Geological time scale (part 1)

I first knew about the geological time scale during my college years, back then the only geological time i knew was “Jurassic” due to a certain Hollywood movie. Learning it was fun but memorizing it for exams was horrible. The lecturers will first show the scale like the one here (very very boring btw), and they will explain one by one what happened with pictures of dinosaurs, plants, ancient humans and etc. It was remarkable, but how did geologists came to this scale always puzzled me, it still does, as we have loopholes in it too. The scale is basically a convention agreed by geologists based on research which were agreeable from time to time.

Here i will briefly explain some key events and how they got there. Most importantly i will put emphasis on how and when life started, the rest is evolution which you can read/view elsewhere. I will be also breaking this topic to a few parts for easy understanding.

Lets start,

After the big bang, the HADEAN period named after Hades begin. The sun was already formed and the rise of giant planets (Jupiter and Saturn) could have happened during this time. This is based on “numerical models“. After the formation of Mars, earth was finally formed in it’s hottest state (hot as hell). It is also postulated that the moon was also formed right after this, and her origins came from earth. Check out the video below on how this could have happened

From here on, our primitive atmosphere begin to arise, which is absolutely hypothetical in case you were wondering. After this particular sequence of events, the building of the habitable earth begins. The first proto ocean were already in play after the cool down effects on earth . There are some speculation that life could have started here; but right after this, the late heavy bombardment (LHB) of comets and meteorite came showering on earth, the planet was destroyed, water evaporated completely and it was a mess. This phenomena is also observable on the moon .If you have wondered why the moon has craters, its because of LHB (despite not having tectonic plates etc).

Now, The ARCHEAN period begins, which is generally the post HLB. Earth during this time has a lot of minerals and more water because of the LHB. In other words, she has received more materials to allow life to flower.

The rest of story is to be continued in the near future, stay tuned

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What makes life work

Life as we know it displays a high degree of organization. All living things look different only on the outside but inside, all of them have the same molecules and systems. The fundamental chemicals of life consist of fats (lipid), proteins (amino acid), DNA/RNA (sugar) and water. This is universal. Basically, Lipid plays a role of the membrane, protein as the building blocks and DNA/RNA as the genetic materials. Amino acids are the monomers of proteins. Interestingly life only utilizes 20 amino acid to form proteins (we call them proteinous amino acids). When amino acid joins each other they become a poly-peptide by forming a peptide bond. Proteins are a combination of large polypeptide. Now when it comes to genetic materials, we have our DNA and RNA which are made up by nucleic acids. Both of them consist of a ribose sugar, a phosphate group and bases. The bases are important since it is used in transcription and translation. Both these processes are fundamental in the building of life. I suggest you take a look at the video below. Every hormones and enzymes which came into existence in your body are through this way. its mechanism is simply amazing (and this happens from the simplest of cells to the biggest whale in the world!!).

When you put all the ingredients together you get life. NO. all this molecules will simply flow aimlessly unless you put them in a cell. This increases the concentration and separates the molecules from the outside world. But then again this is still an impossible feat in synthetic biology. However this does not stop scientist from trying to get this to work. The video below is simply an example on how to make “life” from raw materials and make them “function”.

Generally, origin of life studies are categorized in either being a ‘bottom-up’ strategy or a ‘top-down’ strategy. A bottom up strategy involves using basic chemical mentioned above and putting them to certain feasible environmental stress and see what they do (like the video above). On the other hand the top-down methods, looks at modern biology and uses information from there to extrapolate towards the simplest living entities. Hopefully by using both approaches we can find a mutual meeting point.  But this is going to take time, lots of time.

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Origin of life – a brief history

The study of astrobiology involves 3 things, finding the origin of life, finding aliens and also the future of life. The latter is fully theoretical and often described as the one for the future. When it comes to finding aliens (FA), we are looking for more simpler life forms (bacteria etc), the complex ones are mostly being investigated by the UFO junkies. I will touch on FA in the future. My focus today will be on origin of life (OL).

Viewpoints from all over the world has shaped the philosophy and early sciences in regards to the OL. In 1778, Buffon, a french naturalist was one of the first to postulate the origin of life theory, he claimed that during the early stages, with colder temperature (probably referring to the ice age), organic molecules could produce spontaneous generations, thus producing each species as we know them now. 80 years on, Charles Darwin wrote a letter to Joseph Hooker, a botanist describing a primordial condition on earth:

 It is often said that all the conditions for the first production of a living organism are now present, which could have been present. But if (and oh what a big if) we could conceive in some warm little pond with all sort of ammonia and phosphoric salts,—light, heat, electricity, present, that a protein compound was chemically formed, ready to undergo still more complex changes, at the present day such matter would be instantly devoured, or absorbed, which would not have been the case before living creatures were formed.

Darwin was referring to the OL. He did not define or even hinted about how the origin of life might have been in his famous book. Since his work in “origin of species” involved the history of life, he must have thought that there must have been a starting point. However, OL questions were considered buried once Louis Pasteur concluded that life came from preexisting life-forms. He stood by his words that there is a difference between non-life and life, hence life would not have occurred by inert molecules. In 1917, a young Russian, Aleksandr Oparin begin thinking; How did life first started. He wrote his thoughts in his book The origin of life; published in 1924. During the same time JBS Haldane, a British born geneticist independently publish an essay indicating the similar ideas to those of Oparin’s. Hence, the Oparin-Haldane hypothesis was introduced. Oparin suggested that organic chemicals could have went through a series of reactions which would then lead to more complex aggregates. The aggregates then form a colloidal mixture in watery environment. He calls them ‘coacervates’. Coacervates would be able to perform simple metabolic functions and with evolution become the first life form. Haldane posed a similar idea where the primordial sea would serve as a chemical reservoir powered by the sun. He also added that the group of chemicals was enclosed in a lipid membrane system, thus developing to become the first living cells. He coined the term ‘prebiotic soup’, and this became the expression of the Oparin-Haldane view of the origin of life.

In the early 1950s, Harold Urey, already a nobel price winner for his discovery of heavy water simulated a chemical model of primitive atmosphere. This was done with his then graduate student, Stanley Miller. They put up a mixture of simple gas to an electrical discharge, any products from this will accumulate in the flask below the apparatus. They left the experiment to run for a week. The products of the experiment contained organic chemicals including several amino acid (monomer of proteins). This results were indeed ground breaking and became an instant sensation among fellow scientist. The detection of amino acid shows that natural laws allows them to be synthesized under prebiotic condition. Till date many modified version of this Miller-Urey experiment has been conducted which further enhance our knowledge of creating amino acids from simple gas or molecules. Miller-Urey experiment started the bandwagon, on what kind of life’s chemicals can be created prebioticaly. John Oro showed that the highly reactive hydrogen cyanide under alkaline conditions will polymerize to become adenine, a nucleobase essential to DNA. Lastly in 1978, Dave Deamer and co-workers managed to produce vesicle from fatty acids under certain prebiotic condition. The vesicle here mimics a simple membraneous vesicles. He then used fatty acid extracted from Murchison meteorite (carbonaceous chondrites) to produce vesicle with prebiotic conditions. This indicates that fatty acid formed in space had/has the capacity to form vesicles which can encapsulate DNA or proteins to possibly form the Proto-cell.

The discoveries mentioned above are landmark discoveries which gave scientist the hope that we can get closer to the origin. The experiments (and many more) indicates that under prebiotic condition we can produce life’s chemicals. When it was discovered that Europa could have an ocean below its ice crust; and Mars used to have seas, scientist became excited because if Primitive Earth can yield life’s chemicals towards living beings, then the same could have/had happened in Mars and Europa respectively.

What i have mentioned above is simply a brief history of OL, many experiments have been conducted ever since. Its worth to mention that there are many limitation and unsolved riddles when comes to this study. For example, although we can produce amino acid prebioticaly, there isn’t a prebiotic way where we can polymerize the amino acids to proteins. Also on close examination, life is very selective; only left handed amino acids are utilized to perform life’s activities. But in prebiotic experiments (e.g Miller-Urey), a racemic mixture is always produced, in other words 50% right handed and 50% left handed amino acids. There are many hypothesis that can explain on why these phenomena known as homochirality happens, but there are no explanations on HOW this must have happened 3.5 billion years ago. If we look further into the formation of genetic materials, it is known that DNA denature under prebiotic temperatures (200 C to 400 C). So how did the DNA molecules formed when the earth was hot as hell?. This is only the the tip of the iceberg. Till then this is the story we have.

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Why science can’t define ‘LIFE’

Science defines most things in the world, but do you know that science has no proper definition for life?

World religion including Hinduism, Christianity or Islam adheres to the ‘meaning’ of life more than the definition of life. Many early western philosophers used the similar notion ‘soul’ or vitality elements to define life. However, as much as we see life flourishing in abundance, modern day scientists are still finding the proper definition of life as a staggering act. The spiritual aspects regarding life remained despite the scientific approaches supporting the origin of life (e.g Haldane, Oparin, Urey and Miller etc).

I will present some of the definitions of life and their contradictions in this post. Firstly, its important to know that the definition itself can be broken down in many ways in terms of physiological, metabolic, biochemical, genetic and thermodynamic forms (C.E Cleland, 2002). All of them had/have strong counter arguments.

For example, NASA’s working definition is: “Life is a self sustained chemical system capable of undergoing Darwinian evolution” (Joyce, 1994ab). Despite being ‘considerably’ accepted within the astrobiological community, Darwinian evolution requires the ability to reproduce. Consequently, a conclusion can be drawn that worker ants or mules should be considered as non-life although we know otherwise intuitively.

A second example, Guimaraes defines “The functions, which are called life are metabolism, growth, and reproduction with stability through generations” (Kolb, 2006).  If we look at ‘growth’ as a criteria, the same is also validated for inorganic crystals, which could grow with the right nutrients. Development in organism get adjusted to regulated trajectory, the similar happens when local surface trajectory influence the course of metal oxides crystals (Cairns-Smith, 1982). Even clouds ‘grow’ and become numerous, depending on the weather patterns.

In terms of thermodynamics, life have a low entropy system. This means life maintains a high degree of order. On close examination, life is very selective, for example; only left handed amino acid (protein builders) and right handed sugar (DNA) are utilized to perform life’s activities. This is referred to as homochirality. Even the simplest bacteria Mycoplasma pneumonia when studied in detailed is highly complex. However, a chemical system criteria alone is not enough since many non-living entities do those as well (i.e formation of stars).

Don’t you think it’s rather awkward that we only know life intuitively (on earth at least) but can’t properly define it. The importance of defining life would be very useful since we can streamline all our technical approaches to promisingly identify alien life forms in space (Titan, Europa), unless the green man himself decides to land on earth and say ‘こんにちわ’ (hello in Japanese), millions of dollars could be saved.

On the contrary, the unpopular term “autopoiesis” to define life is slowly making a comeback, despite several misconception and misgauge of the term within science (Boden, 2000). The word ‘autopoiesis’ was first coined by the Chilean duo Humberto Maturana and Francisco Varela in the early 1970’s. (By the way Francisco is the father of Leonor Varela). 

Their definition of life was ill received from mainstream scientist because it was not in tandem with Darwin’s theory of evolution and also DNA making its entry as an important aspect in biology during that time.

Autopoiesis literally means self-producing in Greek. The authors described that life is defined as a unity with a network of producing component (Maturana et. al 1974), in other words an autopoiesis system is capable of organizing the production of its own components that is within a boundary (a membrane is a boundary of a cell) (Luisi, 2003) The term deliberately down plays the importance of genetics (DNA and/or RNA) and focuses on the boundary which holds life’s system. This is simply because Darwinian theory reflects more on the general populations than on the individuals. Before his death in 2001, Varela expressed autopoesis in the following ways: verifying (1) whether the life’s system has a semipermeable boundary that (i.e cell membrane) (2) life is produced from within the system (i.e metabolism) and (3) that encompasses reactions that re-generate the components of the system (i.e transcription) (Varela 2000). Autopoiesis is gaining popularity and few are already using it for synthetic biology (i.e Luisi’s group) and the origin of life field specifically to recreate the proto-cell (Morowitz‘, Deamer‘, Szostak‘ groups).

As mentioned earlier, the specific definition of life is important if we are to understand our origins and to find aliens (i am being real here). But, with the latter, we can’t really rely on earth’s life definition (even if have one) itself since there is a possibility that aliens may be define in other ways beyond our current state of biology.

Ps: I would advice readers who don’t have a formal biology/chemistry background to click on the hyperlinks if they find it difficult digesting the post. I have included wikipedia pages, youtube links and journals (you can download some of it). So do take your time understanding it. Also do give some thoughts on what you think the definition of death might be. 

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Why write a science blog – the reasons

Coming from ‘cell’ and ‘relics’ put together, was registered because the cooler space science related names are already taken. My friends keep on asking me about the purpose of doing this blog, and i almost always replied that i am doing this to get women’s attention. Since online dating is the new way to meet potential love; so why not have a blog to show off your ambitions to future partners.

Now on the nobler part of my intentions; here it goes

Science should be freely available to the public. Despite taxpayers money being used for most grants and post-grad scholarships, the fruits of science are only enjoyed within the academic and research community. Its rather ridiculous when a layperson wants to get his hands on scientific literature, he/she has to pay for it. If you don’t believe me please visit Sciencedirect or Taylor&Francis, these brands are a norm for researchers. Also look at their free sample journals, please take a look at the acknowledgment section; most likely you will see the authors stating that the $$$ is coming from some national/governmental organization, which means your money. By the way, when i use the word ‘scientific journals’ i do mean peer reviewed journals, which means that the data and science has been reviewed from another equally qualified scientist. The reason i am mentioning this is simply because you can get journals which are NOT peer reviewed and are made available. You can find them from pharmaceutical and food related industries, they constantly produce “journals” telling you how their products are scientifically proven. So the next time someone tells you that product X is scientifically proven, ask them if the scientifically proven paper is peer reviewed or not. Always remember, that real science only comes from peer reviewed journals.

So with all the mentioned reasons above, this blog was created to act as a platform where available literature are made understandable to the mass. I do hope that someday, scientific journals becomes completely open access. For now there are some notable ones such as PLoS, which is incidentally highly regarded.

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My first post-Introduction

Hi there, I am Kuhan, a doctorate student doing research on astrobiology (please see my linkedin to know the details).

Astrobiology is about finding aliens and to figure out the origin of life. If you don’t believe there is such a field, please don’t hesitate to google it. The blog is all about my research and what interest me in the field. I will be posting topics which i will be using in my future dissertation. Somehow i hope this will motivate me to write more. I will try not to be super technical and i do hope you will enjoy it. Don’t forget to follow me on twitter and facebook.