Plant Talk! – by Octavia

Welcome to Plant Talk! In this new column, we’ll be looking at new and interesting pieces of plant science and research, and what they mean. This month, I’ll be telling you about how we can use fossil pollen assemblages in salt marshes to reconstruct past climate change.

The Jigsaw within the Rubik’s Cube: Using Fossilised Pollen Assemblages as an Indicator for Sea Level Change.

Science is full of puzzles. Unfortunately, in some cases many of the pieces that look like they should fit together actually come from different boxes. When dealing with something like the history of sea level change (itself part of the larger oceanographic and climate puzzles) there are contributing pieces from the geological, geographical, biological, and other jigsaw puzzles. When pieces from each of these separate jigsaws are muddled together in a single box, it can be difficult to sort out which pieces belong to which puzzle. Instead of one enormous jigsaw, it’s actually easier to think of these larger conundrums as a giant Rubik’s Cube, with each coloured square forming a piece of a disciplinary jigsaw. When each jigsaw is put together correctly, and connected to the other completed jigsaws, the Cube (and the puzzle) is complete.

One of the little squares within the Rubik’s Cube puzzle of sea level change is palynology – the study of pollen. Pollen is an exceptionally good palaeobotanical resource for several reasons. It gives an extensive record due to abundant production. Its hardened outer sheath of sporopollenin helps to protect it from damage resulting from the fossilisation process. Finally, pollen from different species is often very distinctive, allowing for easy identification. The one disadvantage to using fossilised pollen as an indicator species is dispersal – because pollen is very light and often wind-borne, it can travel large distances and spread far from its point of origin. Thus, any palaeobotanical assemblages indicated from fossilised pollen must be interpreted in the light of possible disassociation from the parent plant.

Palynology has often been used to reconstruct past vegetation patterns, which is itself an indicator for sea level and even climate change. A recent example of this can be seen in the salt marshes of South Carolina. Working with fossilised remnants, Pamela Marsh and Arthur Cohen were able to recreate assemblages that could be used to determine regional models of past sea level rise. Pollen fossilises well in estuarine sediments, and so the environment of Marsh and Cohen’s study site – the coast along South Carolina, which, like much of the south-eastern United States, is mostly characterised by tidal inlets, barrier islands and salt marshes – is ideal for recording palynological records. Unfortunately, this is complicated by the fact that salt marsh plants are often insect-pollinated, thus producing less pollen than the wind-pollinated plants seeding the salt marsh from a distance. Also, some salt marsh plants such as Juncus roemerianus reproduce primarily through rhizomes rather than pollen (while simultaneously producing pollen, flowers, and seeds). This complication can be partially mitigated by analysing palynomorphs – when pollen is extracted from a sample of sediment, other tiny organic remains such as spores, insect parts, fungal and algal remains are also extracted, and these are called palynomorphs. This broader analysis can help to provide context and supporting evidence to the vegetation reconstruction. Together, the various pieces fit together like a jigsaw to build a palynological “fingerprint” – a profile representing various ecological habitats on a local and regional scale.

Different types of vegetation can be found within the salt-marsh environment, as vegetation patterns change according to tidal movements: the lowest zones on the marsh are frequently inundated with salt water, while the highest marsh zone is only immersed in spring and storm tides. When patterns of vegetation within the marsh zone change, it can indicate a change in exposure to salt water. For instance, if the vegetation types that typically inhabit the highest zone in the salt marsh move even higher up the shore, it is an indication that sea level has risen, and the less tolerant salt marsh plants have had to migrate even further landward in order to survive.

Because the highest salt marsh plants are least exposed to the turbulence of the ocean waves, the sediment in which they grow is less disturbed than the sediment of the lower marsh plants. This means that their pollen assemblages are less muddled. If these “unmuddled” fossil assemblages can be identified, they give a means of tracing the geographic migration of the highest marsh zone – which is in this case a proxy for sea level rise. Thus, fossilised pollen from salt marsh plants can indicate the rise and fall of sea level along a coast. This is not necessarily an indicator of climate change (other factors, such as geology, may be in play) but this particular pollen “jigsaw” can mesh with other squares from the climate Rubik’s Cube.

In the South Carolina salt marshes, Marsh and Cohen tested palynomorph assemblages from three typical ecological groups, each characterised by a specific type of grassy or herbaceous vegetation: low-level salt marshes (Spartina alterniflora), high level salt marshes (Juncus roemerianus) and salt pannes (Salicornia virginica). Samples were collected from the top two centimetres of sediment, so as to represent a contemporary assemblage. Marsh and Cohen were unable to distinguish a consistent or distinctive jigsaw from either the low level-salt marsh or the salt panne ecologies. However, the high salt marsh areas with a preponderance of Juncus gave a distinct jigsaw pattern for three reasons. Firstly, there was a high diversity in palynomorphs in the Juncus dominated sediments, a diversity that was consistently almost double that found in the other marsh vegetations types. Secondly, over 10% of the palynomorph count was composed of what Marsh and Cohen referred to as Fungal Spore Type A, an unidentified spore found at all tested high-level sites (in contrast, Fungal Spore Type A was found in less than half of the low-level marsh sites, and at only one of the salt panne sites). Finally, a second fungal species, Atrotorquata lineata, was only found in sediments beneath high-level Juncus marshes.

This distinctive assemblage, found beneath Juncus grass, gives a key to a method for tracing sea-level rise over time. Given that this particular jigsaw effect – the Juncus jigsaw – exists, it can be used to identify other high-level salt marsh sites. Whenever this particular conglomeration is found within a sediment sample, there is a strong likelihood that when the palynomorphs were being deposited, they were deposited in an environment characterised by Juncus grass – in grasses that only occurred in high-level salt marsh sites.

Useful assemblages can vary from region to region. In the tropics, for example, mangrove pollen is a useful indicator of sea level change. Pollen assemblage clues like these help to establish the biological jigsaw that makes up one side of the sea level rise – and possibly the climate change – Rubik’s Cubes. And when those little bits of colour connect on the side of a very large, very complicated puzzle, we are amazed and delighted to find something as tiny and everyday as pollen has been the key.

References

Engelhart, S.E., Horton, B.P., Roberts, D.H., Bryant, C.L., Corbett, D.R. Mangrove pollen of Indonesia and its suitability as a sea-level indicator. Marine Geology, 242 (1-3) pp. 65-81, 2007.

Marsh, P.E., Cohen, A.D. Identifying high-level salt marshes using a palynomorphic fingerprint with potential implications for tracking sea level change. Review of Palaeobotany and Palynology, 148 (1) pp. 60-69, 2008.

A Study in the Two Sides of Humility – by gimbol

St. Thomas

These days, the raw material of a saint
Is a bit less than it could be.

There is one that wants to argue,
But he’ll learn in the end.
In his own way, which is less than it should be.
If I got run over by a chariot tomorrow,
He wouldn’t believe it didn’t kill me
Unless he could put his fingers
In the ruts between my ribs and feel my heart.
One day, I tell him. Be patient, and maybe
You’ll learn in time to keep your sticky fingers out of it.

When that day comes, though,
He’ll want the proof of it. Always the proof.
I tell him: Go outside, Thomas!
Scream at the heavens,
Insult the Lord my Father
And bring down his rage upon your head.
That will be your fucking proof.

And Thomas?
God loves you. Just so you don’t forget.

A martyr before her burning

Those who suspect they’re weak try to hide it,
Even from themselves.
Put on a strong face, defy the world.
But those who know they’re weak, those that truly know,
Roll it around themselves, the shadow cloak,
Show their throats
Cut their own flesh to have blood enough to drip

In the end they were glad to burn me,
Glad to sear the voice from my throat –
Sick of hearing me whine:
A great fiery dose of Get a grip already,
You hysterical bitch!

But I could still whine to myself
Panegyrics to my own ability to be tortured…
I am grateful to be allowed to suffer.
But one can only be mild in comparison.

I had successfully provoked them, see.
They were kind at first, especially the young ones,
Too great pains to give me a way out.
But I was weak, determined to be mild, and so
I forced them to be devils.

Interview: KafirGirl

Thanks to a suggestion from last month’s interviewee, Steve Wells from the ASB, this month we’re interviewing KafirGirl, who is currently blogging her way through the Quran. Steve calls it “by far the most entertaining blog I know”, and it is pretty damn fantastic. If you haven’t seen it yet we highly recommend it. KafirGirl is an ex-Muslim who started doubting as a kid and has been an atheist for the past 9 years, and we’re happy that she was gracious enough to let us ask her some questions!

Hi KafirGirl. Can you tell us a bit about your experiences with religion as a child? What does a good Muslim kid generally do to learn about their religion?

My parents taught me to pray when I was really young — 4 or 5, maybe. I don’t really remember praying all that much when I was a kid, though. I started Quran lessons with an imam soon after that. He would come to our house every day after school and teach us how to read the Quran in Arabic. My most distinct memory of those lessons was the way my mom would throw a scarf over her hair when the guy showed up, and immediately yank it off when he left.

When we moved to the States, my parents sent us to Islamic Sunday school at the local mosque. It was a mostly Arab mosque and they were pretty hardcore about learning the Quran and praying. We had to keep charts of how often we prayed and everything. My brother and I got busted for forging our mothers’ signature on our prayer charts. Twice. (Note to any would-be forgers out there: if two of you are going to fake the same signature, only one person should handle the signing part. And also, don’t erase the signature and do it over if you don’t get it right the first time. Seriously.)

Our parents pulled us out of that mosque and made us to go a Pakistani-majority mosque, which was a lot more lax about stuff. No prayer charts, for starters, and it was a lot more informal. Nobody yelled at you if your headscarf came loose, for instance. We had Quran lessons, group prayer and separate discussion group for boys and girls. That was basically where we could sit around and ask questions about how to take a ritual shower after your period ends, or where babies come from. Major awkwardness.

Anyway, that was pretty much the extent of my religious education. I think most Muslim kids have the same general experience: they learn to pray and read the Quran, and they go to mosque, which is just as much of a social thing as it is a religious one.

You started having doubts fairly early: about 8. What prompted this?

I think, in my case, it actually helped that I grew up surrounded by church-going Christian kids. It made me question how different religions could exist. Why was one friend a Baptist while another was a Methodist? Where did Islam fit in with all of this? Why did we pray differently if it was to the same God? I started asking these questions really early on and it set the wheels in motion.

Living as a religious person in a religious community can tend to reinforce faith. Do you find, as a minority within your family community, that a closer knowledge of religion can also help the individual (and outnumbered) atheist to reinforce their doubts?

Before I started reading the Quran, my Muslim friends would say things like, “If you read the Quran, you’ll believe again.” Well, turns out they were wrong. I think reading the Quran has not only reinforced the doubt, but also armed me with better arguments and a snarkier attitude. I highly recommend it! In fact, I’m planning on reading the Bible when I’m done with the Quran. If I still have the will to live, that is.

Your blog talks about your parents’ reactions to your disbelief. Your dad’s comment on his worst mistake, teaching you to think, is pretty brutal. How were you “taught to think”, and how would you suggest more Muslim kids get the opportunity to do the same?

My dad has always been highly critical of rote learning, which is exactly how the Quran is taught. Memorizing something is not the same thing as understanding it, and I think that’s the downfall for a lot of Muslim kids. That’s also why it’s such a huge pain in the ass to argue with a lot of Muslims. They’ll just repeat the same thing over and over again without really knowing what it is they’re saying.

Anyway, my dad taught me think by encouraging us to ask questions and to read everything we could get our hands on. You know those kids’ books with titles like “The Big Book of Why” and “1000 Science Questions & Answers”? He got us a ton of those, and I devoured them. Books like that taught me that it’s important to ask “why” and “how.” Unfortunately for my dad, I started asking those questions about Islam and it turned me into an atheist. Doh!

So what made you start blogging your experiences in studying the Koran? Do you think it’s been an effective way of connecting with others, and getting your point of view across?

I decided to blog my way through the Quran when I realized there was no way I would read the book without some kind of accountability. It’s unbelievably boring, and I’ve had many, many false starts where I’d make it a few pages in before getting bored and moving on to something else. I think putting my thoughts out there for others to read would make me a little more likely to keep up with it, and so far, so good! I’ve connected with some really great people, and they’re teaching me as much as I’m teaching them. It’s fantastic.

What, in your opinion, is the best and the worst bits of the Koran that you’ve blogged so far?

I think the hardest posts I’ve written have been the ones dealing with the Quran’s views on women. How anyone could possibly say that Islam is a feminist religion is beyond me. The best parts — or at least my favorite parts — have been the scientific “miracles.” There is some seriously bad science in the Quran, and that always makes for entertaining reading. Flat earth, anyone?

Please… tell us about the LOLmuslims, we LOVE them. Are they your favourite part of the site?

lolmuslim
The idea for LOLmuslims started when I was Googling for images to use for the blog’s banner. I found some pretty amusing pictures of Muslims at a protest, and it just clicked. It’s been way fun to make them…and it gives me a nice break from reading & writing about the Quran!

I think my favorite part of the site is probably the comments section. And I’m not just saying that to kiss my readers’ collective butt. I’ve learned so much about all 3 Abrahamic religions from people who are way smarter and more knowledgeable than me. They make my brain hurt. Best feeling ever!

What kinds of reactions have you been getting? Are they mostly from religious or atheists, and how much do their beliefs (or lack thereof) govern their responses to you, do you think?

The reaction to the blog has been overwhelmingly positive. The vast majority of responses I get are from atheists, and they’re thrilled that someone is taking on the Quran. I’ve gotten a lot of emails from ex-Muslims — some who are open about their non-belief, and others who have to hide because they live in a country where it’s not really safe to be an open atheist.

The religious response falls into a couple of categories. Christians tend to push the Bible (“There’s none of that hateful stuff in MY book!”). It’s like they think it’s their job to swoop in and bring the ex-Muslims to Jesus. The Jews that contact me are mostly atheists, so we’re cool. And then there are the Muslims. The Muslims who email or comment are preachy and pissed off and insulted. I’ve had a few death threats, which is pretty much expected these days. Mostly it’s just ranty emails about how I’m wrong and headed to hell.

Oddly enough, a lot of Muslims refuse to believe that I’m an ex-Muslim. Readers will occasionally email me some blog or forum with a rumor about my “real” identity. A few weeks ago, I read that I’m actually a Jewish man from Buffalo, New York. More recently, I read that I’m not one person, but a team of Israeli spies, working around the clock to spread lies about the Quran. One site actually said it’s impossible for me to be a Pakistani girl because my writing style is clearly that of a man’s. …yeah.

Unfortunately, you feel safer being anonymous. Many of our readers are life-long atheists from communities where atheism is close to the norm. Can you explain to these readers particularly what it’s really like to always have to be so aware of what you are saying?

It’s funny because in my everyday life, I don’t feel like I have to be wary of what I say. I’m one of those outspoken types — I believe the latest catchphrase is “militant atheist.” I’m actually very open about my atheism with my friends, siblings, and even my coworkers. My anonymity is most just on the internet (see above about death threats from loonies).

The only people I won’t really discuss my atheism with are my parents. They’ve made it pretty clear that they don’t want to argue about it, so I just don’t bring it up.

What’s been the most rewarding part of the experience for you?

I actually know what I’m talking about now! When I argued with Muslims before, I didn’t really know how to respond to some of their claims. And now I can point out specific verses and call them out on their crap.

I also think I’ve been able to dump a lot of emotional baggage when it comes to my family. I feel like I’ve spent my entire adult life hiding who I am and what I (don’t) believe for fear of hurting their feelings, and I finally realize that I don’t have to do that anymore.

The whole thing has been a very positive experience.

And finally: readers of your blog know about your epiphany with pork. What’s your favourite way of eating it now?

If there is a heaven, it tastes like broiled pork chops. Little salt, dash of pepper, a metric ton of diced garlic and you’re good to go!

How Did We Get Here? The Ascent of Life (Numbers) – by Julian

Well, talking of numbers, bacteria have it pretty well sown up in terms of numbers. A tiny scoop of soil contains 40 million bacterial cells. There are probably 5,000,000,000,000,000,000,000,000,000,000 bacteria on the earth. There are only about 9,000 species of bacteria that are named, but estimates vary from 10 million to 1000 million different species in total. Its just that no one has had the time or energy to name and describe them all. Also some bacteria are difficult to culture in the lab, so its typically the cooperative ones, or the killers, that get the attention – so nothing new there then. Bacteria are all members of the prokaryotes, mostly distinguished by not having a nucleus in their cells, their DNA hangs loose, so to speak. We eukaryotes (animals, plants, fungi, and a ragtag collection of single celled organisms called protoists) are more conservative, we like our DNA packaged up in a nucleus, neat and tidy.

But bacteria are so small that it was only with the invention of the microscope that we even had any direct evidence of them at all. So – why are we here, when bacteria are so successful? Why bother to evolve at all?

prokaryotepn3

Well, in the last little piece I keyboarded, we saw that bacteria have a problem with size. Now I know size is not suppose to be important, but it can be if you are not careful. The largest bacteria ever discovered are getting close to 0.5 mm, which is just visible to the naked eye. These are very atypical though. As I talked about last time, the surface area to volume is a key issue for anything that eats and makes energy through its surface. These very large bacteria typically don’t actually have a very large active volume.

Thiomargarita namibiensis for instance, one of those big boy bacteria, has a huge vacuole inside it. This is basically just a store of stuff it is keeping for a rainy day. It doesn’t therefore have a large active volume, more like a thin layer doing stuff, and a big garage full of useful stuff it can raid when it needs. Others get around the issue by changing into long thin shapes, or by having folded membranes to try and offset the problems. All very clever, but it doesn’t make any fundamental leaps in improvement.

actin

What we needed was a paradigm shift. That needed a few things to have evolved first, before it could actually come about. The first step was probably a cytoskeleton. A cytoskeleton does for a cell what our skeleton does for the body. It gives it shape and structure but is inside. The original alternative, the cell wall, was more like the exoskeleton that insects and others use to keep their shape. We’re about to loose the cell wall that most bacteria have, and to stop them collapsing in a heap, they need an internal skeleton. This is mostly made from a rope like protein call actin, together with some securing bolt-like proteins, that hold them in the shape they want to be. A cytoskeleton use to be thought of as purely a eukaryotic accessory, but has been found in a few bacteria too more recently. So obviously some of them managed to make one.

Why develop a cytoskeleton at all if the cell wall is so useful? Well one answer is in things like penicillin. Penicillin is a very effective antibiotic because it interferes with the building of bacterial cell walls, and so they tend to rupture and break. It doesn’t worry us, as we have no cell walls to make or break, so it doesn’t interfere with any of our key process (if you ignore allergies). Lots of things produce anti-bacterial wall substances, its part of the arms race. If you’re a bacteria feasting on some supply of food, and you can pump out one of these substances, then there is all the more for you, as long as it doesn’t affect you. So its possible that one species of bacteria happened along the mutation that gave them a cytoskeleton, and this was another way of avoiding the attacks of their competitors. They could laugh in the face of such attacks.

eukaryotelv0

Now once you don’t need the cell wall, new avenues open up for you. The cytoskeleton is like a series of ropes holding things together. If you shorten one you change the shape of the cell. With a bit of practice you can use this ability to stretch out, contract, or even make funny shadow puppets. One nice feature of this is that instead of sucking in dissolved food, you can extend yourself around food particles and ingest them in one gulp. It doesn’t matter how many competitors there are around now, as you have the food inside ready to digest at your leisure. Of course you can’t do this with a thick rigid cell wall, but you can with a cytoskeleton.

So there we are with a bright shiny new ability, going around ingesting food in lumps and digesting it at our leisure. Cell walls still have their uses of course, they’re tough for one thing and can fend off all sorts of nasty things, so most bacteria stuck with the tried and tested mechanism. The new wall-less organism probably got beaten up on a number of occasions, and were probably humiliated in public places too. One day though, it managed to swallow a working bacteria, and couldn’t digest it. Furthermore, the swallowed bacteria continued to live, sucking in nutrients from the cell attempting to digest it. It is quite possible this happened at the time of rising oxygen levels, and from this a kind of symbiosis happened. The swallower was having a problem with the highly reactive oxygen molecules wreaking havoc with its cellular processes, but the swallowee was already well versed in the handling of this and so consumed it. So the swallowee was getting protection and a source of nutrients, the swallower was finding a way to deal with the increasing levels of oxygen.

Gradually over time the bond got stronger, the swallowee began to discard a lot of DNA, as it could get most of what it needed directly – all the materials for making a new version of itself were there for the taking. Say a defect occurred in the DNA for making cell membrane proteins, no worries just take the ones the host cell has already made. Meanwhile the swallower started to take advantage of the swallowee, by punching holes in its membrane to get hold of energy molecules that it was making directly. In this way the power house of eukaryotic cells, the mitochondria probably came about. Tracing back through genetic history, it seems likely that Rickettsia prowazekii is a modern descendant of the original mitochondrian. Today, our mitochondria still have their own DNA, though now it is pared down to the bare minimum, and they still divide and reproduce independently.

Anyway, these new organelles (as they are called), as well as a giving a way of dealing with excess oxygen, also had another benefit. Suddenly it was not so limited by the volume/surface ratio. If you need more power, then grow more mitochondria. Lots of membranes available then to pump protons across now, the restrictions are lifted. You can’t go completely wild though, as there are still things that are restricted by size. We don’t see single cells much bigger than about 1cm even today, and even those have to play all sorts of structural tricks to get so big. A typical modern cell may have hundreds of mitochondria inside, making all the energy they require. Divide and conquer so to speak, but making sure you are the sole beneficiary. Energy requirements – sorted!

mitochondrion2

So now our cell can grow much bigger and still have plenty of power. It can ingest food in large lumps and so doesn’t have to compete by breeding as fast as possible. It can be much more leisurely about breeding. This in turn means that DNA is not so much of a limiting factor. It can start to accumulate junk in its genome. Duplicate copies, broken versions and so on. Sure it costs a bit more to replicate, but its not a life or death issue any more.

Its not just energy factories that were swallowed. Chloroplasts, those organelles that plants and some protozoa use to turn sunlight into sugar seem to have suffered a similar fate. They also have their own DNA and replicate themselves. They would be much more important if we were a plant based species, but as we’re not, I’ll skate over them. Another theory, without quite so much support is that the nucleus is also an ingested item. Anyway, these cells with all their new found machines were one of the steps that led to us. Although these new cells, the eukaryotes are much bigger than bacteria, most of them are smaller than the naked eye can see, and stay that way.

So how did they get bigger?

Fiery Oven Baked French Fries – by Isolde

oven-fries
Fiery Oven Baked French Fries
adapted from Passionate Vegetarian

4 medium-large potatoes, peeled and cut in 1/4″ French fry strips
4 cloves garlic, pressed
1 tbs olive oil
2 tbs soy sauce
1-3 tsp Tabasco sauce
2 tbs white or rice vinegar
black pepper

Line a baking sheet with foil, then spray with nonstick spray. Preheat oven to 375F with the rack in the highest position.

Toss the potatoes with the garlic and olive oil. Add soy sauce, Tabasco and vinegar, then toss again.

Transfer potatoes to the baking sheet, spreading them into a single layer. Add some black pepper. Bake, turning and flipping the potatoes about every 10 minutes, for 20-35 minutes. Test for doneness – continue to bake until they’re browned, cooked all the way through, and getting crisp on the ends.