RQ#03 Is there really a non-natural selection?

I haven't done a random question in a while. This is the third one, apparently.

A grocery store still life, primarily Brassica oleracae

Lately I've been involved in some fairly theoretically discussions about evolution, which tend to push one to pay more attention to terminological precision. Or get very confused And get very confused regardless. Additionally, I hang around some biologists with minority opinions on certain aspects of evolution, and ultimately end up talking about evolution differently, to the point of using different words or same words differently. The usual side effects of specialisation. This becomes particularly evident in heated argument with someone outside your tribe – you start speaking slightly different dialects, if you will. Of course, where there's variation, there's opportunity to pick the variant that suits you better. Ideally, that has something to do with accuracy, since we are, hopefully, still attempting to do science and what-not.

Let's start with the easier of the usage and terminology discrepancies – the term 'natural selection'. Is it useful or does the simpler 'selection' make it redundant? I tend to drop the 'natural' part; laziness and word limits may help, but I think there may be valid theoretical or philosophical merit in doing so:

1. 'Natural selection' was initially proposed in contrast to 'artificial selection', which was used as an effective pedagogical/explanatory move. It got the point across, particularly in an age when humans were unquestionably special and distinct from the natural world. Nowadays, few scientists would seriously make a distinction between human and non-human nature in the context of biology, and thus there really is no artificial selection per se. 'Artificial selection' is 'natural selection' performed by humans to pressure their organisms towards traits the humans find favourable. In this case, the humans are part of the environment, playing a similar role to predators, except they breed the variants they like instead of instantly culling them. With no need for an 'artificial selection', is there still a need for 'natural selection', since there no longer is a valid contrast?

2. 'Natural selection' is often equated with adaptation. This isn't to say 'selection' by itself isn't, but 'natural selection' is the variant used most often in popular writing, some of which can be careless and inconsistent with its terminology. While presumably many of the authors do truly understand that selection and adaptation are different things, adaptationism has led some to consider the difference irrelevant. If adaptation is the sole phenomenon responsible for all the observable or cool things in biology, does it really matter if it's used interchangeably with natural selection? When a term is learned and frequently used incorrectly, it is extremely difficult to fix even in an individual, let alone a population. While 'natural selection' is not meant to be conflated with adaptation, it is, and has thus been tainted.

3. Use of 'natural selection' implies that phenomena like sexual selection and kin selection are somehow distinct, or special. These are secondary phenomena, special cases or manifestations of selection. That is, sex and kin selection are subtypes of 'natural selection' and do not lie on equal hierarchical level as it may first seem. While most of the scientific community has no problems understanding this, it is perhaps not the clearest delineation of the terms for the general public or students. This way, we can also keep 'artificial selection' to refer to domestication (although I don't see the necessity in doing so) without it contrasting with the 'natural' kind.

4. This is the least important point, but rather a more personal one. I dislike Darwin-worship; I'm not a 'Darwinian' (nor a "Neo-Darwinian), don't know what that means and frankly don't consider this question relevant now, over a century after Darwin's death. While history of science is indeed fascinating and undeniably worthwhile to learn about, we shouldn't trap ourselves in our history. In fact, I think equating evolution with Darwinism is a bit offensive to all the hard work and frustration of subsequent researchers that have contributed to the field – do they not matter? They work for evolution, not Darwin. 'Natural selection' has been too often tightly associated with 'Darwinism', and often plays a part in Darwin-worship. In other words, the term has acquired some baggage; mind you, not through Darwin but rather through his fervent supporters afterwards.

5. Population geneticists seem perfectly happy with just 'selection'. They're the ones who actually study the mechanisms of this stuff, so if it works for them, perhaps it should be adequate for the rest of us?


I don't mean to nitpick on words and 'mere semantics', but given the difficulty of conveying ideas to those outside your field and the general public, any site of potential confusion is worth trimming if we can. Those on the writing end are also prone to sloppiness and mistakes, so we too are susceptible to the confusion potential. That said, 'natural selection' has stuck around for this long – perhaps there is a beneficial reason I missed out on? This is an honest question – I've never really been formally trained in evolutionary biology save for a basic first year level, and may thus miss large chunks of theory. As I mentioned before, I'm being 'brought up' in some minority circles of evolutionary thought.

Why should we still use 'natural selection'?
Your turn. Just be gentle with the philosophy – I'm rather slow at following complicated abstract theoretical discussions, which is why I do experimental science ;-)

A stats question RE T-tests and U-tests

So I'm in the midst of the "Oh fuck, must get actual numbers and graphs for publication" stage of my project. This means I must not only generate piles of data, but also make it talk, and speak the truth. Which means I get to interrogate it with statistics, mwahaha. I actually enjoy this part of the process, since you can magically convert piles of numbers into pretty p-values and sexy graphs showing how earth-shakingly significant your data is...oh, well, statistically significant anyway. That is, if your stats is being done correctly, otherwise the whole activity is a futile waste of taxpayer dollars, more so than it usually is.

So I noticed that for situations where I'd expect some sort of significance (they're bloody obviously different, but I never thought/said that because I'm a 'good scientist' and all that...), the p-values were...well, maybe a little bit too high. Like, they were kind of insane -- 10^-45? Oh come on... it would be awesome boring if biological data were so clean! But both the t-test, and the Mann-Whitney U test showed extreme significance, with the latter being more trustworthy in my case, or so I've been told (I have a prominent shift in distributions rather than means; that is, cells in the drug treated case get really big, while in the mock they don't get really big.)

So I decided to test the data I know shouldn't be significant -- treatments of two wild-type ecotypes, and another case where the drug had no effect. So here's my data that SHOULDN'T be significant:

The first graph shows means and st dev errorbars, second graph shows quartile box plots of the same data (that is, no obvious shift in distribution either). Then I have t-test results from Excel, which show significance regardless of whether we assume equal or unequal variance, although F-test shows equal var. The Mann-Whitney U-test, while not being as striking as the results for the data that should be significant, is still somewhat... acceptable-ish. That is, 'significant'. But that doesn't correspond well with the data in the graphs, does it?

Would anyone know what the hell is going on here? Could the difference in sample sizes come into play? All involved data has a normal distribution, but under some conditions (not in the data above though), there is evident shift in skew in the data. I was told a U-test should sniff out differences in skew and kurtosis. I ran my data by a stats-ish guy (ok, ecologist...) a while back, and he said there's no doubt my significant data (not shown), is actually significant, but I can't trust my tests if they show 'significance' between wild types (not shown) and treatments that don't make any noticeable difference whatsoever (above).

This is really REALLY frustrating because I have a total of like 10 different lines, each treated and untreated, with massive sample sizes considering the work it takes to get the data (microscopy and measurements and all that), and I'd like to wrap up very soon with a complete graph with significant results pointed out, and finally start writing. This will be my first time writing up a part of a manuscript, so it's really exciting (and scary), but right now I've got damn stats in the way!

And I am aware Excel is not a stats program. We don't have anything else though...

I'd really appreciate any input, thanks! =D (even if it leads to rediscovering that I'm actually a huge idiot...)

UPDATE 07.02.10 2am

Ok, so Aydin recommended PAST, which turns out to be quite a nice stats program =D Thanks!

But it shows the same thing.

Actually, looking at the confidence intervals (and repeating the calculations back in Excel), the 95% CIs don't overlap, nor do the 99% ones. What's even more frustrating, is that the drug that generally causes cells to get bigger (ploidy, etc), in this case "significantly" shows smaller cells. Which is weird. And rubbish.

Ok, fine, this isn't really a proper control. Let's compare our wild type ecotypes -- the ultimate negative control. There's no bloody way Col-0 and Ler (ecotypes) should have different responses in this situation! Right?

Amazingly, it baaaarely scrapes by for 95% confidence! We use 99%, so we can call it non-significant, but still... it shouldn't be anywhere near barely scraping by! I mean, the damn p-values should be like 0.5 or something, no? Again, these are two WILD TYPES! Sketchy...

And, hang on... F-test comes out significant? Owww, headache!

Do I need more data then? It'll take another couple of months to double the sample sizes, especially for these ones, where there's much lower count per view, so I'd have to image waay more specimens. Grrrrr...

OMG, IT DOES HISTOGRAMS? And in a HUMANE way, unlike Excel? Aydin, I owe you for PAST!
So here's the obviously significant case:

The non-significant (histograms can be really misleading when the sample sizes differ, I find...)

And now the really weirdly 'pseudo-significant' case: (again, n = 280, 352)

I can see how there's a bit of a shift, but significant? Really???

Great. So while the phylogeny course has beaten out any faith in phylogenies out of me, now goes my faith in statistics. I mean, this is the thing we're supposed to rely on to avoid introducing our own biases and judgements... but if done wrongly, it can really make a mess. And I suspect I'm not doing something right.

Or am I just being too paranoid?

Random Question #02: So where do YOU think the root of Eukarya lies?

Things have been a bit quiet here lately. Let's start up a fight.

What are your views on the root of the Eukaryotic tree?
In the Unikonts, Bikonts, between them, don't recognise either as any valid group, etc?

Feel free to use abrasive language when defending your position. TC-S-like hyperbolic assertions are perfectly welcome to spice up the discussion.

If you're totally out of the loop (lucky bastard), how about this random more general argument: Holophyly or monophyly? =P
(I find this one always works when you wanna start up a lively discussion/raging war with some taxonomy/phylogeny friends...)
Also, see some musings in the comments for the previous post.

Random question: Does evolution require selection?

Got a midterm tomorrow, so should must be studying tonight, and may well be undergoing EtOH treatments tomorrow night (haven't dared to drink'n'blog yet...), so I've got a question for you guys to ponder over/discuss:

Does evolution require selection?

(context can be found in this comments thread on Sandwalk)

Go!

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Update 16.11.09: I've mentioned this in the comments, but it's kind of a new question so I'll repost it here:

An evolutionary system, regardless of its medium (biological, linguistic, cultural, etc), has finite resources, and must abide by laws of physics. The former necessitates some form of positive selection eventually, the latter invokes negative selection right from the start, provided variation exists. Some forms will end up being unable to self-propagate, regardless of which system we are dealing with. In the biological system this is very obvious - fuck up DNA replication, and the organism's lineage ends there.

My question was invoked partly by the commonly accepted statement that evolution fundamentally requires three things: Heredity, Variation, Selection. As much as I like fighting commonly accepted statements, this one seems strong thus far. Also, I've heard strong proponents of Neutral Theory use these preconditions as fact, so it's not in any way conflicting with a more neutral view of evolution. So I referred to it in the discussion on Larry Moran's blog, and the selection component, to my surprise, was shot down entirely.

So I often hear that evolution is change in allele frequencies (or their equivalent in non-biological systems) over time. Can this change occur without positive selection? Well, yeah, we've got genetic drift. But what about negative selection? Surely, for allele frequencies to shift, the population size must be finite; else the proportions would remain the same (ignoring positive selection). Stuff must die. Even if we assume no selection at that level, the new variation must be 'proof-checked' via negative selection, especially considering many changes are actually deleterious.

I guess if we remove all mutation, then we could have a system devoid of any selection, where stuff just randomly dies and then the allele frequencies would drift, and evolution can be said to occur.

But then, would weather patterns be an evolutionary system? They can be argued to be heritable in a non-discrete sense. Say we have each sq km being rainy, sunny, foggy or whatever. It inherits its next weather state partially from its previous condition (and obviously influenced by neighbours; lets call it LGT). The percentage of sq km in a given population experiencing rain or shine changes randomly selection-wise (although non-randomly if we consider it from the physics perspective; but the same applies to biology).

I'll argue here that, unless I've missed something, the weather system is akin to the biological system minus selection (the variation and heredity are still there). Does it still evolve?


(and thanks, this discussion is really helping me wrap my head around certain things! I don't learn well by just listening and digesting; I have to constantly prod at stuff until I'm ready to accept it!)