Is there anybody out there?

This piece in November promised a lot more and I have failed to deliver on my promise so far. This is my first attempt to catch up with what I had promised. This post will deal with the chemicals that one finds in asteroids that land on Earth and with it questions the possibility that the raw materials for life on Earth could have started by the availability of these chemicals and also discuss the possibility of panspermia.

First, I will start with astronomical spectroscopy. This is the method by which chemists identify the compounds present in space. When light or any electromagnetic radiation is passed through a sample, the sample absorbs and emits certain wavelengths of light better than others and the wavelengths that are emitted and absorbed can be used as a fingerprint analysis of the chemical nature of the compound itself. Unfortunately, the science is not as simple* as I mention here but will suffice for the discussion that follows.

There have been many meteors that have hit the Earth's surface and some of these impacts have been seen as the reason for major climate change in the Earth. The interest in astronomical spectroscopy was purely to understand the physical and chemical nature of the universe around us. But as soon as astronomical spectroscopy developed into a reliable science, it stood to reason that it could lead us to understand how life on Earth originated and whether there are traces of life elsewhere in the universe. Afterall, if life evolved on Earth, the chemicals responsible for life should have been present on Earth before that (and possibly elsewhere) and hence the chemical nature of these meteors became important to biology as well, but all these studies have not been localized to the meteors alone.

The interstellar medium is divided into the dense and diffuse kind. The diffuse interstellar medium is cold and icy material that is not too dense and is made up of neutral and charged ions of compounds of C, H, and N, and also contain compounds such as naphthalene, which are aromatic compounds. In the dense interstellar compounds, the temperature is close to 10K to 200K (freezing point is 273K) important compounds such as hydrogen gas, carbon monooxide, water, carbon dioxide, methane, methanol, ammonia and hydrogen disulfide were found among others. That is, it has a source for H, C, N, O, and S. Later, in some clouds they have also found organic acids and higher alcohols such as ethanol (pure delight!).

The meteorites that have hit close to home were found to be quite rich in the lower and higher organic compounds of the classes mentioned above but were also found to have trace quantities of natural as well as unnatural amino acids (natural defined as biologically natural), purines, and pyrimidines (the base compound in DNA and RNA). In addition trace quantities of phosphonates and other P containing compounds were also found (also found in DNA and RNA). What was also interesting is that some of these amino acids was found to be chiral in nature (like in biological systems). In other words, there is a way in space to make optically active compounds and not synthsize all the isomers in equal quantities. It is actively debated whether these meteors were contaminated by biologically active components on their way to the ground even though there is evidence that says that it was not contaminated.

To summarize, the raw materials for life to start could be found in meteors and other components of space and indeed, these compounds under the right condition could lead to life anywhere. I will deal later with attempts by scientist these days to understand how life started from these raw materials.

I would like to end with panspermia and I think wikipedia has a good definition - Panspermia is the hypothesis that "seeds" of life exist already in the Universe, that life on Earth may have originated through these "seeds", and that they may deliver or have delivered life to other habitable bodies.

It is kind of a whacky theory and people either do not believe it or do not want to believe it because it is a theory like intelligent design - once you have said it, there is no way to prove it right or wrong. It is a theory which is unscientific in nature. But one of the leading scientists believing in the theory was none other than the Nobel Laurette - Francis Crick. Finding these organic chemicals in space has only led to more evidence for this hypothesis.

* Before one performs spectroscopy of a sample, one has to attempt to purify all the compounds present in the sample which is not an easy job because the chemical nature of the substance is an unknown at the beginning. A variety of chromatographic techniques are used for this. In addition, even after the spectroscopy of the individual samples are performed, it does take some time to realize the exact chemical nature of the substance being examined.

References:
Wikipedia as usual - on Origin of life and Astronomical Spectroscopy and Panspermia.

Extraterrestrial Organic Matter: A review - William M. Irvine - Origins of Life and Evolution of Biospheres - Volume 28, 1998, 365-383.**
** I can provide the pdf of this document on request.

Starting with the parts and ending with the whole

The focus of today's blog post is going to be statistical mechanics. In statistical mechanics, one starts with the properties of the atoms/molecules/ions in a system and try to understand how the whole system will behave. So, one starts with the microscopic properties of the components of a system and tries to understand the macroscopic properties of the whole system. The macroscopic properties here implies properties such as volume or temperature or pressure that one measures in an experiment physically. I will provide an example to make one understand how difficult this task is:

Now lets consider a box or cylinder filled with gas molecules. As each individual gas molecule is small in volume, to fill up the whole container, one would require a very large amount of gas molecules, lets just say, something in the order of a mole (A mole contains 6.023 * 10^23 molecules of the gas. This might sound enormous but is actually a small number in terms of molecules. To place things in perspective, 1 mole of water is contained in only 18 grams of water, and a liter of water typically contains 55.556 moles of water). Let us assume for simplicity that these molecules obey Newton's laws of motion and do not undergo any quantum effects.

Even under these conditions, the molecules are all moving and the total energy of the system would be the sum of each molecule's individual kinetic energy and potential energy. In addition, there will be forces acting on each molecule due to the neighboring molecules as well as the ends of the container. So, by Newton's law of motion, each particle will have a unique acceleration induced on it and the position and velocity of each particle continuously changes within the box. It becomes a hopeless situation to even try to follow an individual particle's position and velocity as the position of the other particles affect the potential energy and force of the particle we are interested in.

Hence, what one does is try to come up with a probabilistic approach as to how the system's macroscopic properties are affected by it's microscopic properties. Most of the theory that is dealt with in statistical mechanics are valid only when there is a sufficiently large number of particles (as the derivations that will come up in the coming weeks will show) and will not hold true under other conditions. Using statistical mechanics, one can go beyond the simple Newton's laws of motion and try to derive/explain the laws of thermodynamics that one can measure experimentally.

Books to understand Statistical Mechanics:
Chandler, David (1987). Introduction to Modern Statistical Mechanics.
McQuarrie, Donald (2000). Statistical Mechanics.
R.K.Pathria (1996). Statistical Mechanics.

Book to understand Thermodynamics:
Above books and
Callen, Herbert B (2001). Thermodynamics and an Introduction to Thermostatistics.

Some of the above discussion was also inspired from the Wikipedia article on statistical mechanics.

New Hope For Infertility

In July 2006, Prof Nayernia published a paper in Developmental Cell where he showed that he and colleagues had created sperm cells from mouse embryonic stem cells and used these to fertilise mice eggs, resulting in seven live births.

Now, he has published in Gamete Biology another breakthrough paper. A team of scientist lead by Professor Nayernia has isolated mesenchymal stem cells from the bone marrow of the male volunteers and coaxed into becoming germ cells (partially developed sperm cells called spermatagonial cells). The genetic markers showed that these mesenchymal cells had indeed developed into spermatagonial cells. While in most men, the spermatogonial cells develop into mature, functional sperm cells, this natural progression was never achieved in this experiment.


(Image courtesy: Mail On Sunday)

Earlier Prof Nayernia had shown that when spermatogonial cells were created similarly from mouse bone arrow and transplanted into mouse testes, they underwent early meiosis but did not develop any further.

Talking about his newly published research paper, Prof Nayernia, of Newcastle University, said : "We're very excited about this discovery, particularly as our earlier work in mice suggests that we could develop this work even further. Our next goal is to see if we can get the spermatagonial stem cells to progress to mature sperm in the laboratory and this should take around three to five years of experiments.”

The experiments open a whole new avenue for not only infertile males, but also for gay couples. What was done with the male blood cells, could be done with female bone marrow. Exciting times, lie ahead.

A word of caution before the media rings this in as male infertility solved.
Firstly, the cells in this case have not developed into mature sperm.

Secondly, the earlier experiments with the stem cell redirected sperms had resulted in mice that had severe problems - they were all infertile and had breathing or walking difficulties. They also were growth impaired, either abnormally large or or small. And all had reduced life expectancy - they died within three days to five months of being born (normal lifespan is two years for healthy mice). Prof Nayernia had acknowledged then the abnormalities were probably due to genetic defects that arose in the creation of the sperm.


Of course, the technique has already provoked an ethical storm (and it was just published on the 11th!) and could soon be banned by the Government over concerns about the safety of using artificial sperm. Critics say that the treatment breaches moral boundaries, mostly because it would effectively render males redundant!! The technique could be adapted to grow eggs in a lab (and thus helping infertile women), but this seems to the critics a way of children being born through entirely artificial means!

Precaution needs to be taken before the use of this technique - the scientist themselves claim that work needs to be done, the process is far from perfect. But to blanket ban it would hurt several hundreds of infertile men (natural or those who underwent chemotherapy)..

Heights! Mapping the "Toy" Gene

Domesticated dogs are amazing in their variety - pocket size Yorkshire terriers to Great Danes! Ever wonder what accounts for that disparity?

Wonder no more. This week's issue of Science sees a study published that gives us a clue to how a mutation in a single locus regulates size in these creatures.

A team of more than 20 scientists from eight institutions (United States and the U.K.) toured the dog show circuit and collected blood from 3,241 canines of all sizes and shapes. They found that the reduced growth mapped to a locus, near the IGF1 gene. In human IGF1 plays a role in the growth from birth till adolescence.

In all the "toy" dogs tested (distantly related and reproductively isolated), there were mutations in the region next to IGF1. This is intriguing to see a single change map to all the small breeds, indicating that the change probably maps to the time when dogs evolved from their wolf-like ancestors. The same "small dog marker" however, is not found in the modern wolves.

Why is this so fascinating? Mostly because the entire study pinpoints a single allele to be responsible for the phenotypic variation (small size) and the result was achieved without doing a single cross!!

Longevity- What needs improvement?

S. Jay Olshansky, Robert N. Butler, and Bruce A. Carnes ask a simple question, What if Humans were designed to last? in the latest issue of The Scientist.

A coordinated network of molecular processes providing cells with nearly flawless surveillance, maintenance, and repair capabilities exemplifies the "perfection" of the human body. Living things need this precision in order to survive to reproductive
maturity in the face of a hostile environment and the toxic debris that the
cellular machinery of life generates. Meanwhile, subtle changes and imperfections at every level of biological organization give rise to the diseases and disorders associated with aging and impose limits on the duration of life, but ultimately, these changes and imperfections drive the evolutionary process itself. The juxtaposition of Michelangelo's perfection and Darwin's flaws embodies the linked stories of reproduction and death..

I particularly like that the authors say,

Our goal is not to create new methods of combating disease, but rather, to
spark an idea, trigger a thought, and inspire others to think outside the box by
first imagining a new future of human health that is better than the present -
and then working to make it so.

What do you think? If you could embark on making a long lived perfect human what would you change and why?

Discuss!

A Species Concept...How hard could it be??

People have thought about the origins of closely related species for decades. In fact, scientific research on speciation can be traced all the way back into the early 19th century. By looking at older literature, we can understand old arguments, as well as, provide us with ideas toward current problems. The evolution of biology is a like a history of unanswered problems that have been worked on by some of the most original thinkers of our time. This is very different from a field like molecular biology, where much of the older literature may be irrelevant due to advancement of the field. One of the first things that you should know is that researchers cannot come up with one universal definition of a species. Speciation is a process that can be looked at from many points of view, whether it be by Behaviorists, Phylogeneticists, Systematists or Evolutionary biologists. So, when trying to decide on a single definition, many conflicting ideas come into play depending on the angle you are examining it from. Most often, the definition for a species, depends on the specific criteria you have set for boundaries. As you can see, this is not as easy to define as it initially seemed. So, how do we begin to understand speciation? First and foremost, it is best to understand the current definitions that are accepted for a species. Then, tackle the problem of understanding the difference between concepts to finally be able to choose a definition that works best for you. Species Concepts for Speciation: 1. Biological Species Concept (Isolation Concept) (BSC) "Groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups" (Mayr 1963) "Systems of populations, the gene exchange between these systems is limited or prevented in nature by a reproduction isolating mechanism or by a combination of such mechanisms" (Dobzhansky 1970) 2. Recognition Species Concept "The most inclusive population of individual biparental organisms which share a common fertilization system [specific mate recognition system]" (Paterson 1985) 3. Cohesion Species Concept "The most inclusive population of individuals having the potential for phenotypic cohesion through intrinsic cohesion mechanisms [genetic and/or demographic exchangeability]" (Templeteton 1989) 4. Phylogenetic Species Concept (Character-based) "An irreducible (basal) cluster of organisms, diagnosable distinct from other such clusters, and within which there is a parental pattern of ancestry and descent" (Cracaraft 1989) 5. Genealogical Species Concept "exclusive' groups of organisms, where and exclusive group is one whose members are all more closely related to each other than to any organisms outside the group..." (Baum and Shaw 1995) 6. Evolutionary Species Concept "A single lineage of ancestor-descendant populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate" (Wiley 1978) 7. Genotypic Species Cluster Definition "Distinguishable groups of individuals that have few or no intermediates when in contact..." "...clusters are recognized by a deficit of intermediates, both at a single loci (heterozygote deficits) and at multiple loci (strong correlations or disequilibria between loci that are divergent between clusters)" (Mallet 1995) From this list, 1-3 are process based, while 4-7 are pattern based. Many researchers are adamant that pattern not process should form the basis of any species definition while the others are just as adamant for the opposite. A generally defined and consistently applied definition of species is vital for the study of diversity, as well as, phylogenetic investigations of diversification...which ultimately gives valuable insights into the study of speciation. However, what previously seemed easy to define, is in fact a hot issue being debated to this day... with the science community still not using a single, general concept of what exactly defines a species. I hope this opens up conversations as to what is a species, as well as, leads to interesting topics of speciation. I have given a foundation....so off you go now...

Do We Or Don't We?

Carl Zimmer brings up a very important point that conservation biologists (and all the rest of us who care about this Earth) are facing right now. As climate changes occurs, species move away in search of their natural habitats (as previous records show). However, we now know there are several species that might die if we don't find them a habitat.
The pros for human assisted moves are obvious - we save a threatened species. The cons are numerous - such moves in the past have rarely succeeded, when they did it resulted in threatening the natural habitat where the species was moved or it end up producing "hybrid zones" to name just a few.
As Zimmer puts it, "Which is worse: the risk of creating a new invasive species through assisted migration, or just watching a species become extinct? "
We have a moral dilemma in front of us - I wonder what step to take?