Archive for biology

What’s This About Methane On Mars!?

Posted in astronomy, biology, personal views with tags , , on May 6, 2010 by cpolsonb

I have had at least a few people ask me directly “what exciting stuff is there left to discover in science?” Other than the obvious fact that there are definitely exciting answers to questions we haven’t even conceived of yet, there are also many major scientific mysteries answerable in this lifetime. I do not look think badly of these people, they likely haven’t had the exposure to learn about cutting edge modern scientific mysteries. It is also true that many of these mysteries, like those potentially answered by the LHC, require a deal of background knowledge to wrap your mind around. Nevertheless a few hours on wikipedia browsing major concepts in physics and astronomy is all anyone needs to appreciate the awesomeness of things like black holes, dark matter, entanglement, supernovae, exo-planets or the Higgs Boson.

This blog entry is about what I consider possibly the most exciting scientific question easily answerable in my lifetime. That question is “What’s with the methane on Mars!?”

What is so exciting about some gas leaking from Mars you might ask? First a little background. Methane on Mars was first discovered by a team at NASA back in 2003 using infrared telescopes fitted with spectrometry devices that break down incoming light into it’s constituent spectrum and can infer chemical composition from the signature or absorbed wavelength. This methane is being released annually (Martian annual) during the warmer periods at a number of locations. The gas is released in a series of plumes which can release as much as 19,000 tons of methane each!

So what does this all mean? Well we begin by considering all possible explanations for these methane plumes that scientists consider plausible. A likely explanation is that some geologic process is going on underneath Mars that is creating this methane. The only known way this could be happening on Mars is if water, carbon dioxide and the planet’s internal heat are converting iron oxide (rust) into serpentine minerals (common rock-forming hydrous magnesium iron phyllosilicate minerals). One major stumbling block with this explanation is that Mars is not thought to be geologically active and the required heat has not yet been found. It is possible that pockets of methane created in aeons past are stored beneath the surface and released annually as fissures form from cracking permafrost but this adds in another layer of complexity. There are other geologic questions that need to be answered before a complete explanation could be established and any such answer would still provide fascinating and as yet unknown information about ongoing activity on the Red Planet previously not thought to exist.

Another explanation, recently discounted by published research suggested that the methane might be left over on Mars from meteorites. Calculations have shown that the amount of meteorites needed to continually maintain the levels of methane found on Mars is far beyond what could be considered possible. There are other gaping holes in this hypothesis, such as why would the methane be confined to a few discrete pockets and why is it only being released annually. After considering the possible explanation of geologic activity and the unlikely explanation of meteoric activity we are left with one other major hypothesis.

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Chronicle of Belief: Part 3 – Nature’s Value

Posted in biology, personal views, Philosophy with tags , , , , , on April 4, 2010 by cpolsonb

This third installment of Chronicle of Belief is about a subject very personal to me as a budding Biologist; nature. It is very easy to say that the natural world is a thing worth protecting and few fellow skeptics or rationalists would disagree, but why? What is so important about nature and is there an objective rational justification for why nature has value? To begin with let’s look at what my particular field, Conservation Biology is really all about.

For many people I imagine conservation conjures images of protesters and hippies, marching in the streets or standing in front of bull dozers. That sort of naïve environmentalism is however often irrational, counter-productive and/or used as a means to push some other ideological agenda. Conservation Biology is a scientific discipline that looks at how biological communities react to change, how different species and the environment interact with one another and how we as humans can ensure the continued existence of these systems. At it’s core Conservation Biology has a number of guiding principles:

Principles of Conservation Biology

1. Evolution is the basic axiom that unites all biology. Conservation biologists do not aim to conserve the status quo, nor stop the evolutionary process but to ensure that populations can adapt naturally to environmental change.

2. The ecological world is dynamic and non-equilibrial. Conservation based on a static view of nature is fundamentally flawed and a mis-representation of the natural world. A dynamic view allows for a deeper understanding.

3. The presence of humans must be included in conservation planning. Conservation biologists aims to integrate humans into the equation and study their impact.

These principles are text-book simplifications of a complex scientific field and highlight the dynamic, integrated approach that conservation biologists must take when approaching questions. It is also valuable to note that conservation biology is a ‘crisis discipline’, having been born from the outrage at anthropogenic mass extinctions and environmental destruction of the last few centuries. In this way it is also a science of eternal vigilance, there can never be a complete theory conservation biology as it is reactionary and time dependent. It is also not an exact science, biological systems are far too complex to ever predict with the certainty of say for example, a chemical reaction.

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“Science is the Poetry of Reality”

Posted in biology with tags , on March 26, 2010 by cpolsonb

In “enemies of reason” Richard Dawkins states that he thinks of Science as “the poetry of reality”. That idea may soon be more fully realized than perhaps Dawkins ever imagined, thanks to Canadian poet Christian Bok. Bok is a world renown experimental poet most famous for his poetry book Eunoia in which he only uses a single vowel per chapter (of which there are five). His latest attempt at experimental poetry is to literally insert a poem of his into the DNA of a living organism.

The organism in question is the bacteria Deinococcus radiodurans, the choice of which was no arbitrary decision. Deinococcus radiodurans is nicknamed “Conan the Bacterium” because it holds the world title for most resistant organism to radiation. The amazing resistance to radiation that this bacterium shows is thanks to a unique ring structure into which it’s DNA is formed. What the ring structure means is that pressure is applied all the way along the chain in such a degree that the normal severing of DNA by radiation does not occur. Radiation is still able to split the polypeptide chain in the DNA molecule but instead of the pieces floating away like in a normal DNA strand the pressure caused by the circular structure holds the pieces in place until they are able to “glue” themselves back together. This unique structure is therefore important if Bok wants his poetry to be preserved in future generations. If the poetic sequence were encoded into a different species of bacterium then over time radiation would sever and re-arrange the words into nonsense.

So the questions remains of how this will be achieved and what the poem will be. While I haven’t found much information on the specific mechanism that will be used to encode the sequence the most likely candidate is via plasmid integration. Without going into too much detail plasmids are small rings of DNA that occur separately in the cell to the chromosomal DNA in the nucleus. Plasmids are not considered life as they do not encode any genes for replicating or reproducing. Instead they are physically passed from one bacteria to the next through a process called conjugation. To cut to the chase, scientists are easily able to insert new plasmids into a bacterium that will integrate permanently into the chromosomal DNA. This is process is so easy that undergraduates like me are even able to do it!

As for the particular poem that Bok is going to insert, that remains to be seen. Unfortunately for Bok the genetic alphabet consists of only four letters; A,G,C,T which correspond to the nucleotides Aadenine, guanine, cytosine, and thymine. In order to construct an intelligible piece Bok is in the process of developing a cipher in which particular each triplet of nucleotides (i.e. AGT, TCA, AAG) will correspond to a particular letter of the English alphabet. All Bok has said so far about the content of the poem is that it will likely have an incantatory quality similar to a spell or ritual.

Australian Critter of the Week: Potorous gilbertii

Posted in Australian Animals, biology with tags , , on March 3, 2010 by cpolsonb

Well it’s Wednesday again and time for another Australian critter of the week. This week I’ve chosen an animal that is very precious to me as an aspiring conservation biologist in Western Australia. That little animal is the Gilbert’s Potoroo (Potorous gilbertii), a cute little marsupial with a tragic past and shaky prospects. Gilbert’s Potoroo were first discovered in 1840 and as you might expect are named after English naturalist John Gilbert. It was not long after their discovery that all trace of them was lost, and after a short while they were presumed extinct. Of course our story doesn’t ended there and out of the blue in 1994 a shocked researcher discovered what she later identified as a Gilbert’s Potoroo in a trap she had set for wallabies. Thus the extinct status of Gilbert’s Potoroo was removed, 120 years after they were declared so!

But the elation of rediscovering these cute little critters soon wore off as the critical plight they were in became apparent. Researchers struggled in vain to find a large breeding population of Gilbert’s Potoroo but to no avail. Historically the Gilbert’s Potoroo had very few predators, and those it did have were unable to follow it into the thick undergrowth of it’s habitat. Not so for introduced foxes and cats who while they hadn’t succeeded in wiping them out completely had successfully reduced the Gilbert’s Potoroo population to less than 50 individuals! Stack on top of this habitat destruction and disease and we’ve got ourselves one unfortunate little marsupial. Gilbert’s Potoroo has the ghastly title of Australia’s most endangered animal and is indeed one of the world’s rarest mammals.

In order to protect the remaining few individuals their location at Two People’s Bay was deemed a Class A nature reserve, meaning no unsanctioned humans are allowed to set foot within it’s bounds. This is course did not stop the foxes and cats from continuing their carnage and so in 2005 three specimens were translocated to pest free Bald Island. Since that time a few more individuals have been taken to the island in an attempt to establish a breeding population. Despite Biologist’s and Conservationist’s best efforts the number of Gilbert’s Potoroo surviving today is estimated at less than 40 individuals. This dis-heartening excerpt from the conclusion of a report by the Department of Environment sums up the plight of the Gilbert’s Potoroo succinctly:

Gilbert’s Potoroo is known from one population in the wild of less than 30 individuals. Its geographic distribution is precarious for the survival of the species. The species and its habitat are subject to a number of ongoing and potential threats including a catastrophic or uncontrolled fire, predation from foxes and feral cats, low recruitment of young to the adult population, the impact of the dieback disease caused by the root pathogen Phytophthora cinnamomi on fungi host plants and the clearing of areas of suitable habitat within the species extent of occurrence.

Next weeks won’t be such a downer I swear…

Australian Critter of the Week – Moloch horridus

Posted in Australian Animals, biology with tags , , on February 24, 2010 by cpolsonb

Moloch horridus or the “thorny devil” as it’s commonly known is one kick ass lizard. These little guys grow to around 20cm long and live throughout the scrub and desert of central Australia. We are lucky enough to have the highest density population here in Western Australia! As well as being used for defense and camouflage the thorny scales all over its backs contain tiny little canals that carry water to its mouth, how awesome! The thorny devil is also an example of convergent evolution; where genetically dissimilar species evolve similar characteristics. As it has been isolated geographically for many million of years Australia contains many interesting examples of convergent evolution. In the case of the thorny devil it has evolved physical, dietary and activity patterns similar to the North American Horned Lizard. Perhaps the cutest thing about the thorny devil is it’s unusual gait, involving freezing on the spot and rocking as it moves around searching for food (namely ants).

Another awesome thing about this little guy is that it actually changes its colour depending on the amount of sunlight in its surroundings. It also has the crazy little “second head” at the base of it’s neck. The use of this second head is still somewhat of a mystery although leading hypotheses suggest it may be used to confuse predators or even to store fat and water. Whilst not endangered they are protected under the Wildlife Conservation Act. Unfortunately they are sometimes killed on roads as they bask for sun and absorb the heat from the tarmac.

That’s all for this week!

Belated Darwin Day Post

Posted in Trips and Visits with tags , , , on February 14, 2010 by cpolsonb

So Friday was Charles Darwin’s 201st birthday. I was hoping to get my blog set up in time to do a happy birthday post but things kept cropping up and distracting me. Nevertheless I thought I’d give my shout out to the father of evolutionary theory today.

For those few of you who may be unaware, British naturalist Charles Darwin was the man who at the right place and time managed to put together the pieces of the puzzle that formed evolution through natural selection. Why did I phrase it like that? It is important for science lovers and rationalists to understand that very rarely (if ever) have great scientific discoveries been whipped up by a single person from a vacuum. It is not widely known that simple and somewhat flawed versions  of common descent and transmutation of species have been around for thousands of years. Philosophers in Greece, Rome, Persia and China all toyed with ideas that to contemporary man sound strikingly similar to evolution.

Even Charles Darwin’s grandfather Erasmus Darwin developed much of the thinking that helped inspire Darwin to formulate his theory, especially with regards to the relatedness of all forms of life. To cut to the meat of my post, Darwin’s publication of ‘On the Origin of Species’ presented evidence to the world that evolution through means of natural selection is the driving force behind the diversity and history of all life on Earth. Darwin’s famous voyage on the HMS Beagle provided a good deal of evidence and inspiration that would help him solidify his ideas years later.

In Sydney Australia in 2009 an exhibition was held at the Maritime Museum focusing on Charles Darwin’s famous voyage with the Beagle, particularly in regard to his visit to Australia. Despite the fact that Darwin described Australia as dull and uninteresting I was able to forgive him long enough to make a trip to the museum while on a work trip in Sydney.

I present for you a small collection of photographs I took of objects at this awesome exhibit “Charles Darwin: Voyages and Ideas that Shook the World”:

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