Friday, 30 November 2012

AHS Southern Conference 2012, this Saturday at The University of Southampton

The National Federation of Atheist, Humanist and Secular Student Societies (AHS) have their Southern Conference 2012 this Saturday, Dec 1st. It's on Highfield Campus at The University of Southampton, hosted by the Student's Union Atheist Society. One of the speakers is The Tippling Philosopher, whose blog I frequent when time allows (and who also reposted one of my posts on ID Creationism). Nice to see that they're heading to The Crown - my favourite pub near the Uni - afterwards for a pint or two and dinner. (Mmmm... Crown Burger!)

Although I am a member of The Rationalist Association, I've never actually attended an atheist or Humanist event since moving to Southampton, so I will try and get along if I can. If you're in the area, why not check it out?

Saturday, 24 November 2012

Differential survival, (inclusive) fitness, selection and evolution

In my last post about Multi-level selection and The Selfish Gene, I neglected probably the most famous and important aspect of the "Group Selection" debate: "inclusive fitness", which (along with its specific form, "kin selection") can potentially give rise to counter-intuitive adaptive behaviours such as altruism and self-sacrifice. To understand inclusive fitness and how/why (a) it works, and (b) it is important, we have to revisit the importance and meaning of heritability in selection.

The key point is that "fitness" and selection are about more than just differential survival. Differential survival is sufficient for evolution - the population will change with time - but without the heritability aspect, this is not selection and there can be no adaptation.

It's easiest to think about this in terms of purely random events. Imagine two populations of beetle (there sure are a lot of beetles!) living in two trees who, by chance founder effects have different frequencies of an allele that causes melanism (a dark colour morph). Now imagine that one of those trees experiences a rare catastrophic event - perhaps a meteor-strike, or it is on a cliff-top and collapses into the sea - that wipes out its entire beetle population. The frequency of melanic colour morphs in the beetle population has changed - there has been differential survival - but because it was totally unrelated to the causal reason for the differential survival, this is not selection.

Evolution without selection happens all the time and can easily lead to certain traits becoming fixed in a population, even if they have no direct (or only a very weak) fitness effect on those with the trait relative to those without. (Fitness is always relative.) Most changes at the molecular level, for example, are neutral changes occurring through random genetic drift. This is still evolution, it is just not selection - it will not give rise to adaptation. (Although a change of environment - and the environment for genes is never static - could render a previously neutral trait as good or bad.)

So where does kin selection and inclusive fitness come in? Well, a key - and sometimes confusing - point about fitness and selection is that the individuals expressing the heritable trait and the individuals benefiting from the heritable trait do not have to be the same individuals. This is critical because it reinforces the special place that genes have in multi-level selection.

In the last post, I wrote:
Yes, selection can potentially act at some of these different levels - the collective properties of the family, tribe, species or ecosystem can affect the fitness of the genes therein - but only the genes make copies of themselves. Only the genetic information is passed on - all of the physical aspects - the DNA, the chromosomes, the cells, the bodies, the tribes, the ecosystems - are transient vehicles for this information. Only if this genetic information gives rise (in an appropriate background) to the trait that influences fitness - whatever the level that fitness is manifest - will that trait be heritable and selection happen.
This is the difference between "replicators" (in Dawkins parlance) and mere reproducers. The crucial thing about genes is that they make copies of themselves, which are then carried by different members of the population. A particular genetic variant will increase in frequency if the sum total of all its effects is to the collective benefit of carriers of that genetic variant, even if some of its effects are detrimental to some of its carriers. Hence altruism can still spread if it has a genetic basis and the net product is increased survival/reproduction of carriers of the altruism "gene(s)".

There are two more important points about inclusive fitness:

1. Kin recognition is not required. Crucially, there does not need to be a conscious awareness by the altruistic individual; it does not need to be able to recognises its kin or fellow gene-carriers. (Although, clearly, if it can then it will be even more successful.)

2. All fitness is inclusive fitness. Inclusive fitness is one of the few unifying principles of biology that, as far as I can tell at least, applies across the board. Whether you are talking about Artificial or Natural Selection, Individual or Group Selection, it all comes down to inclusive fitness. Even when all of the phenotypic effects of gene are limited to its carrier - pure "Individual Selection" - inclusive fitness comes in to play: as long as it benefits more individuals than it impairs, it will still spread. (The same gene can have different effects in different individuals.)

The nice thing about inclusive fitness is that it works irrespective of the nature by which the sum total of its effects benefit its carriers. These effects can occur at any level of biological organisation and may, indeed, have effects at multiple levels; thanks to inclusive fitness, far from being in conflict, multi-level selection and The Selfish Gene are one and the same.

Thursday, 22 November 2012

Multi-level selection and The Selfish Gene

Yesterday, I attended a seminar run by the University's Institute for Complex Systems Simulation by Samir Okasha, a Professor of Philosophy of Science from the University of Bristol and author of the book "Evolution and the Levels of Selection" (among others). The talk was entitled 'Individuals versus Groups in Evolutionary Biology' and Prof. Okasha gave a very interesting presentation about some of the history and issues surrounding the discussions (and sometimes arguments) about "Group Selection" and its modern incarnation, "multi-level" selection.

It looks like an interesting book too and is on my ever-growing reading list. I'd particularly like to ponder some more his thoughts on emergent group properties - something I do not currently have the time, space or philosophical nonce to explore further in this post.

There was one key aspect of the debate that, in the interests of time, was not covered in detail in his talk: the issue of heritability and what that means for "Units of Selection". The more I think about it, the more I think it is a real barrier for people understanding the problem and, in my opinion, leads to all sorts of confusion about how evolution and selection work.

This is a quote from an Amazon review of his book that sums up the key issue quite nicely:
So often we are bombarded with 'scientists' giving us their metaphysical views as if they were 'scientific fact'. It is therefore refreshing to find a philosopher looking at a science and seeking to clarify the various concepts in that science.

Okasha observes that the various life forms are arranged in a hierarchy:

Generally reproduction occurs at the same level in the hierarchy: organisms reproduce to give organisms; chromosomes divide to give chromosomes; colonies divide to give colonies, and so on. According to the logical formulation of the theory of `natural selection' a) variation, b) differential fitness (different rates of survival and reproduction) and c)heritability (parent - offspring correlation) are required to produce evolutionary change. All these may be present at each of the levels in the hierarchy so there is nothing that necessarily restricts selection to any one level, say at the level of the gene. To claim that selection always occurs at the level of the gene is to confuse the result of selection (the proportion of the various genes in the gene pool) with the process of selection (where in the hierarchy the winnowing actually occurs).
[My emphasis]
This is an argument that I have come across a few times on internet forums and like - often by non-biologists. (I'm not sure why the reviewer puts quotes around 'scientists' - perhaps this is an unfair dig at Dawkins. When these arguments appear, they are often accompanied by a barrage of anti-Dawkins nonsense about dogmas and how our old, flawed understanding of evolution is being overthrown etc. At best, this is a gross exaggeration. In my opinion, it is utter hogwash.)

Quite simply, I don't think this argument works because it overlooks something very important. I have highlighted the key phrases in bold. This review has the matter utterly backwards. To say that selection is occurring at a level other than the gene and not the gene (and "gene" in this context must have the correct evolutionary meaning not the biochemical meaning) is to confuse the agent of selection, which can be gene, cell, organism, family, whatever, and the target of selection - the "gene". This is because, for selection to work, there has to be heritability and this heritability is not simply "parent - offspring correlation".

(At this point, I would like to make it clear that I do not think Samir Okasha makes this mistake. I've not read his book yet but in his talk he was very clear to make the distinction between causality in selection - what we call direct and indirection selection, which correspond to causal and correlative changes in gene frequency. He also pointed out that there is no conflict with multi-level selection and "The Selfish Gene".)

For selection to work, there has to be a causal link between the heritable trait and differential fitness. Mere correlation is not enough. It is enough for evolution - there will be a change over time - but it is not enough for natural selection. And this is where genes are special. Yes, selection can potentially act at some of these different levels - the collective properties of the family, tribe, species or ecosystem can affect the fitness of the genes therein - but only the genes make copies of themselves. Only the genetic information is passed on - all of the physical aspects - the DNA, the chromosomes, the cells, the bodies, the tribes, the ecosystems - are transient vehicles for this information. Only if this genetic information gives rise (in an appropriate background) to the trait that influences fitness - whatever the level that fitness is manifest - will that trait be heritable and selection happen. Reproduction in the important sense - heredity - does not occur "at the same level in the hierarchy".

Has anyone actually demonstrated non-genetic inheritance of any higher-level trait? I'm not aware of any and whenever I have raised this in online discussions, I am normally just met with a barrage of anti-Dawkins nonsense or some vague notions about epigenetics, behaviour and "emergent" properties (which I advocate in general, by the way,) without any specific demonstration or model as to how these higher levels reproduce and pass on their traits to the next generation. Crucially, you have to do more that demonstrate that it could work mathematically or in a computer simulation - you have to demonstrate that there is a corresponding biological reality.

Which brings me to another important point. I would also question the notion of "fitness" at some of these higher levels. Ecosystems do not reproduce at all. There can be competition between groups of organisms, certainly, and long-term differential survival, which will result in evolution - just as random events such as floods and meteor strikes can influence long-term evolution through differential survival. But this is not selection. The ecosystem is changing because of individual success or otherwise and individual success is being influenced by the environment - the changing ecosystem - but an ecosystem is not directly spawning a new ecosystem that inherits its properties and goes off into the world to compete with different ecosystems. (It seems to me that there is one higher level entity capable of non-genetic inheritance - something championed by Dawkins himself. The cultural replicator, or "meme". This is not what multi-level selection is about, though, as far as I can tell.)

A final problem for non-genetic multi-level selection is that many of these "levels" don't really exist in a fashion that makes selection possible - they are part of continua rather than discrete entities. An ecosystem, for example, does not really mean anything specific. I am an ecosystem from the perspective of my gut microbes. The whole planet is an ecosystem. It is useful to drawn the boundaries at different points for specific study but we should remember that these distinctions are arbitrary. Even an "individual" is a woolly concept thanks to symbiosis - and we are probably all symbionts at the end of the day.

The only thing that is absolute is that you can break everything down to genes (genetic information) and their environment. The flow of information is one way. Genetic information is modulated - but not created - by the environment. (Even accounting for epigenetics, which modulates the environment but not the genotype, though this is for another post.) The Selfish Gene (and its Extended Phenotype) still wins.

Or does it...?

There is one problem that remains for the "Selfish Gene" and it is the same one that plagues almost all of biology. Just like all the levels above it, a "gene" (in the evolutionary sense) is just a mirage. In many ways, there is no such thing as a gene. There is just genetic information. We like to talk about a "gene for X" but really what we mean is "heritable genetic information that has a causal but environment-dependent tendency to produce X". This is just a problem of conception and language, though, not the underlying mechanism and theory. Selection is still ultimately acting on genetic information, and it is still selection at this level that gives rise to adaptations, but how you package this genetic material up into genes is, again, context-dependent and (thanks to recombination and mutation) can be complicated.

It fascinates me how we love to try and split continua - life, species, development, genes - into discrete packets even when no such packets exist and then tie ourselves up in knots because we can't let go of those arbitrary (and false) divisions we have made. Ultimately, I think the issue of Individual versus Group Selection might just be this problem, taken to another level.

Wednesday, 21 November 2012

#ProjectEvoMap (not "Project EvoMap"!)

Social media and public engagement are increasingly important for scientists in the modern age. Resources like the University of Oxford's 23 Things are springing up to help young (and old!) researchers harness the power of "Web 2.0" activities, such as Blogs, Wikis, Podcasts and Twitter. Although a blogger and occasional Tweeter, I think I should probably do the course myself; I am sure that I could make better use of social media than my current attempts. (As with most activities, though, the biggest obstacle is time and energy!) I think that one has to be careful about getting obsessive about such things (I went through a phase of trying to post every day, which is not always healthy or productive) but anything that helps communicate science to a wider audience is usually a good thing.
One such project that caught my eye a while ago was ProjectEvoMap - A global map of evolutionary biology research groups, started by an English PhD student in Sweden, Robert Griffin (#ProjectEvoMap). I'm not 100% sold on the name - if, like me, you try to find it and insert a space after "Project" you get all sorts of other stuff - but I really like the idea. It's a pretty simple aspiration: to enable people to locate evolutionary biology labs near places of interest and to generally raise awareness of what (and where) evolutionary biology is being done. I've added my lab and if you're an evolutionary biologist reading this, I hope you'll add yours too.

Friday, 16 November 2012

Artificial Selection versus Natural Selection

One of things you will probably encounter quite quickly if you ever discuss evolution with a Young Earth or Intelligent Design Creationist is a deep confusion about Natural Selection. Often this is as simple as claiming that it doesn't exist and explains nothing, which is clearly and demonstrably utter nonsense. Recently, I experiences a more unusual extension of this claim:
"Natural Selection does not exist. It is all Artificial Selection."
This is usually an attempt to discredit experimental evidence for Natural Selection that comes from direct laboratory manipulations, such as the long-term experimental evolution of bacteria in the lab of Richard Lenski and colleagues.

A less extreme position is to claim that lessons learnt from artificial selection, generating different breeds of dogs, for example, are cannot be extrapolated to nature because Natural Selection is fundamentally different. Both variants of the argument are utterly wrong.
[Image credit: Science Museum.]

So, what is the difference between Artificial Selection and Natural Selection?

Philosophically, I think it is the difference between being directed or undirected. This is different to it being a case of directional versus undirectional. All selection is directional - that's the point. Evolution without any direction happens - neutral evolution and Random Genetic Drift - but this does not give rise to adaptations. Selection, on the other hand, imparts directional constraints to the evolutionary trajectory because some variants do better or worse than others.

This is most clear with "Negative" or "Purifying" selection, in which certain directions are closed because carriers of those variants are less competitive. This is what produces a signal of evolutionary conservation. More dramatic are the cases of "Positive" selection, in which particular variants have increased "fitness" compared to the population (i.e. the genetic material for that variant is more likely to be passed on to the next generation than a random bit of DNA in an individual without that variant) and thus it "sweeps" through the population. (Contingent on the strength of the effect and the population size.)

The point is, though, that while Natural Selection has direction it is not directed - it has no goal it is striving towards. The direction is imposed by the environment that a particular variant finds itself in at the time. This environment includes all the other variants in the population: fitness is always relative.

The direction of selection can also change from generation to generation, even within a generation. (Think of adaptations to hot or cold weather and consider climate variability, for example.) This means that populations can evolve themselves into an evolutionary dead-end, or lose a gene/trait that could prove useful in the future. Evolution by Natural Selection reacts to the now, it does not predict the future. The bills of Darwin's finches are specialised for certain foods they have encountered during their radiation - they have not all remained versatile generalists, ready to adapt quickly to changing food availability.

I think this is the real reason that many religious people have a problem with evolution by Natural Selection: there is no goal, no target, so humanity cannot be the goal. We are not the pinnacle that evolution has been working towards, we are just a by-product of past selection and chance events. (There are, of course, ongoing discussions about the predictability of evolution but this is really a question as to whether, if evolution were re-run, something like us (i.e. intelligent life) would inevitably appear. I can't imagine that any evolutionary biologist would seriously entertain the notion that we would re-appear if life were restarted.) The root of the argument against Natural Selection (but accepting Artificial Selection) is born of the belief that all evolution is directly governed and directed by some kind of deity. (Even if this deity is dressed up as an "Intelligent Designer".) Often, this is coupled with claims along the lines of "there is no such thing as random mutation" and other such arguments, which simply do not account for observations of the world around us. (Not unless, for reasons unclear to me, you postulate a deity who is deliberately out to deceive and make things look random and undirected. I'll save this one, and the randomness of mutation, for another post!)

The directed/directional distinction is just one aspect of the difference, however. To really qualify as Artificial Selection, I think that the directing agent has to be directly choosing (selecting) who reproduces and who does not. This is distinct from Natural Selection, in which the differential breeding success is just a consequence of reactions to the environment. This is why claims that experimental evolution in the lab are Artificial Selection are normally wrong. Laboratory evolution is normally directly studying Natural Selection, albeit with a tightly controlled environment. (One of the key approaches in science is to try and remove as much random variability and simplify the system as much as possible.)

In some ways, it is easy to see this by examining the spectrum of selective regimes used in the lab. Some can be quite complex in terms of responses, such as changes in temperature or the addition (or removal) of certain common or key nutrients. Others are much more defined, such as the addition of an antibiotic resistance, in which a very specific trait - resistance - is being sought. This is still Natural Selection: the environment being controlled and the organisms are surviving differentially based on their genotypes in response to this environment.

It could be - and sometimes is - argued that this is actually Artificial Selection and that the specific antibiotic regime is merely the mechanism by which the human is artificially selecting. It could be argued - blurring the boundaries between the two, which I'll get back to - but it shouldn't be argued, for I think it is a wrong (if forgivable) position to take. Even antibiotic resistance experiments are not purely selecting one trait. There will also be more subtle selection pressures due to the choice of media or growth conditions. As well as resistance, there will still be pressure to grow fast. There may even be complex biotic interactions where a subpopulation protects the rest of the population, such as biofilm formation. Even though the desired outcome might be antibiotic resistance, the experimenter is not (normally) actively selecting individuals. (S)he is not manually screening individuals and picking which ones to propagate.

This is quite different to selective breeding in dogs, for example. Here, a breeder is picking a particular trait - such as the ridge in a Rhodesian Ridgeback and selecting specific individuals with that trait to breed from. This is so powerful as a selective force that it can over-ride normal fitness considerations and evolve a trait that is otherwise downright detrimental to the individuals concerned. A number of pedigree dogs have severe health problems, for example.

This distinction of active versus passive selection of individuals with specific traits is certainly one way to view the Artificial Selection versus Natural Selection issue. There is another way, however, which I tend to err towards and makes the statement that there is no Natural Selection and only Artificial Selection even more erroneous: Artificial Selection is actually just a special case of the more general process of Natural Selection: one end of the continuum. Far from there being no Natural Selection, it is all Natural Selection!

The fact is, philosophy aside, there is no real biological difference between the two. Yes, it's easier to spot and define the selection when it's directed and tightly controlled - which is why it is so useful in the lab - but the basic mechanism of differential reproduction of heritable variants holds true for both. Furthermore, there is a direct analogy for Artificial Selection in nature, in which decision-making agents actively choose which individuals get to reproduce based on specific traits - Sexual Selection. (Intersexual selection, specifically, in which mate choice (as opposed to direct intrasexual competition) is a determining factor in reproductive success.) Sexual selection and mate choice abound in nature and can produce some quite absurd phenotypes that, like the products of artificial selection, are not necessarily healthy. From the perspective of the organisms experiencing the selection, a human imposing Artificial Selection is just part of the environment in just the same way as a choosy mate might be.

One possible example of this is the antlers of the (now extinct) Irish Elk. The photo above (from WEIT) shows male (right) and female (left) Irish Elk skeletons from the Museum Building in Trinity College Dublin. The sexual dimorphism - only the males have the monstrous antlers - is a clear sign of sexual selection and the antlers of male Irish Elk are so massive that it is thought they probably contributed to their extinction.

It's not actually the best example, to be honest, because the initial sexual selection on antlers was almost certainly intrasexual selection between fighting males and even though the Irish Elk antlers are too big for such behaviour, their monstrous size could be linked to increases in body size rather than intersexual selection for big antlers. That said, there must have been some force maintaining such impractical ornamentation and female mate choice is a prime contender. I mainly picked it because my brother works in the Museum Building and I used to see these elk quite regularly when I lived in Dublin. There's also an alternative YEC explanation for their extinction (right, also from WEIT; cartoon by Chris Madden)! If you don't like the elk as an example, there is always the peacock. (Whole books have been written about it if you want to know more.)

So, in conclusion: not only do Artificial Selection and directed evolution provide good tools for investigating aspects of Natural Selection, in very real terms they are Natural Selection. Anyone who claims that Natural Selection does not exist and everything is Artificial Selection has got the situation entirely backwards.

Monday, 12 November 2012

The Cabbages of Doom 2.2

A new edition of The Cabbages of Doom is now available on the Kindle for only 99p (or $1.59). Thanks to some editorial advice (thanks, Karen!), a few grammatical errors and typos have been fixed here and there. It also features a new cover. Following some changes at Amazon Kindle Direct Publishing, it can be lent too. (Though only in America, I think.) The iBooks and Lulu versions will be updated when time and energy allows. (Unless I discontinue them and enrol in "KDP Select".)

If you are curious, visit Amazon to download a free sample, read the blurb or view the sample chapter (PDF). If you need more encouragement, here it's one review so far (for the Lulu PDF version, which is yet to be updated):

This exciting and entertaining first novel exceeded all of my expectations. The story itself is a very imaginative chase across the English country side involving inter-dimensional travellers culminating in an entirely unpredictable hilarious and action packed final confrontation. The story had me laughing out loud and genuinely invested in routing for the good guys (okay, cabbage and small animals). Unlike most self-published first novels in this price range this one was very well spell-checked and surprisingly grammatically correct. If you are in the mood for a smile, a fun story and groan or two for some amazing puns and references to classic films, then this is the best 99p you can spend.
Go on. You'll make my day.

Thursday, 8 November 2012

Standing up for Genetic Modification

It's my 300th blog post and so I wanted to try and post about something that captured the essence of the blog, hence the delay! What could be better than to combine food, science and The Cabbages of Doom?

Actually, The Cabbages of Doom is a bit of a red herring for this post. Just in case there is any confusion, The Cabbages of Doom is not a negative reference about Genetically Modified (GM) foods. (It's a surreal science fiction story about some marauding cabbages from another direction invading Swansea. And only 99p! Review here.)

In fact, I could not be much further away from an anti-GM position. For me, the success of the anti-GM lobby in the UK and across Europe in the late nineties represents one of the biggest scientific, political and media disasters of the modern age. A well-organised and probably well-intentioned but horribly misinformed group of scaremongers managed to hijack the public debate over use of one of the most promising technologies ever to be developed in the history of mankind.

Let's make one thing clear from the outset: there is nothing inherently unnatural about Genetically Modified Organisms (GMO). For a start, many GMO just involve targeted mutations within a strain or introduction of genetic variants from related species. These could potentially be achieved by conventional breeding and artificial selection at much greater expense of time and money (and death). The more advanced GMO involve taking DNA from one organism and inserting it in another. Even these GMO are not really unnatural, even if the techniques used to create them are: although it is rare in multicellular plants and animals, "Horizontal Transfer" of genetic material between organisms - including eukaryotes - does occur in nature. (See Keeling & Palmer (2008) Horizontal gene transfer in eukaryotic evolution. Nature Reviews Genetics 9:605-18 for some examples and discussion.)

It is true that the level of modification desired is unlikely to be achieved by natural mechanisms within the lifetimes of the scientists involved. This, though, is one of the key benefits of GM: it greatly speeds up our ability to generate and evaluate possible genetic solutions to environmental problems. We don't need to wait around just trying to get lucky.

Furthermore, far from being inherently dangerous, many GMO are probably safer to the environment than non-GM alternatives. Why? GM is far more precise and targeted than "traditional" methods of creating mutants for screening, which involve chemicals or radiation and produce something much less predictable. The more we understand the nature of the modification, the easier it is to both predict possible risks and also detect or mitigate them. You only have to look at the problems of "invasive species" to realise that entirely "natural" organisms in the wrong place can be an environmental calamity. By eliminating the ability to customise and refine appropriate native organisms through GM, inappropriate introduced species might be used instead. (Often it is not clear what the problems might be until they are released.) The other reason is that, done right, a GMO can permit reductions in uses of chemical fertilisers, pesticides and herbicides.

Food safety is more of a concern but the solution here is not a blanket ban nor even a blanket hysteria, it is adequate food testing and common sense. If a gene has simply been removed from an organism or repressed, as in the "Flavr Savr" tomato, it is no more dangerous than a new hybrid from natural breeding - DNA is digested when we eat food, so if the product itself is not toxic, there is no obvious risk. If, on the other hand, the GMO is producing something like Bt toxin, one obviously needs to be more careful. Even here, though, it is not obviously the case that using chemicals, or even "organic" alternatives (all GMO are organic!) like spraying Bt strains of bacteria, would be any safer. Preferably, all new foods would undergo appropriate toxicity and allergy testing, whether they were the product of conventional breeding or GM. If there is a genuine problem, clearly that specific GM food should be withdrawn, just as one would do with anything containing, or grown with, new bacteria or chemicals.

So, what went wrong? One of the big problems was the old chestnut of "balanced reporting" in the media. All too often, this seems to equate to equal air time for both sides, no matter how uneven the evidence supporting the two sides was. A calm and cautious (and often already pretty balanced) scientist is paired up with a volatile and definitely one-sided activist. Clearly, this is going to end up biased towards the activist even if their position is weaker and founded on misunderstanding and/or misrepresentation of the science. Worse, the journalists chairing the whole thing often fail to interject when one side is just plain wrong about their facts.

The second problem was education. I don't think it would be such a big problem today because DNA and genomics is in the news so much more but, at the time, a scary proportion of the British public did not think that a non-GM tomato had any DNA in it, for example. (At Nottingham, we had a public debate on the issue and a someone had to be removed because they just kept shouting "I don't want to eat DNA!" and would not stop to have it explained that he was eating DNA in all his regular food.)

The final nail was economics. The anti-GM campaign was good enough at scaremongering that public confidence was weakened, despite (inadequate?) attempts by the scientific community to set the record straight. Supermarkets perceived that they would lose enough custom to warrant pulling the plug and so they did. GM has been largely vilified in the public domain ever since, although I think the EU has now relaxed its zero-tolerance stance. After all, if a supermarket is advertising itself as "GM free" as a good thing, GM must be bad. Right? (Obviously, the consumer desires of someone like me, who would rather eat the cheaper, tastier, less wasteful GM tomatoes, are not so important.)

GMO are not universally good and I am sure there have been situations where big corporations have used GM just to make more money or to increase herbicide resistance and thus use more herbicide, which is bad for the environment. Like any technology, the applications need to be considered on a case-by-case basis.

That said, there are some clear situations where GMO can be a force for good, such as the Golden Rice Project, which seeks to use "biofortified rice as a contribution to the alleviation of life-threatening micronutrient deficiencies in developing countries". Drought- and salt-tolerance maize and other such crops could also be important in our changing world.

The sad irony is that, by resisting the development of government-funded GM crops in academic institutions, the anti-GM lobby have actually driven it all into the hands of large corporations that can get round legislation by doing tests overseas and are far more likely to create the kind of GMO that we don't actually want. (Or, even more scary, unregulated amateur biohackers.)

Whether you think it's man-made or not (it is), Climate Change is a big problem and the more we ignore it, the worse it's going to get. This is a problem so big that we need to throw every weapon in our arsenal at tackling it head-on, and that includes taking a chance here and there. There is a reason that food security is one of the major focuses of UK science funding. We have to feed a growing population on dwindling resources. It's not rocket science. (And I haven't even mentioned biofuels.) Genetically modified organisms represent one of the best - possibly the only - chance we have, short of a massive reduction in the global population. (Population crashes and extinction are natural responses to Climate Change - let's make no mistake here, "natural" is not always good.) It's time to let the genie back out of the bottle and let it be a force for good.

Sunday, 4 November 2012

Intelligent Design is Creationism, just not Biblical (or Young Earth) Creationism

In their FAQ, the Discovery Institute write in response to the question "Is intelligent design theory the same as creationism?":
"No. Intelligent design theory is simply an effort to empirically detect whether the "apparent design" in nature acknowledged by virtually all biologists is genuine design (the product of an intelligent cause) or is simply the product of an undirected process such as natural selection acting on random variations. Creationism is focused on defending a literal reading of the Genesis account, usually including the creation of the earth by the Biblical God a few thousand years ago. Unlike creationism, the scientific theory of intelligent design is agnostic regarding the source of design and has no commitment to defending Genesis, the Bible or any other sacred text. Honest critics of intelligent design acknowledge the difference between intelligent design and creationism."
Well, I am an "honest critic" and I will acknowledge the difference between ID and the restrictive definition of Creationism that they choose to use but I will not acknowledge the difference between ID and Creationism in general. Creationism is the belief that some being outside nature (as we know it) created everything, as opposed to everything arising naturally without any causal agent or intervention. This totally encompasses ID.

The fact that they try to make claims that their designer need not be a deity - and, in particular, is not necessarily the god of the Bible - is irrelevant and demonstrates their intellectual paucity and/or dishonesty. The only ultimate conclusion that can be drawn from the ID "hypothesis" is that the Universe was created by a non-physical intelligence. That sounds a lot like a deity (and Creationism) to me. If "aliens did it" then ID also predicts that those aliens must be the product of ID and the problem is moved but not removed.

The only thing that could part ID from Creationism would be if they came out and stated in pure black and white that they are willing to accept that the proposed Designer of this Universe and/or life on Earth was itself the product of purely natural processes and devoid of input from an external Intelligence. In other words, state clearly that their extrapolation of design ONLY applies to the observed Universe. It wouldn't help their "scientific" claims at all but at least they could honestly cut the ties to their clear and documented Creationist ancestry. (I predict that they will not because I think that even they can see that making this statement would be tantamount to admitting that ID is a wholly unnecessary hypothesis - the only thing that keeps it alive is a stubborn refusal to let go of certain key (flawed) assumptions.)

Even should they take this extra step, the DI and their ID friends have a serious problem that cannot be ignored. The reason that so many critics make the link between ID and Creationism is that, when it comes to the scientific observations and interpretations, ID has the same core ideas as certain flavours of "Theistic evolution" Creationism, and thus all the same criticisms and problems apply.

Creationism is a spectrum with Young Earth Creationism at one end and an almost entirely naturalistic Theistic Evolution at the other. In the former, the Designer ("God") did essentially everything. In the latter, the Designer just kicked things off at the start - designing the Universe to be able to support life - and did nothing else. ID, as described, is indeed incompatible and different to both of these. (They do accept evolution - ruling out YEC - but do not accept that it was a purely naturalistic, unguided process - ruling out naturalistic Theistic Evolution.)


There is a whole spectrum of Theistic Evolution Creationism in between that invokes an on-going intervention of the deity to a greater or lesser extent.

Possibilites include:
☛ intervening to start life by making the first replicators (abiogenesis). Note that this (and designing the Universe) is a wholly separate question as to whether evolution could occur by purely natural (unguided) means
☛ intervening for the "major transitions" in evolution. (The first cell, multicellularity, eukaryotes etc.)
☛ intervening at key points throughout to drive the evolution of complexity
☛ intervening to drive all "macroevolutionary" events but staying out of "microevolution". (A false dichotomy in itself but that's one for another post.)
☛ intervening to drive all evolution by directing all mutations

ID sits at some fuzzy point along this spectrum, as do Creationists. The fact that, for a Biblical Creationist, the Designer was God is largely irrelevant - unless they go the whole hog and deny evolution entirely as a Young Earth Creationist. (A much more intellectually honest position than ID but also so demonstrably wrong position that even the DI appears to disown it on their homepage.)

In fact, ID has a bigger problem than Theistic Evolution Creationism - the motives of the Designer. As ID advocates will be free to point out when critics point out the numerous apparent design flaws in nature, one can only really talk about "good" versus "bad" design if one knows what the design is for. Natural Selection provides an inherent discriminator for things that work better than others - that is how Natural Selection is able to facilitate the evolution of complex adaptations. Theists can argue from their holy books that the end-point was mankind (or whatever) and although I suspect they cannot really get a good handle on their Designer's objectives (why, for example, the inordinate fondness for beetles?), they can probably rule some things out. The ID crowd do not even have that.

Instead, ID is just "God of the gaps" rebranded as "Designer of the gaps". They refuse (but not refute, for their rebuttals are all flawed) possible natural explanations for certain observed phenomena - a Universe "fine-tuned" for life, complex macromolecular machines in biology, and life itself - and make an alternative proposal that is based on unproven and erroneous extrapolations combined with a woeful ignorance of information theory and biology - all cloaked in pseudoscientific language. (Another post for another day.) They then try to find examples of where the theoretical natural explanations for specific phenomena (such as a specific protein complex or specific past evolutionary event) have not been demonstrably proven (despite having a sound theoretical explanation) and insert their Designer with no clue as to its motives or rationale for intervening at that particular point in time and space.

That certainly sounds a lot like traditional Creationism to me. (And whatever it is, it sure ain't science.)

[Edit note: although most YEC and ID leaders are clearly at odds, it should be noted that ID does not actually rule out a Young Earth, it just does not promote it. Given the overwhelming scientific evidence for an old Earth and lack of Biblical Flood, the fact that the ID movement does not explicitly reject these is another indication of its utter lack of scientific motivation. Then, of course, there is Of Pandas and People, a Creationist text that similarly neither accepts nor rejects YEC and is famous for doing a find and replace for "Creationism" (and similar words), replacing them with "Intelligent Design". How can you have a coherent view of biological origins if you can't even decide on something of such fundamental importance?]

Saturday, 3 November 2012

The 2nd Law of Rocking

The 2nd Law is the 6th album of Muse and my initial reaction after a few listens is that it is one of the best. It's a pretty eclectic miss.

Supremacy is a good a Muse song as you will find anywhere, full of orchestral/classical influences as well as their rock genius. Madness is Lady Gaga meets Queen (plus Muse, of course). In Panic Station, they out-Darkness The Darkness. For me, it's the difference between being great musicians and being great song writers (and musicians). Survival was one that I had already heard from its Olympics release but it actually sounds much better in context, I think. (The previous track, Prelude, sets it up nicely, as the name suggests.)

I've always thought that Muse had a touch of Radiohead about them and this is never more obvious than in Explorers, which has more than a little No Surprises about it in my book. (Not a bad thing.) Another band that I really enjoy is The Qemists and The 2nd Law: Unsustainable reminds me a bit of them, in a good way. It is a bit of a departure for Muse vocally, as they seem to have a Cylon doing guest vocals. I like it, though! (I think their interpretation of the 2nd law of thermodynamics is a bit flawed though - it's the same mistake that the Creationists make: the Earth is not a closed system. All the time that we get energy from the Sun, continued growth is indeed sustainable (in theory)!)

Overall, in The 2nd Law, I think Muse have achieved something quite unusual. Somehow, it contains both a wide range of styles but also an overall coherence that all fits together well. And it rocks! A definite contender for my favourite Muse album to date.

Friday, 2 November 2012

Why? Why? There is no why!

One of the oft-repeated claims of those who maintain that religion provides something that science/materialism cannot is that religion can answer "why" questions. The standard re-used metaphor seems to be that used by theologian John Haught about making tea. In response to the question of "why is the kettle boiling?", the argument goes, the scientific answer will be something about heat, energy and the motion of water molecules inside the kettle, whereas there could be an equally valid answer of "because I want a cup of tea". In other words, science tells us what the Universe is like whereas religion can tell us why.

I have lots of problems with John Haught's metaphor and might give it a post of its own one day but it is already dealt with quite nicely elsewhere, such as this Skeptico blog post. In essence, though, the problem is this: none of the answers to the "why?" question that Haught proposes are outside the remit of science. Yes, there were several possible levels of causation that could be correctly introduced as explanations but science could address them all.

It's really just a problem of the recursive "why?" One could go on to ask, why did you want a cup of tea? And there would be a potential scientific explanation for that too. Perhaps you were thirsty. Why were you thirsty? Well, the body loses water through respiration, perspiration and excretion and that needs to be replaced? Why? We are mostly water and our bodily functions all need to be performed in a primarily aqueous environment. Why? Life originated in an aqueous environment. Why? And so and so forth.

Anyone who has spent any time around young children will be familiar with the recursive why problem - you can answer any response to the question "why?" with another question "why?" until, eventually, the answerer reaches the end of their patience and/or knowledge. At the end of the line, there is no why - there is just "because". And while religion claims that the "why" is their domain, they have the same problem. It may be true that they can insert a god in there near the end so that the answer is "God wanted it that way", there is still a "why?" And we end up with "because that's what God is like" rather than "because that's how things are" as our final "answer". It's just like the Origin of Life/The Universe question: if God made the Universe then who made God? If God always existed or popped into existence, then why not the Universe? It doesn't answer anything - it just increases the "unknowable" layer before you give up.

The other thing that really annoys me about religious claims to the "why" questions, though, is that religion really sucks at providing reasons for things. Take "The Problem of Evil" for example. This one still gives theologians major headaches. For science, on the other hand, there is no problem. The "why?" is simply a feature of the natural world - albeit one that we'd rather did not exist. Evolution is another one. Theistic evolutionists can come up with contrived reasons as to why a divine being might want to use the extremely lengthy, wasteful and unpleasant mechanism of Natural Selection to generate the complex life-form that is Homo sapiens but they are no where near as convincing as the more obvious answer to the question as to why did it take over 4.5 billion years for humans to appear - long, slow evolution and Natural Selection is the only way that something complex like humans could appear.

I have not encountered a single question regarding the physical or metaphysical Universe where religion provides a more satisfactory answer to the question "why?" than science and materialism. That's probably because science remains the only way we have of finding out if a given answer is right. (Or, at least, less wrong than our previous answer.) And that is my other problem with the how/what versus why claims: religion can suggest answers but it does not actually provide any way of knowing whether any of them are true.

Thursday, 1 November 2012

Avenged Sevenfold - my kind of Nightmare for Halloween

Not as cute as black cats but it seemed appropriate to make a Halloween post about an album with death and graves and stuff on the cover. I've already covered Rage (although I notice that Blogpress has eaten my pictures) so now is the turn of a band that are a much more recent discovery for me but remind me somewhat of the Scandinavian riffmonster rockers: Avenged Sevenfold and their most recent offering, Nightmare, which is my album of the moment. (I only got it last week.)

Avenged Sevenfold (or A7x to fans, as I now consider myself,) were recommended to me by a good friend. I was a little put off by the first album I got through emusic, Waken The Fallen as the vocals tend a bit too much towards screaming for my tastes in places (although the music still rocks) but I was reliably informed that it gets more rocky and less metalcore as the albums progress. It's true, and Nightmare is a fantastic collection of tunes for those who like crazy drums and wild fret-wanking guitar riffs - as well as good tunes, of course. (I do!)

Besides, how can you go wrong with a band whose lineup consists of M. Shadows (vocalist), Synyster Gates (lead guitarist), Zacky Vengeance (rhythm guitarist) and Johnny Christ (bassist). Their (replacement) drummer for Nightmare, Mike Portnoy, needs to do something about his name if he's going to join the band on a permanent basis!

A couple of black cats for Halloween

And if Halloween is not your thing, the latest Henri video might be for you. This is not a happy time of year for a black cat who does not suffer fools.

(The pumpkins are getting a lot of love from the trick-or-treaters this year, which is gratifying.)