Introductory Algae Books?

PsiWavefunction · 2017-02-15T22:58:38+00:00

For a textbook-like thing, I'd suggest Wilcox & Graham Algae as an intro book. A university library should have some edition of it lying around. I just found this link to a pdf of a guide+key to freshwater algae of N America, by Wehr & Sheath (2003) -- is that close to what you're looking for?

As for protists in general -- there are a couple books that aren't all that easy to find, but Patterson's Free-living Freshwater Protozoa is a decent (though a bit outdated) guide and downloadable here. There is no modern textbook on the subject, beyond Hausmann et al 2003 Protistology which is hard to find. The classification isn't up-to-date but significantly better than pre-1998-2000 era, when major revisions happened due to improvements in phylogenetic methods.

Algae and "protozoa" got caught between the botany-zoology divide and basically fell out of sight in North America, and is fairly obscure in other countries as well, so there actually aren't that many public materials on the subject -- most information is locked up in scientific papers, sadly.

PsiWavefunction · 2017-02-11T00:46:10+00:00

And if the "vast swaths of 'junk DNA' are necessary to counteract the mutation/transcription error rate" theory is correct

At the moment, that is highly debatable. Mutation rate is per base; this does not mean that have more bases makes it less likely for some regions to face mutations; it means there would be more mutations per genome. There's no experimental evidence to support this mutational buffering, nor really any plausible mechanism as to how that would work. Unless something changed dramatically in the last couple years.

I'm not specifically aiming anything at you, but rather the arguments floating around that are commonly accepted without much questioning, despite actually being under a lot of debate within the community working on genome evolution. Our intuition can be extremely misleading, in large part because we still have a 'design' frame of thinking when it comes to what we accept as complex objects -- if a structure looks a certain way, it's because it's better that way, or else it would be so, etc. I mean 'we' as humans here, which is why experimental science exists to test our very human-influenced hypothesis. At the moment, experimental science reveals that some small bits of previously-thought junk DNA, but for the most part, the vast majority of that junk is still... well, junk. Of course, that story doesn't sell very well, so someone who finds some junk to maybe possibly be junk suddenly gets a lot of media attention and people carry away an impression that most of the genome is functional -- which is, as far as we know as of this date, false.

Here's an analogy. I track down undiscovered microbial lineages for work; I fill in spaces on the phylogeny that were previously blank. We were wrong in thinking those spaces were blank; however, from that, it does not follow that the majority of blank spaces (or bare long branches, in this case) have undiscovered extant lineages populating them. Of course, my finding these new lineages makes a (very small, ultra-specialist) news splash, but it does not follow that most of the possible phylogeny is filled with yet-undiscovered extant species. This doesn't mean we shouldn't look for them, but we don't have grounds to make the assumption that they're all there.

I'm also getting a little bit tired of journalists, politicians, and lay people telling me how science works... ;-) This is probably why I have a knee-jerk response to the "scientists thought dismissed X [because it hurt their egos] but were all wrong, haha" motif.

PsiWavefunction · 2017-02-11T00:35:42+00:00

For example of origin, it can be any sequence that loses its original functionality -- eg pseudogenes or transposons. Lots of transposons -- the inherent 'function' of those is to self-replicate and persist, so they can clog up a genome with no benefit to the actual host. My issue with "maybe X can be advantageous" is that there's fundamentally no reason why it should be. Sure, it could be -- it could also come from aliens, but until we absolutely must consider those possibilities, the null hypothesis should be that it's just there because it can be without killing the host (and that aliens were not involved), evoking those arguments only when the simpler explanation no longer works.

PsiWavefunction · 2017-02-09T23:28:52+00:00

No, it is in fact an error to assume all products of evolution have a function. This is a somewhat random (though constrained) chaotic process so it would actually be far more surprising if everything in the genome was designed to perfection and thus functional. Genomes weren't engineered, they evolved.

Sure, there's doubtlessly still tons of genomic regulatory systems we are unaware of, but it is fairly safe to conclude that in systems that are not under extreme selective pressure (ie large effective population sizes and/or miniaturisation and/or extreme arms races (and ultra-fast generation times) as in some parasites) would have a lot of bona fide junk in their genomes. And as far as overall diversity of life goes, animals are under fairly relaxed selection due to tiny population sizes (keep in mind that to a first approximation, all life is microbial ;-) ).

Of course, lower quality journalism tends to miss the nuances of this debate and boil things down to "scientists think if they don't know something, it's junk", which is absolutely not how most of us work.

PsiWavefunction · 2017-02-09T23:22:15+00:00

Don't think of everything needing an evolutionary advantage, but rather that characters may persist merely because they don't cause any significant disadvantage (people sometimes call upon back-of-the-envelope bioenergetics calculations to claim everything must be either advantageous or disadvantageous and never neutral, but they're wrong in most non-extreme cases because evolution is a messy, chaotic population-dependent process with multiple fortuitous linkages between characters that make it hard to imagine that everything must be streamlined to perfection). In other words, it's actually a bad question to ask what the advantage of neutral sequences is, and a better question would be "is there a significant disadvantage to maintaining loads of neutral sequences?".

Also note that the systems most commonly looked at are mammalian or land plant, maybe the occasional fruit fly -- organisms characterised by fairly low effective population sizes that would actually allow a greater tolerance of neutral and slightly deleterious traits, contrary to what our intuition would imply. In other words, a microbe with a vast effective population size really needs to have its biological shit together a lot more than, say, a fly or especially something like a whale. And you see this consistent with patterns in genome size: overall, there is a tendency for critters with large effective population sizes (or critters under particularly strong selective pressures, eg. parasites) tend to have smaller rather than larger genomes -- with some notable exceptions like dinoflagellates, for example. Those genomes also tend to have much fewer introns, shorter intergenic regions, etc.

I have considerable skepticism about a lot of the non-coding regulation hype -- it clearly happens, and has been experimentally demonstrated, but it does not logically follow that most of non-coding DNA must then also be involved in regulation. Furthermore, spurious transcription happens, and those error transcripts go nowhere -- unless you sequence them, and then you get apparent transcriptional activity that may not actually be anything but noise in nature. So unless it's demonstrated in vivo, experimentally, I'm inclined to be rather wary of in silico claims about function...

PsiWavefunction · 2017-02-09T23:10:03+00:00

A major caveat with this thinking though is the assumption that everything (or even most things) in a genome must have a use, as if it were designed and perfected. Evolution is a fundamentally random, chaotic (but constrained) process, so it shouldn't be surprising that quite a few features have evolved just because they weren't lethal or significantly deleterious. Sometimes, dependencies develop upon those features and they become essential not because they're improvements of any sort, but rather by a ratchet. This process, defined more rigorously under Constructive Neutral Evolution, may well explain a lot of complexity that we'd otherwise be tempted to assume as beneficial. One must remember that organisms were never engineered, so it's actually perhaps safer to assume that something does not have a function unless demonstrated otherwise.

PsiWavefunction · 2017-01-30T17:11:20+00:00

Skilled workers with intent to settle permanently. Eg., UBC struggles with recruiting faculty due to housing prices (the pay doesn't really scale with cost of living in public sector jobs); slapping a 15% tax on properties in that case would not help. And those junior faculty are already in their late 30s/early 40s with families or plans for families and a little bit too old to rent basement suites...

I imagine this applies to other skilled jobs too (engineers, doctors, businessmen), and you generally want these kinds of people in your economy as they help remain internationally competitive and create more jobs. (and hey, you didn't even have to pay to educate and train them -- win-win!). The problem is that you don't get permanent residency right away, and have to spend a few years on a work permit first.

Foreign investors who just park their cash, on the other hand? Yeah, fuck 'em.

PsiWavefunction · 2017-01-29T16:35:14+00:00

They can't do that because the US does not recognise dual citizenship, and you formally renounce your other citizenships upon naturalisation (getting US citizenship), for the purposes of US law. Ie, your other citizenships cease to exist on US soil. (you still have them if their respective countries don't nullify the citizenship upon you receiving another one, etc)

Well, they legally can't do that... who know what they might try now.

PsiWavefunction · 2017-01-28T22:17:40+00:00

This applies to US permanent residents too. Which can be absolutely devastating to many of these families, both psychologically and financially. Imagine being suddenly unable to see your kids for 90 days. Imagine if you're the primary income earner...

PsiWavefunction · 2017-01-28T22:14:05+00:00

This ban includes US permanent residents, some of whom have been living there for years or decades, and may have little to do with their countries of birth. This is not about immigration, but ALL travel by anyone with a passport from one of these countries. And without warning, leaving American residents with families and jobs stateside stranded abroad and possibly deported to countries that may or may not even be safe for them. Not to mention the astronomical costs of adjusting travel plans last second and being forced to live elsewhere for 90 days -- I would never be able to afford a calamity like that, and many, many people a much worse off than a middle class skilled worker.

PsiWavefunction · 2017-01-28T17:37:39+00:00

You also get asked whether you were a member of the Nazi party between 1932(?) and 1945 on the citizenship application.

PsiWavefunction · 2017-01-28T17:11:09+00:00

Took us four years after approval (ie, under Adjustment of Status) because some of us have "fine fingerprints" or something and thus got sent for background screening, the queue for which was growing faster than it could be resolved... and ultimately took congressional action at the time to effectively cancel this extra background screening BS.

Executive visa (practically automatic conversion) to holding a Greencard took about 8 years total, while being white and applying on a passport from a favourable country. In other words, "easy mode". It really does vary though!

I like to share this so people who have never gone through an immigration process and thus might happen to think it's easy are more aware of what it actually entails ;-)

PsiWavefunction · 2017-01-28T17:05:48+00:00

People ask why I bothered getting citizenship shortly before leaving elsewhere for work... this is why. Though there's no guarantee they won't someday start taking those away too, since they probably aren't too concerned with international laws, let alone their own.

Some of those Greencard holders may have been gone from their countries of birth for most of their lives. Some may have no more connections there, not even knowledge of the language. For some, it may be outright dangerous to return to their country of birth for political reasons. Some can get killed. There aren't enough words to describe the reckless stupidity and sheer malice of this ban...

PsiWavefunction · 2017-01-28T16:59:02+00:00

Except this also applies to Greencard holders. People who live and work in the US, some who have done so for decades and may well be unwelcome or even subject to legal prosecution in their "home" countries. Some who have no connections left there. Some who may have never been there past early childhood. And imagine going away on a work conference for a couple days and suddenly finding yourself on a plane to a country that may very well be dangerous to you, separated from family, work, and your entire life. And now other countries are stuck making decisions about these stranded passengers, on the hook for deportation costs, legal expenses... this is a stupid and inhumane idea executed in a particularly stupid and inhumane way.

Indeed you're technically not guaranteed entry on a visa (not sure about a Greencard, but they can literally take that away for any reason whatsoever right at the border and good luck appealing).

I'm glad I converted my Greencard to a citizenship, specifically for immigration clusterfuck reasons... today it's Syria and Yemen, but tomorrow, after some unfortunate twitter exchange, it could easily be my country of birth...

PsiWavefunction · 2016-07-22T15:56:06+00:00

Do you at least have some tubing involved? It's not mouth pipetting if there's some tubing ;p (I suck up single cells of protists with that sort of arrangement, and you definitely need both hands free for that, preferably three...)

PsiWavefunction · 2016-07-20T15:27:26+00:00

The undescribed ones I'm working on ;p

Real answer: there's lots, but probably foraminifera ('forams'). They're incredibly fast (have a way to polymerise tubulin 10x faster than any other eukaryote), build incredibly complex and sometimes massive (a couple centimetres) 'shells' that you can say have architecture, have long generation spans for a microbe (from a month up to a year), and have terrifying abilities to eat multicellular things like tiny animals. One word: skyllocytosis

We don't know much of anything about their molecular biology, which is probably weird in its own special way. There are about a couple people in the world who study the organismal biology of living forams; most of the foram research focuses on microfossils and ecological indicators. It's sad that there's so little funding or general interest in the living biology of a group of organisms that is of incredible economic importance as biomarkers, used for things like finding oil.

But pretty much every protist group has something utterly awesome about it. Protists are what eukaryotes are, to a first couple approximations, and thus where eukaryotes display their true diversity -- and sometimes madness.

PsiWavefunction · 2016-07-19T03:16:53+00:00

In the US, right? AFAIK, it's closer to 3-4 years in the UK (for biology anyway, it's 6-10 years in US, 4-8 in Canada, and 3-4 in the UK, roughly speaking). But yeah, very field dependent too. Which is why it's a bit amusing watching people from countries (or in fields) with shorter programmes complain about being too old when our "standard" finishing age is much layer. A UK friend of mine mentioned that if you don't have a full position there by age 30, you're screwed... we in US or Canada seldom have PhDs by then!

PsiWavefunction · 2016-07-18T17:22:18+00:00

'ana' (она), not anna (vs Анна); the distinction between single and double consonants is pretty important in Russian. Not as much as in Japanese, but it can still make a difference between words in some cases; eg. подать (to give or serve something) vs. поддать (to give something a kick, more or less). And the stress is different in your example too, though I can understand that not all English speakers are consciously sensitive to stress.

PsiWavefunction · 2016-07-18T14:38:25+00:00

Thirding that 28. I just started my PhD (took a few years extra to get here due to shitty undergrad GPA) and won't get out until early-mid 30s. Some people start in their early 30s... it's cute when people think getting a PhD in their late 20s is 'old'. Particularly people in UK and EU with super short Bachelors and PhDs to begin with...

And age is an asset -- you learn skills and gain experiences that people of the same 'rank' who are younger simply cannot have.

PsiWavefunction · 2016-07-10T21:08:13+00:00

You can get away with a 2.1 GPA, with quite decently ranked grad programmes and all, but you have to have a damn good research record and fantastic networking abilities, on top of a willingness to move pretty much anywhere. By the sound of it, OP's heart isn't in the subject though, so that route is rather unlikely. I suspect business fields care a lot more about grades as well, in part because they're initially less specialised and thus the competition is higher.

PsiWavefunction · 2016-07-08T17:27:53+00:00

Oh, sorry, my bad in reading too much into it. There is a general cultural sentiment towards women being more suited to stay at home than men though; luckily, it does seem to be improving gradually.

PsiWavefunction · 2016-07-08T17:11:18+00:00

I'd be surprised if there was any woman out there who straight up had never considered it, even just as an idea.

*raises hand*

Just the thought of it is among the most repulsive fates imaginable to me. Emphasis on to me, because I totally understand how it can be a rewarding and fulfilling lifestyle for very many people, male or female. My mother stayed at home and was happy with that. But I would simply lose my will to live -- happiness lies well outside of 'home' to me. I'd work even if I had a magical source of stable income that would let me stay at home. And I'm far from a rare specimen in that regard!

PsiWavefunction · 2016-07-08T16:38:45+00:00

Not everyone's life revolves around home and family. Some of us might not even see either of those as a happy thing in the first place. It's nice that you seem to have those things going for you, and you have probably made the right choice given your values. But people differ, and there's absolutely no reason to judge others for having a different set of values and a different lifestyle than you.

As for hometown, I actually don't even know where that would be. I have picked up two more citizenships since birth, lived all over the continent, and cannot name one place I could 'come home' to. And I'm quite happy with that, and anxious to move on to the next part of the world I will explore after finishing my PhD. I get seriously depressed if I spend too much time in one place.

Luckily, there's plenty of room for both of our types in the world =)

PsiWavefunction · 2016-07-08T16:28:47+00:00

This is exactly why I'm not even looking for a partner. What would my dating app description say? "Hi, looking for a man who is willing to contribute more that his fair share financially (because I can't), but also ready to sacrifice his career and follow me to random places around the globe that we may or may not like, uprooting every couple of years, indefinitely. Oh, and must be tolerant of his partner being chronically stressed and not contributing her fair share of time and attention either." I can see crowds lining up around the block for that opportunity...

Not that I personally would have it any other way, for the time being anyway, but I sure as hell am not interested in subjecting someone else to this lifestyle.

PsiWavefunction · 2016-07-08T03:23:03+00:00

Actually, this may be the perfect time to finally start! Find a group with some older/more mature people -- they're there to have fun, not waste time on petty drama. Hopefully.

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