish evolve into the proto-legs of Tiktaalik. Now Doctors Shubin and Daeschler, along with a few of their colleagues, have published a new paper comparing the limb-fin of Tiktaalik to those of related, and thought to be ancestral species, Sauripterus taylori and Eusthenopteron foordi.

First the researchers used CT scans of the fossil remains to construct 3-D models of not only the bones in the animals fins but also the cartilage and dermal (skin) rays. The 3-D model allowed the researchers to rotate and examine the entire skeletal structure bringing out details that are commonly lost in removing the bones from the rock encasing them.

Dermal rays of the pectoral fins of T roseae. (Credit: Thomas A. Stewart et. al.)

What the scientists discovered was that the evolution from the earlier species to Tiktaalik involved a reduction in the dermal rays of the fins. At the same time the top and bottom of the fin lost their symmetry, the top growing faster than the bottom leading to the formation of a ‘palm’ in the fin of Tiktaalik. Such a structure would have been able to act as a support base when Tiktaalik rested on the bottom of a pond, or on land.

The water to land transition was one of the most important events in the history of life. Thanks to the work of Doctors Daeschler and Shubin we are now filling in some of the minute details of the anatomical changes needed to make that transition. Bit by bit other paleontologists are filling in the details of other events as well giving us a clearer picture of how life evolved into all of the many the living things on Earth today.

It probably didn’t happen this way! (Credit: Thumbpress.com)

Have Scientists taken a critical step in understanding the Chemistry of how life began and an update on our Interstellar Visitor.

Ever since Charles Darwin’s ‘On the Origin of Species’ had demonstrated that all of the multiform types of living creatures here on Earth had evolved over millions of years from a single primitive type of life scientists have sought to understand how that first living thing came into being. Much has been learned in the last 150 years but many of the details of the chemistry involved in the development of a complex, self-replicating molecular system, i.e. a simple living cell, are still unknown.

Now researchers at The Scripps Research Institute (TSRI) have published a paper in which they claim to have found a chemical compound that played a key role in assembling short nucleotide chains (early genetic material) with peptide chains (short version of proteins) encapsulated in a lipid vesicles (early cell walls). Finding a catalyst that could combine these three distinct types of chemicals, and which could have existed on the primitive Earth has been a goal of ‘Origins of Life’ researchers for the past several decades.

The scientists at Scripps have given their compound the name diamidophosphate or DAP for short and have published their results in the journal ‘Nature Chemistry’. The figure below shows the chemical diagram and the structure of DAP.

Chemical Formula for DAP (Credit: Ramanarayanan Kirshnamurthy)

Structure of DAP (Credit: Ramanarayanan Krishnamurthy)

According to lead researcher Doctor Ramanarayanan Krishnamurthy DAP “would have allowed other chemistries that were not possible before, potentially leading to the first simple, cell based living entities.” “With DAP and water and these mild conditions, you can get these three important classes of pre-biological molecules to come together and be transformed, creating the opportunity for them to interact together, ” Krishnamurthy said. The image below shows DAP and the three classes of chemicals needed to build a simple cell.

DAP linking three classes of pre-biological complex compounds (Credit: Ramanarayanan Krishnamurthy)

Whether or not DAP was THE chemical catalyst that enabled the formation of the first living cell will be difficult to prove four billion years after the fact but Dr. Krishnamurthy and his co-authors intend to continue their study of DAP and other phosphorylating compounds. If you’d like to read the press release put out by the Scripps Institute click on the link below.

https://www.scripps.edu/news/press/2017/20171106krishnamurthy.html

Before I go I’d like to take a moment to update one of my posts of just last week (4Nov17) about the interstellar visitor that entered our solar system and is now on its way back into the void between the stars. Well A/2017 U1 has been given the new name of 1I Oumuamua. The 1I indicates that it is the first interstellar object ever discovered while Oumuamua is a Hawaiian word meaning scout or Messenger. 1I Oumuamua was discovered by the Pan-STARRS telescope in Hawaii after all. The image below shows Oumuamua’s path through our solar system.

Path of 1I Oumuamua through our Solar System (Credit: NASA-JPL-Caltech)

 

More importantly a group of Astronomers are preparing a paper in which they give their estimate as to the place of origin of Oumuamua along with how long it took to reach our solar system. Working backward along the trajectory of Oumuamua Eric Gaidos and Jonathan P. Williams of the University of Hawaii along with Adam Kraus of the University of Texas are of the opinion that Oumuamua originated in the Carina and Columba Associations, clusters of young stars at a distance of 215 to 365 light years. (Carina and Columba are constellations in the southern sky).

Current research estimates that the Carina and Columba Associations were an active star-forming region about 45 million years ago. If Oumuamua had been thrown out of a newly forming solar system in the direction of our Sun at a velocity of 1-2 kilometers per second it could just now be arriving in our solar system!

Even though Oumuamua was only near enough for us to study it for about a month we have already learned a great deal from it. This is only the start, in the years to come I have no doubt that we’ll be learning a great deal more.