Word of the day: Microbiome

This is clearly a portmanteau word: microbe + genome. Microbe refers to microscopic organisms - in this case, bacteria; genome refers to the sum total of genetic material in an organism.

There's a community of bacteria living within humans that performs functions essential for human life. Scientific American (Mar-2012) says there's at least 10 times as many bacteria cells as human cells in the human body (but those bacteria are a whole lot smaller, with much, much simpler genome).

So microbiome is the genetic material of the [useful] bacteria in the human body. In such a situation, it differs from human to human, so things like this are usually measured on a sampling basis.

According to that Scientific American article (Backseat Drivers, p11), the sum total of all genetic material housed in a human body is then called the hologenome.


Small bone to pick here. The human genome is generally thought of as referring to the genetic material (23 chromosomes of DNA) housed in the nucleus of each cell. But there's extra DNA not in the nucleus: mitochondrial DNA, used to generate energy, passed on only maternally, and originally passed to humans by bacteria. This DNA is often left off discussion of genomes.  In this case, I'd say they'd be including mitochondria for the sake of completeness.

Another small bone to pick. Microbiome is listed in Wikipedia as the sum total of microscopic organisms in a particular environment, and hologenome is used as an idea of co-evolution with microbes, roughly speaking. So the Scientific American article is pushing the envelope a bit.

So even within a scientific community the meaning of words can change over time until/unless locked down.

Further reading (both from Scientific American, as it happens):

• What happens when those useful bacteria disappear
• The appendix is useful - for the microbiome

Word of the day: Cardiomyocyte

A cardiomyocyte is a heart muscle cell.

Paraphrased from New Scientist, 5 May 2012: After a heart attack, fibroblast cells form scar tissue on the damaged areas, but they don't pump properly like cardiomyocytes. Dzau (Duke University) used a virus to deliver four microRNAs to switch the fibroblasts to cardiomyocytes. Viruses are, more or less, RNA (or DNA) factories. That is, they are much smaller than normal cells, and spend their lives using a host cell's own mechanisms to manufacture more genetic material.  Preferably its own, but with the benefits of modern genetic engineering, clearly they can be taken advantage of for the benefit of the host cell.

microRNA: short strips of RNA that bind to messenger RNA to stop genes being expressed.

It's not clear to me whether this happens at transcription inside the cell nucleus (like epigenetics, but acting on the RNA), or translation (that is, preventing the ribosome properly decoding some of the RNA into proteins outside the cell nucleus. Either way, it's pretty clever to be able to:
a) identify the switches that change a fibroblast to a cardiomyocyte. Possibly just a function of what proteins are expressed at the ribosome
b) engineer a virus so that it expresses the right set of RNA strands to do the trick
c) deliver the virus to just the right cells. 


(I note that there's been another effort to achieve the same outcome - fibroblast to cardiomyocyte - in a completely different way: using stem cells: http://stemcells.nih.gov/info/scireport/chapter9.asp) 



Where did I encounter this word? Yesterday, in that New Scientist (I'm behind in my reading!)


 

Chomsky's trajectory of complexity

I read today an interview with Noam Chomsky in New Scientist.

I have a lot of respect for Chomsky.  Although the interview started on a scientific footing with his academic speciality (language), it was nearly as wide ranging as he is.  What he said was all eminently sensible albeit not especially novel, but there was one comment that was more memorable than the others.

It's rather a throwaway line, but it struck a chord with me, because it coincides with a trajectory that I've been more or less following.  Bar the psychology (which, incidentally, my wife is currently studying).

In your new book, you suggest that many components of human nature are just too complicated to be really researchable.

That’s a pretty normal phenomenon. Take, say, physics, which restricts itself to extremely simple questions. If a molecule becomes too complex, they hand it over to the chemists. If it becomes too complex for them, they hand it to biologists. And if the system is too complex for them, they hand it to psychologists... and so on until it ends up in the hands of historians or novelists.



I don't know where he might place economics... maybe as a voodoo science?

In mitigation, I have to say that much as I'd like to, it's extremely unlikely I'll get around to a novel :)

Frogs and hybrid fungi

A few days ago I posited that humans are affecting ecosystems globally on a scale that rivals extinction events in the distant past.

Subsequent to that I unsealed an old copy of New Scientist that I'd been saving for a rainy day.  The 12 November 2011 issue mentioned  a disease that is "decimating frogs around the planet."

The cause is a fungus lethal to frogs called Batrachochytrium dentdrobatidis.  Sixteen of the 20 samples collected globally were a genetically identical strain (called BdGPL), ie they were of the same origin.  And they are "extremely virulent."

That strain was clearly a hybrid, formed in the past 100 years, most likely due to the "20th-century pet and food trade", which enabled the strains to meet.

Madagascar and south-east Asia are the regions most at risk right now, being "hotspots of amphibian diversity" and free of this fungus right now.

Globalisation is an inevitable process in the development of human society.  Such collateral damage need not be inevitable, but it takes political will which in turn, at the very least, would entail using one's vote wisely.

SETI, Open source, and the socialisation of productivity

What does SETI have to do with Microsoft's furrowed brow?

We all know the Search for Extra-Terrestrial Intelligence, whereby the universe is scanned for signals throughout the electromagnetic spectrum which can be interpreted as originating with intelligent life. Some of us have run SETI@home: you download a screensaver, which runs in the background, borrowing your unused computer time to run a parcel of number crunching for SETI. Everybody wins: only your idle computer time is used, and it can have some wider community benefit - you may even be responsible for the first discovery of extraterrestrial life.

That was the first distributed grid computing project to gain widespread publicity. But the software is now available to turn any general project requiring major computer time into a socialised project. The Herald recently ran an article on Australian use of such software: specifically, BOINC, The Berkeley Open Infrastructure for Network Computing. The article said over 32,000 Australians were currently running BOINC projects, out of 1.7 million people worldwide.

The scope is tremendous, not just for general scientific research, but also for any community-sector project that may not otherwise have the resources to get off the ground.

For the moment, here's a list of projects you may wish to take part in. Those are all scientific research, mainly in biology, physics and maths, but there's also a World Community Grid, which is specifically aimed at humanitarian projects.

As for Microsoft, the other side of community computing is software: open source, to be specific: generally an open source project is contributed to by many, with no profit-oriented copyright - and generally available for free. Open Office may be the most famous - a direct competitors to Microsoft's Office suite. And as a method of developing software that is freely available to all, it has gained acceptance in most areas of my professional focus, business intelligence. Apart from the well-known mySQL database, there are also open source tools available for most related areas. As well as database and BI software, there's also ETL, data profiling, and so on.

Over time, you should expect prices to tumble in all types of software directly affected by open source initiatives. Yes, the likes of Microsoft can expect some buffering from these forces due to brand-name strength. But yes too, Microsoft is worried enough that they are already working on alternative revenue streams, including jumping into the cloud. Those alternatives shouldn't see a collapse of capitalism any time soon, but the long-term trend can only benefit the public, particularly those who might not otherwise be able to afford such computer resources, particularly in the developing world.

In a wider sense, distributed computing and open source are simply harbingers of a globalisation and socialisation of productivity, for the benefit of all.

The cell as computer

Making sense of the material world is a gradual process that we all achieve to different degrees over the course of our lives. The further removed a paradigm is from a day to day human experience, the harder it is to put it in a meaningful context. Whether too vast or too small in size (stellar phenomena or microscopic to sub-atomic action), or too long or short in time (evolution; quantum actions), it helps to find a way to express meaning in terms we live each day.

Living cells are computers. This is a very succinct analogy which can help to conceptualise the complexity of cellular life and action.

Of course this metaphor is not new, but it looks to be very well put in a new book, Wetware: a Computer in Every Living Cell, by Dennis Bray (and reported in New Scientist).


Stentor Roeselii is a pond-dwelling single-celled organism. It exhibits behaviour that is akin to being directed by a brain. If a jet of water is squirted at it, it will duck down, then come back up cautiously. Another, identical squirt would be ignored. Squirt an irritant chemical at it, and it will "arch its stalk-like body out of the way, move from side to side", retreat, then finally tear itself free from its mooring and drift off to a new home.

Bray characterises such an organism as a chemical computer. Ultimately, the programme written out in the DNA (and so it cannot be reprogrammed per se). But the complex set of actions (output) are all induced by chemical reactions that occur as a response to stimulus (input). The chemical reactions are not simple, but they are effectively laid down by DNA, which also dictates the form, that is the composition of this "bag of biochemistry". We cannot yet come close to duplicating this because we haven't broken the barrier to the point where we can build computers at anything more than an electronic level.

In a similar fashion, a multicellular organism could be seen as a large group of chemical computers that includes complex mechanisms (chemical interactions) to bind them to working collaboratively. (By the time we get to the sophistication of an animal with a decent-sized brain, though, the ultimate outcome could be said to be non-deterministic, simply because of the complexity and miniturisation... but that determinism is another debate altogether.)


Comparing biochemical action to advanced miniaturised computing is a very useful way to help understand how life builds up from its building blocks to the level of complexity we now see.

Evolution: DNA basics

It's been difficult to grasp the subtleties of some of the discourses on evolution without having a precise grasp of genetic biology. A general understanding can only help so far. In fact, I've found that some of the reason for my difficulties has been that much of the terminology has been used quite loosely, particularly when discussion escapes into the realms of mass communication such as journalism. In particular, the term 'gene' has been tossed about with such reckless abandon that it's all but lost useful meaning in the popular press.

Ideally, Wikipedia would always be a clarifying resource, but I've found that it's often not as clear as one might expect. In days to come, I hope to nail down some basics, starting with DNA.


Deconstructing the term DNA
Schematically, the shape of Deoxyribonucleic acid is the well-known double helix. To be literal, the name is broken down thus. An Acid by definition has hydrogen ion activity greater than that of pure water - this corresponds to a pH of less than 7 (which is neutral). Nucleic acid - mostly either DNA or RNA - is typically located within a cell's nucleus, although there are exceptions. The ribose part of the name refers to the backbone spirals - they are made of repeating groups called nucleotides, each of which is built on a nitrogen base, a phosphate, and ribose sugar. Further, in DNA the ribose sugar has an oxygen atom removed, thus the sugar is effectively deoxyribose.

These molecules are long - about 1.8 metres in humans! - but 46 of them are wrapped into each cell nucleus in our body - these are the 23 pairs of chromosomes.

The two spirals of repeating nucleotides are just infrastructure. The true value lies in the rung that connect one nucleotide to its opposite. Each nucleotide contains one of four bases, at their simplest C, G, A and T. They are paired (via hydrogen bonds) with their opposite number in one of four combinations: C with G, G with C, A with T, and T with A. There are up to 220 million of these base pairs in a human chromosome. Three base pairs in a row, called a codon, provides the blueprint for an amino acid, the building block of a protein. One codon sequence denotes the end of the DNA strand. (There are 64 possible codon sequences but only 20 amino acids, so some redundancy exists in ways of describing them.) A somewhat involved process uses the whole sequence in the manufacture of proteins, which are ultimately responsible for the development of an organism.

Before a cell divides, the two arms of the spiral separate and unwind. This requires the DNA molecule to spin at several hundred turns per second. I can't say my reading has given me a clear understanding of this process, although DNA molecules are located in specific areas of the cell nucleus, so there's unlikely to be any entanglement (and thus interference) between the different strands of DNA in a cell.

Junk DNA
Better described as non-coding DNA, this term refers to coding sections of DNA for which no function has been detected. This currently constitutes about 80% to 90% of the information stored in DNA. There's a variety of thoughts on the reason for this non-coding information. Most of it may be repetitive elements. A lot of it may be historical artifacts of evolution. It's plausible that the function of some of these sequences simply remains to be discovered. Some consider the sequences as stored away for potential future use. This is an interesting puzzle that may speak volumes on evolutionary processes. The evolutionary narrative finds demonstrated that redundant features of an organism don't tend to survive too long: carrying extra baggage costs, and the mutations that ditch unneeded baggage tend to be more successful. Either this precept doesn't apply at the DNA level, or there is some evolutionary benefit in this "junk" being maintained, which we just haven't yet fathomed.

There is some to suggest organisms habitually absorb DNA from other sources (as seen recently, bdelloid rotifers seem particularly good at this), although it's hard to say what part this plays in the mystery.

Other DNA
Mitochondrial DNA is that located outside the cell nucleus, in an organelle (an organ of the cell) called mitochondria, which are used to produce energy. This DNA is circular in shape, as is that of bacteria. In fact, it's thought that it originated from bacteria absorbed by eukaryotic cells. mDNA is inherited entirely matrilinearly; it has been found that mDNA in sperm cells have been marked for deletion. There are hundreds to thousands of copies per human cell, each with around 16,000 base pairs, which correspond to the same set of functions in most higher organisms.



References
Jones, S & Van Loon B (1993): Genetics For Beginners. Icon, Cambridge.
Lafferty P & Rowe J (eds, 1994): The Hutchinson Dictionary Of Science. Helicon, Oxford. [of the sources, this one has proved the most lucid, despite the brevity.]
Wikipedia: DNA, Base Pairs, Junk DNA and Mitochondrial DNA.

Evolution: what are microbes?

Once biology terminology breaks out into the world of popular press, the sense of a word is often lost or misconstrued, or never well understood in the first place by either communicator or recipient.

Soon I hope to dive into the sordid mess of genetic terminology. Right now, it's microbes.

Microbe is simply a synonym for micro-organism, or microscopic organism. However, therein lies a welter of misinformation; much of the time, it's rendered synonymous with bacteria - but that's only part of the story. Here is a list - not necessarily complete - of microbes.

Bacteria. Domain: Bacteria - yes, they're a whole grouping unto themselves, which animals, plants and fungi are not, being of domain eukaryote. Bacteria are unicellular with no nucleus (thus prokaryotic). They reproduce by binary fission. There are ten times as many bacteria cells in the human body as human cells, although as prokaryotes they are an order of magnitude or so smaller than human cells.

Archaea: Domain: Archaea. Also prokaryote, reproducing by binary fission. It was thought until relatively recently that they were restricted to extremophilia - that is, only living at the extremes of tolerable ranges of temperature, acidity, etc. Since then, they've been found to be far more common. Possibly the most ancient lineage (hence the name), although there's whole worlds of debate in that issue.

Protists: a paraphyletic grouping (a Kingdom), ie a bucket for things that don't belong together, but don't fit elsewhere. They include unicellular animals (protozoa), plants (protophyta), and fungi (slime molds, water molds).

Amoebae: or amoebas, also lumped in with protists, ie Domain: eukaryota; Kingdom: Protista; phylum: sarcodina. Unicellular.

Algae: again paraphyletic. United by their focus on photosynthesis, they can be either unicellular or multicellular. Cyanobacteria was once called blue-green algae, but this is not accurate.

Plankton: Not a grouping per se, but actually defined by their ecological niche: pelagic (nearer surface) oceans. They encompass animal, plant, bacteria, etc. The bottom of the ocean food chain, and what all other pelagic animals feed on - a mixed diet, but uniformly microscopic.

Virus: Don't really belong here, as they're not classified as living: just bags of DNA seeking hosts, and which cannot live without those hosts. There are viruses for every type of living organism, including those for bacteria (bacteriophages).

Interestingly, genetic information infiltrates and is exchanged in all sorts of ways between these and other, larger organisms. That's quite a story in itself, and hopefully will be tackled soon.

Science: New science snippets

New Scientist (right), the weekly British science news magazine, is often an embarassment of riches. When I had a weekly subscription, I ended up with rather a backlog of issues to consume my reading space.

The occasional issue is most welcome; this week's had a number of interesting items, some of which appear here today.


Creationism and science teachers
The US is the only western country for which creationism is a significant issue. Most of the rest of the world is accepting of scientific reason; or more correctly, most of the rest of the world doesn't have a powerful fundamentalist christian lobby voice.
A survey of science teachers (presumably secondary level) from Pennsylvania State University has found some interesting statistics - as well as a fair bit of the bleeding obvious. A quarter of the 900-odd respondents taught about creationism, and about half of those presented it as a valid scientific alternative to Darwinism.
Sixteen percent of these science teachers believe humans were created in the last 10,000 years.
So, half of those who raised the concept of creationism didn't teach that it was valid; and there was a number who thought it was valid, but didn't teach it.
Interestingly, it notes that the amount of class time given to evolution was higher, the more science education the science teachers themselves had. Making a rather good case for science teachers to be properly trained.
The study suggested that less-trained teachers felt less confidence engaging in the subject (ie responding to questions).
However, I strongly suspect that even where science is taught properly, a lot of those teachers would have a somewhat weak grasp of the two fundamental tenets of random mutation and natural selection, let alone the myriad implications that stem from them.

Inbreeding and genetic disorder
A review of studies from Murdoch University in Western Australia examined genetic disorders amongst the offspring of first cousins. This would be a rather surrogate measure, of course, of the effects of inbreeding. The study found a 1.2% higher rate of infant mortality of offspring of first cousins, compared to the overall population. Another such (review) study in 2002 found a similar order of magnitude: less than 3%.

Artificial legs as a boost for runners
Recently was shown a prosthetic foot design that enabled high performance sprinting, notably in double amputee Oscar Pistorius. Claims then made that this unfairly boosted performance - which have now been tested.
Again, a proxy measure was used to determine any advantage conferred: the amount of calories burnt per distance - ie whether it was cheaper to fuel the prostheses.
The answer given was no - it wasn't more efficient. So Pistorius is free to compete in the Olympics - unless some other hurdle appears.

Evolution: Crocodilians, and clarity of terminology

What is a crocodilian? This came up in one of my kids' home readers - little books that five to eight year olds practice on each night.

You might intuitively suggest crocodilians are the group comprising crocodiles and alligators - fair enough. You might add caimans/caymans and, if you were really knowledgeable, gharials.

Gharial: the lesser-known crocodilian

But from here, we come to a point that is somewhat illustrative of a certain lack of clarity in the common usage of terms. Catalogues, descriptions, narratives of animals frequently refer implicitly to extant species, but are silent on extinct ones. Thus a narrative may be wholly accurate in a current context, but misleading if evolutionary groupings are considered.

This is particularly true in the case of mammals. Most living mammals are, of course, placentals (eutherians, more properly). Some are marsupials (metatherians, which can also be considered placental), and a few are monotremes (non-therians, less correctly prototherians, taking in the platypus and echidna species). Metatherians are placental, but give birth to partly-developed young, while monotremes are egg-layers. But are non-therians exclusively egg-layers? There is divergence even in scientific material. This for another post.

Crocodilians are, correctly, an order of tetrapods in the class Sauropsida (reptiles) - they are the closest living relatives to birds. There is an applicable superorder: Crocodylomorpha.

To its credit, the aforementioned book Crocodilians also enumerated a few extinct species. To wit, Orthosuchus, Terrestrisuchus, and Desmatosuchus. I looked up those three species. They're all from the late Triassic; all united in the Sauropsida class. However, the first two belong to the Crocodylomorpha, while the latter is a bizarre armoured, vegetarian species of the order Aetosauria. According to both Paleos and Wikipedia, on current phylogeny this is a only a sister clade to the Crocodylomorpha.

Interestingly, Paleos and Wikipedia agree on this, but disagree on how they are organised: see Paleos on Suchia and Wikipedia on Crurotarsi. Without tracking all the sources, I'd sooner trust Paleos, although in this case Wikipedia actually gives direct sources for that cladogram. Sometimes such differences are due to different sources that are in disagreement; sometimes they're due to one of the two being updated more recently. To Wikipedia's discredit, the piecemeal nature of its updating structure often leaves details between articles in disagreement.

the now-orphaned Desmatosuchus

So, as I suspected the herbivore Desmatosuchus didn't really belong in that book aimed at children. Pity, because the writers did make an effort. It's possible thinking had changed since it was published, however, the only detail I now have is the book's name.

Incidentally, my 1988 Britannica is silent on crocodilians - at least at the index level.

Phylogenetic wallpaper

Amira told me about her vision for what would be a phylogenetic wallpaper: that is, one that lists all organisms cladistically around the wall, showing the evolutionary relationships (and degree of closeness) of everything.

Sounds great - if you're that way inclined, which I am too. I said to Amira that you'd need one that could update - pretty much on the fly - because our understanding of evolutionary relationships is changing all the time. Whereas in the past, taxonomy was based largely on morphology - physical relatedness - this is being broken down by molecular analysis, which is showing up much of our morphological classifications to be "mere" cases of convergent evolution.
Visual technology is such that we're not too far away from being able to "paper" a room with very thin, bendable computer displays. The result would be garish but fascinating. Garish because the technology's not good enough to make it easy on the eyes. Fascinating in that at the fringes you'd be seeing more or less constant movement, ripples of change that reflect ongoing corrections in the tree of life. Then every so often there would be a major cracking like an earthquake, as a fundamental adjustment is made.

Sometimes there are hazes, where differences of opinion result in toggles between different states.

Tomorrow, Amira, I'll go into some of those hazes. A recent article on linkages between arthropods and nematodes, vertebrates and echinoderms, speaks to some top-level cladistic relationships - but these are not without contention.

Seaweed linked to parasites

A brief article on the Herald's website heralds the discovery of a type of brown algae whose closed relatives include a couple of parasites, cryptosporidium and plasmodium.
This is the closest yet to linking those parasites to algae.

The link is already understood in general terms, because the parasites contain relics of chloroplasts, the mechanism for photosynthesising sunlight into energy. The parasites thus evolved from feeding off sunlight to feeding directly off hosts, leaving residual traces of their origins.

Previously, the closest link between those parasites and algae was a group of dinoflagellates (some parasitic simple algae); this discovery brings the link much closer.

The resonance with Sydney is that they were found in Sydney harbour, while seeking algae living in coral.

Brown algae tends to manifest as seaweed.

Cryptosporidium and plasmodium are both single-cell eukaryotes of the phylum Apicomplexa (classes Aconoidasida and Conoidasida respectively - differing in the absence/presence of the conoid, an organelle comprised of a "funnel of rods").

Brown algae are distinguished by chloroplasts with four membranes, suggesting an origin in symbiosis between two eukaryotes. While Brown algae, dinoflagellates and those parasites are all eukaryotes, in the kingdom chromalveolata. Brown algae are multicellular; the parasites are unicellular, and dinoflagellates are... _mostly_ unicellular.

The online report raises more questions than answers. It refers to the print edition, but it's not been published there. What is the name of this new algae? Which dinoflagellates? The findings are said to be published in Nature, but maybe the paper hasn't been published yet, because a search of Nature's archive doesn't turn it up.


And finally... hello to Dee Carter, microbiology Associate Professor at Sydney University, quoted in the report. Based on this photo (not so much the current one at the university!), looks like the same Dee Carter who was in my class at school (Onslow College). Small world.



Other references: Wikipedia [beware, however, there are inconsistencies in classifying organisms: some use unhelpful paraphyletic groupings such as protista.]