Most people have heard of "The Selfish Gene" and many will know what it's about. For those that don't... in essence, it is about "genes" as the primary driving force of evolution. A "gene" in this context is a piece of DNA within some form of entity that replicates that DNA. The rules are simple: if that piece of DNA does anything to increase the chance of its future replication and persistence, it will spread. Usually, we perceive this as a "gene" having some positive beneficial effect on the organism to which it "belongs" (or, perhaps more accurately, within which it is carried and replicated). Life, as usual, is more complicated than that, however, and examples exist of "genes" that spread at the cost of their replicator host - viruses and transposable elements being two such examples.
The point is, though, the genes are "in it for themselves". Yes, they often form complex cooperatives - genomes - that build intricate organisms but only because the members of those cooperatives replicate more successfully in this fashion than going it alone. Natural Selection is not about the good of the species, or even the good of the individual, it is the good of The Selfish Gene.
As you can tell, I am a big fan of this gene's-eye view of evolution. It begs the question, though, if the units of evolution are genes, where does this leave organisms? Species? Even genomes? How does this marry with the standard "Tree of Life" (TOL) model of evolution, in which all species are gradually splitting and diverging over time, carrying their genes with them?
In their recent Biology Direct paper, The public goods hypothesis for the evolution of life on Earth, James McInerney et al. summarise the issue quite nicely. "Horizontal Gene Transfer" (HGT) - essentially the passing of genetic material from one organism to another, other than to offspring (and often a different species) - is widespread, especially in bacteria. So widespread, in fact, that the TOL hypothesis just does not hold up. Instead, we should take a economist-style view of genes as "public goods", with the evolution of Life on Earth as the product of sampling (and retention) of different genes over time, rather than a TOL pattern of bifurcation and divergence.
Of course, the story is a lot richer than that and builds on a body of other ideas. It is also not without criticism. I strongly encourage you to read the paper and the interesting discussion with reviewers that can be found at the end of the manuscript. Time will tell whether the Public Goods hypothesis really offers something more than TOL+HGT but it's definitely something worth considering.
So what does this mean for evolution? Does questioning the TOL put evolution in peril? Well, no. It is important to point out that the genes themselves are still evolving in a tree-like fashion. Molecular evolution and molecular phylogenetics is not substantially altered by this idea. What is altered is the way we interpret this molecular data in terms of trying to determine the relationship of "species", especially bacteria. This is nothing new - the "species" concept for bacteria has been dead for a long time, to be honest - but it potentially gives us some new tools and ideas with which to probe the Natural History of prokaryotic life with more clarity and insight than ever before.
And what about all the claims us evolutionary biologists make about the molecular evidence for evolution, and how we get remarkably consistent trees when looking at different genes from a set of animals? Was that all lies? Well, no. It is also important to point out that the problems with the TOL are largely restricted to bacteria, viruses and the like. For eukaryotes - e.g. plants, animals, fungi - the tree picture is still pretty solid. The authors themselves make a nice analogy with mechanics. Quantum Mechanics did not stop previous observations about Newtonian Mechanics being right, it just extended our understanding into realms where our old Newtonian understanding began to break down. I am not sure whether this idea represents such a game-changer but I do know that it's a exciting, if slightly head-wrecking, time to be a microbial geneticist.
Wednesday, 24 August 2011
Tuesday, 23 August 2011
It's a workout, Gym, but not as we know it
Today, I went to the gym for the first time in quite a few weeks. Too many weeks. So many weeks, in fact, I couldn't even remember when I last went to the gym, so I looked it up. It was June 22 - exactly two months ago, almost to the minute.
Last time, I got a free trial session with a personal trainer. It was pretty good but I was literally still hurting a little a week later - part of the plethora of lame-assed excuses that stopped me going back since. Another part was the shame of seeing said personal trainer, having seemed so keen at the time and then failed to turn up again.
So why go now? Well, the time has come to reverse the polarity of the shaming beam. A friend has just signed up at the same gym and went first thing on Sunday morning, of all times. Then, my wife went earlier today. Finally, of course, there is Rule #1: Cardio. It was time to climb back on the horse. Or, more accurately, back on the treadmill. Without a horse: that would be cheating.
This blog is the final cog in the wheel of shame. My wife and friends are too nice to really make me feel shame for my non-attendance. Instead, therefore, I shall here record my triumphs, or acknowledge my lazy lameness, to be forever electronically recorded for posterity. Or, at least, until the inevitable EM pulse from World War III takes out Google.
Machines used: treadmill
Time run: 30 min
Distance: 5km
Rehydration: lucozade sport, raspberry
Last time, I got a free trial session with a personal trainer. It was pretty good but I was literally still hurting a little a week later - part of the plethora of lame-assed excuses that stopped me going back since. Another part was the shame of seeing said personal trainer, having seemed so keen at the time and then failed to turn up again.
So why go now? Well, the time has come to reverse the polarity of the shaming beam. A friend has just signed up at the same gym and went first thing on Sunday morning, of all times. Then, my wife went earlier today. Finally, of course, there is Rule #1: Cardio. It was time to climb back on the horse. Or, more accurately, back on the treadmill. Without a horse: that would be cheating.
This blog is the final cog in the wheel of shame. My wife and friends are too nice to really make me feel shame for my non-attendance. Instead, therefore, I shall here record my triumphs, or acknowledge my lazy lameness, to be forever electronically recorded for posterity. Or, at least, until the inevitable EM pulse from World War III takes out Google.
Machines used: treadmill
Time run: 30 min
Distance: 5km
Rehydration: lucozade sport, raspberry
Monday, 22 August 2011
McGuigan Bin No. 528... what can I say?
I like wine. I never used to like wine. Then I discovered that I didn't like cheap wine. This was unfortunate, as all I could afford (or, at least, was prepared to fork out for) as a student.Now, my palate (and wallet) have improved a touch, my enjoyment of wine has likewise increased. That said, I still like a bargain, and don't know that much, so I like to go for the half price wines, like this one (£5 at Sainsburys):
Sadly, while my palate has improved enough to increase my enjoyment, it has not yet resulted in an ability to describe wine with anything resembling sophistication. This one's nice for drinking, though!
Location:Southampton, UK
Saturday, 20 August 2011
Bug-Bombing Biofilms
This weeks's Science Now has a really cool example of the awesome power of genetics and genetic engineering. Published in Molecular Systems Biology, a paper by Nazanin Saeidi et al. describes the construction of a bacterial bomb designed to take out Pseudomonas aeruginosa, which is a nasty biofilm-forming human pathogen.
Traditionally, we think about bacteria a single-celled organisms but this is often not really the case. In many situations, populations of bacteria form multicellular masses called biofilms. These can be a big problem, particularly for human disease, because the biofilm structure can make the bugs resistant to regular antibiotic attack.
Bring in the Special Forces. Saeidi et al. took another bacterium - workhorse of the molecular biology lab, Escherichia coli - and pimped it out to be a Pseudomonas aeruginosa killing machine, using many of the own pathogen's weapons against it. Essentially, the system was comprised of three parts:
1. The E. coli were engineered to recognise the "quorum sensing" signals that the Pseudomonas naturally produce to communicate during biofilm formation.
2. The quorum sensing receptor was genetically wired up to a gene that produced a toxin, pyocin, that had been modified to kill Pseudomonas. (In fact, they modified the very toxin that Pseudomonas uses to kill other bacteria during biofilm formation.)
3. The sensor was also wired up to a self-destruct mechanism, switching on expression of a lysis protein that, once enough had accumulated, would cause the cell to burst.
The net result is an E. coli that can sense when it is near Pseudomonas biofilms and, once the density is high enough, will start producing the pyocin toxin and the self-destruct lysis protein. After a period of accumulation, the cell bursts and all the surrounding Pseudomonas are exposed to the toxin, hopefully killing them.
The paper was just proof of principle, really. They were able to kill 90-99% of Pseudomonas aeruginosa with their new bug-bomb but there are still a lot of hurdles to overcome before this could be considered as a treatment for Cystic Fibrosis and other biofilm-related diseases. For one thing, it is not clear how harmful the E. coli, itself a human pathogen, or its toxic cargo would be to the patient or the other "friendly" bacteria in their bodies.
Despite this, though, I still think it is cool. Just being able to engineer something like this that works is a demonstration of how awesome molecular biology and genetics is in the 21st Century. Even if human diseases cannot be targeted directly with such techniques, biofilms also cause problems outside the body, such as in water pipes or on surgical instruments, and having another potential weapon in the arsenal to fight them is always welcome.
Traditionally, we think about bacteria a single-celled organisms but this is often not really the case. In many situations, populations of bacteria form multicellular masses called biofilms. These can be a big problem, particularly for human disease, because the biofilm structure can make the bugs resistant to regular antibiotic attack.
Bring in the Special Forces. Saeidi et al. took another bacterium - workhorse of the molecular biology lab, Escherichia coli - and pimped it out to be a Pseudomonas aeruginosa killing machine, using many of the own pathogen's weapons against it. Essentially, the system was comprised of three parts:
1. The E. coli were engineered to recognise the "quorum sensing" signals that the Pseudomonas naturally produce to communicate during biofilm formation.
2. The quorum sensing receptor was genetically wired up to a gene that produced a toxin, pyocin, that had been modified to kill Pseudomonas. (In fact, they modified the very toxin that Pseudomonas uses to kill other bacteria during biofilm formation.)
3. The sensor was also wired up to a self-destruct mechanism, switching on expression of a lysis protein that, once enough had accumulated, would cause the cell to burst.
The net result is an E. coli that can sense when it is near Pseudomonas biofilms and, once the density is high enough, will start producing the pyocin toxin and the self-destruct lysis protein. After a period of accumulation, the cell bursts and all the surrounding Pseudomonas are exposed to the toxin, hopefully killing them.
The paper was just proof of principle, really. They were able to kill 90-99% of Pseudomonas aeruginosa with their new bug-bomb but there are still a lot of hurdles to overcome before this could be considered as a treatment for Cystic Fibrosis and other biofilm-related diseases. For one thing, it is not clear how harmful the E. coli, itself a human pathogen, or its toxic cargo would be to the patient or the other "friendly" bacteria in their bodies.
Despite this, though, I still think it is cool. Just being able to engineer something like this that works is a demonstration of how awesome molecular biology and genetics is in the 21st Century. Even if human diseases cannot be targeted directly with such techniques, biofilms also cause problems outside the body, such as in water pipes or on surgical instruments, and having another potential weapon in the arsenal to fight them is always welcome.
Friday, 19 August 2011
There is no such thing as "The Theory of Evolution"
There is the fact of evolution - the undeniable* accumulation of data and observations that lead inescapably* the conclusion that all life we have encountered shared, and evolved from, a common ancestor. (*Undeniable and inescapable without some serious mental gymnastics, buckets of untruths (either through forgivable ignorance or less forgivable deceit) and, most importantly, an agenda to deny this scientific truth.) Then, there is evolutionary theory - a body of different theories put forward to explain different aspects of these observations and data. Best of all, in my humble opinion, there is the application of evolutionary theory - my own field of research - in which we use the fact of evolution, the theories about the underlying mechanisms, and the enormous quantity of data we have accumulated to make predictions about areas of biology for which we have less data. Evolutionary theory is used to design lab experiments, manage conservation projects and find cures (and causes) for diseases.
If you are confused about the whole evolution fact/theory thing, it is explained really well in this recent blog post by Larry Moran. In it, he points out that "The Theory of Evolution" (singular) does not really exist. There is no single theory that encompasses all aspects of evolution. (Even the current observation that all life on Earth evolved from a single common ancestor is not "The Theory of Evolution" - evolution would be just as true if it turns out there are multiple unique ancestors, although it would take some serious new data to suggest this.) So, he argues, let's stop using the phrase, which gives Creationists something to distort and confuse people with. I agree.
It's late, so my own summary will be more succinct... Evolution. It works, bitches!
If you are confused about the whole evolution fact/theory thing, it is explained really well in this recent blog post by Larry Moran. In it, he points out that "The Theory of Evolution" (singular) does not really exist. There is no single theory that encompasses all aspects of evolution. (Even the current observation that all life on Earth evolved from a single common ancestor is not "The Theory of Evolution" - evolution would be just as true if it turns out there are multiple unique ancestors, although it would take some serious new data to suggest this.) So, he argues, let's stop using the phrase, which gives Creationists something to distort and confuse people with. I agree.
It's late, so my own summary will be more succinct... Evolution. It works, bitches!
I eat waffles, therefore I waffle
I just changed my profile picture to this one of me eating a lovely Belgian waffle in Bruges and it got me thinking about food/verb homonyms - words that are food but also verbs. Like waffle. I like waffle. And, I like to waffle, as you (and my poor students) can tell.
But then I got thinking about other ones: cake, chip, chop, cream, fish, jam, juice, milk, toast... all yummy things. Sprout. Hmm. (Actually, I like sprouts.)
Some of these of course, are foods named after verbs. Chips, for example, are chips because they were chipped from potatoes. Likewise, chops were chopped and toast was toasted. Some are the other way round: you fish to get fish, milk to get milk and juice to get juice. Not so sure about cake, though. And back to waffle... Where does that come from?
Then we can cast the net wider with homophones: I drink wine, I whine; I eat meat, I meet; I eat a plum, I plumb. OK, so I might be scraping the barrel with that one. (I'm a bad plumber, clearly.) I'm sure I had some better ones when I started writing this post but my mind's gone blank. Oh well. Perhaps they will come back to me. In the meantime, I think I shall go and chock a lot.
Thursday, 18 August 2011
Even by Homeopathic standards, this is stupid
This story is covered much better at sciencebasedmedicine.org but it's so gob-smacking, I just had to write something. It's seems that the industry does a good job of convincing people that homeopathy is the same as "natural" or "herbal" remedies. It isn't. It literally has no active ingredients and apparently they don't like little people pointing this out.
Basically, a large multinational corporation (Boiron) is threatening a lone Italian blogger for pointing out that one of their products did not contain the active ingredient they claimed. No surprises there, given that homeopathy is expensive water and has no active ingredients of any kind. (According to geeks who have done the maths, the stated dilution is approx. equivalent of diluting one teaspoon of substance in a volume of water the size of the Universe.)
What is more surprising is that the "active ingredient" - oscillococcinum - almost certainly does not even exist before it is diluted! All the evidence points to it being an early Twentieth Century microscopy artefact. There is certainly no evidence that it does anything, let alone cause the symptoms of flu, which is at the heart of Homeopathic nonsense (despite an utter lack of any theoretical or empirical scientific basis, remember). Naturally, as even the existence of oscillococcinum is unproven, the idea that the duck liver extract being diluted to non-existence is high in oscillococcinum is pure speculative fantasy.
Even by Homeopathic standards, oscillococcinum appears to be sham. While every single step of the Homeopathic method lacks evidence and totally contradicts modern scientific understanding, oscillococcinum seems to contradict the homeopathic principles too. No wonder they don't want anyone drawing attention to it.
Basically, a large multinational corporation (Boiron) is threatening a lone Italian blogger for pointing out that one of their products did not contain the active ingredient they claimed. No surprises there, given that homeopathy is expensive water and has no active ingredients of any kind. (According to geeks who have done the maths, the stated dilution is approx. equivalent of diluting one teaspoon of substance in a volume of water the size of the Universe.)
What is more surprising is that the "active ingredient" - oscillococcinum - almost certainly does not even exist before it is diluted! All the evidence points to it being an early Twentieth Century microscopy artefact. There is certainly no evidence that it does anything, let alone cause the symptoms of flu, which is at the heart of Homeopathic nonsense (despite an utter lack of any theoretical or empirical scientific basis, remember). Naturally, as even the existence of oscillococcinum is unproven, the idea that the duck liver extract being diluted to non-existence is high in oscillococcinum is pure speculative fantasy.
Even by Homeopathic standards, oscillococcinum appears to be sham. While every single step of the Homeopathic method lacks evidence and totally contradicts modern scientific understanding, oscillococcinum seems to contradict the homeopathic principles too. No wonder they don't want anyone drawing attention to it.
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