I woke up at 7am this (Saturday) morning to an amazing realisation: I’ve wasted weeks of work because one of my tests was completely futile.

I’ll tell you the steps of my work; see if you can pick where I went wrong.

Aim: Create a copy of an E. coli gene on a plasmid.

1. Amplify tiny piece of DNA (gene) from E. coli, using PCR.
2. Put gene inside bigger piece of DNA (plasmid).
3. Put plasmid inside of E. coli so that it multiplies and makes lots of plasmids for you.
4. Check whether plasmid inside E. coli has the gene by doing a colony PCR, which contains all the DNA inside one E. coli colony.
5. Regrow colonies that contain the gene, get plasmids, continue with more steps.

I’m up to step 5 at the moment and I’m having trouble regrowing the colonies, which is why I have been thinking about this. Anyone guess what’s wrong with what I did?

Well, I’ll tell you…

I’m cloning (that’s what this whole process is called, has nothing to do with creating sheep or dinosaurs or copies of humans) an E. coli gene; I tested all the DNA inside my transformed E. coli cells to see if the gene was in the cell.

Of course it’s in the sodding cell! It’s even the same strain of E. coli that I got the gene from in Step 1! There’s no way to tell with PCR where you’re amplifying DNA from: it could be from the genome or a plasmid. So my results told me that all the colonies I picked had the gene, presumably on the plasmid. Since I haven’t been able to grow them again, I don’t think they do have plasmids, or they lost them. If you have any knowledge of what I’m talking about you’ll know that we use antibiotics to make sure there’s a plasmid — I did, but maybe over time the antibiotic broke down or something.

I feel stupid! Not as stupid as I could feel though, because my lab supervisor told me to do what I did. Normally the technique would be okay because he works with genes from a different species, which would not be in E. coli… I think I can rectify the situation without too much extra work, but I’ve been battling with these cells for at least two weeks now. What a waste of time!

Kangaroo farts could fight global warming

When I first saw the line “Australian scientists are trying to give kangaroo-style stomachs to cattle and sheep in a bid to cut the emission of greenhouse gases blamed for global warming.” I thought, “What the heck?!”

It turns out they’re not going to try to transplant cows’ stomachs – just some bacteria in kangaroos’.

Thanks to special bacteria in their stomachs, kangaroos’ flatulence contains no methane and scientists want to transfer that bacteria to cattle and sheep who emit large quantities of the harmful gas.

Those crazy scientists! Actually, it’s a novel idea – I like it. I didn’t realise it was extra bacteria in kangaroos’ stomachs rather than an absence of other bugs that meant they don’t produce methane.

Do you think about what you throw away, the things you never lay eyes on again? Do you think about the things that get washed away from your sight? Much of it never really goes away.

Today, October 15th, is Blog Action Day. A day for us to spread awareness abut environmental issues.

This semester at university I’m doing a project about the remediation of industrial sites at Homebush Bay (Sydney) and sediments in the bay. Particularly for the Union Carbide/Lednez site. Union Carbide left the site long ago, with a cap on chemicals buried in the soil to try to prevent their further spread. However, during industrial activities, which included the reclamation of land, plenty of toxins were released into the soil and bay sediments.

This Homebush Bay site was used for industrial chemical production, including timber preservatives, herbicides (I think Agent Orange was produced here at some point – breakdown of Agent Orange releases dioxins), DDT, and many others. Over the course of activity at these sites (1890s-1970s) it was considered normal to dump waste products in the near-by water (perhaps for some things it’s still the norm). Contaminated soil was used for the reclamation and run-off from normal activities and weather went into the bay.

Think about the substances that went in there: products that preserved dead tissues (timber), substances that killed organic material (Agent Orange) and pesticides (DDT). The thing about many of these chemicals is that they’re not naturally occurring, so they’re not able to be broken down naturally, i.e. they’re not biodegradable. They’re not biodegradable and they accumulate up the food chain to cause some nasty biological problems.

At the moment a large remediation project is going on in Homebush using thermal desorption to get rid of dioxins from the area. I believe a significant motivating factor is to build residential apartments on the site, as well as a marina. I don’t know if the area can support that sort of expansion, but another reason that was proposed for doing this was that it just shouldn’t be left for the next generation to deal with. I thought that was a right response.

There’s no value in pointing fingers now, what’s done is done. People and industry were happy to release this sort of thing into our midst. Heck, DDT was sprayed on the walls of people’s homes to combat malaria. What we can do now is learn from their mistakes and make an effort to clean things up.

I don’t really think very hard about what I throw away, but I’m sure I could be less wasteful and more observant of what I just release into the world to rot (or not rot as is the case for many chemicals, including plastics). What bout you? Do you think about what you wash down your sink? Do you think about what you throw in your trash, which then gets in a hole in the ground? Do you think about what you can reuse?
I’d love to hear about anything you’re careful to dispose of or inventive ways you’ve reused things.

Traditional models of economic decision-making assume that people are self-interested rational maximizers. Empirical research has demonstrated, however, that people will take into account the interests of others and are sensitive to norms of cooperation and fairness. In one of the most robust tests of this finding, the ultimatum game, individuals will reject a proposed division of a monetary windfall, at a cost to themselves, if they perceive it as unfair. Here we show that in an ultimatum game, humans’ closest living relatives, chimpanzees (Pan troglodytes), are rational maximizers and are not sensitive to fairness. These results support the hypothesis that other-regarding preferences and aversion to inequitable outcomes, which play key roles in human social organization, distinguish us from our closest living relatives.

This is an excerpt/abstract from an article published by Science that I thought was kind of interesting. You have to pay to see the whole article, so I haven’t seen the rest.

I’m left wondering what it means that chimps are “rational maximisers”. Why aren’t they just maximisers? How do we know that chimps are really in it for themselves and humans aren’t? Perhaps humans have a better grasp of consequences. Perhaps humans are the rational maximisers because they know that if they’re not fair today it could bite them in the bum tomorrow.

Of course there are people who do things because they think it’s the right thing to do… it’s nice to remember we’re not all ape-like. :P

A limited view of science

What do you think science is?

At dinner last night one of our lab demonstrators, who has a BSc (Honours), claimed that he got into science because he wanted to prolong life. Quality life, not life plagued with alzheimers, for example. Somewhere in his speech about long-life, money management and a drastic change in society he said that he thought that prolonging life is what science is about.

In a discussion about science and god someone said to me “if something cannot be proven to exist, if something cannot be observed (directly or indirectly) … it doesn’t exist”. He seemed to think that science was some kind of absolute.

I’ve never thought of science in either of these ways. To me it is simply exploration. Science asks “Why?” Not an existential kind of why, more of a how kind of why. Why does the electron transport chain create an electron gradient? So we can make energy! Why does potassium pretty much explode when it hits water?

Broadening our horizons

Being fairly informed yet young in the field I’ve had a look at what others have said.

Wikipedia tells us the origins of the word science came from the latin scientia, knowledge (and also the name of a building UNSW :P). That’s a start. Knowledge in itself has no real purpose except to be known. There’s no assumption of motive, for people to live longer or cure disease or anything else.

Part of a university course reading gave an exposition of what science isn’t. Overall, an excellent summary of what science isn’t and in comparison what it is.
Science is not technology didn’t sit quite right with me. However I think I see where they’re coming from. “People doing science often use sophisticated technology, but science doesn’t require it.” That’s true, without the original scientists and philosophers we couldn’t have gained the knowledge to create new technologies (the way we know things know at least). Just as science isn’t the pursuit of long-life it’s not the pursuit of technology, but it’s so intrinsic to engineering and technology that I don’t think the distinction needs to be emphatically stated.
I don’t necessarily agree there’s no “extent to which knowledge changes through time” or “extent to which future changes in knowledge are expected by user” in religion. Of course generalisations can’t apply to everyone, there have been plenty of noteable religious people that have been stubborn and earnt this stigma.

The American Physical Society has a short defintion, which exemplifies that science isn’t infallible truth or the sum of all existence.

The success and credibility of science are anchored in the willingness of scientists to: Abandon or modify previously accepted conclusions when confronted with more complete or reliable experimental or observational evidence.

Obviously, in the pursuit of knowledge, denying the existence of anything that you haven’t observed is absurd. If that had been a part of scientific method we would be decades, perhaps centuries behind the knowledge we have now (they couldn’t see DNA when they thought of genetic material).

This essay is so throughly constructed that I have little to say expect “Read it!” Some of my favourite quotes:

It means is that scientific education for the masses will do little good, and probably a lot of harm, if it simply boils down to more physics, more chemistry, more biology, etc., to the detriment of literature and history…

The idea that science means a way of looking at the world, and not simply a body of knowledge, is in practice strongly resisted.

At the moment, science is on the upgrade, and so we hear, quite rightly, the claim that the masses should be scientifically educated: we do not hear, as we ought, the counter-claim that the scientists themselves would benefit by a little education.

I highly appreciate MusEditions’ thought process about what science may be. Including, “So, “knowledge” is not a set-in-concrete concept, either.”

Science can be fun!

Free your mind

There may be many people that have a balanced view of life, science and arts. There are many more that have such a limited view of science that their science becomes almost dogmatic.

“There must be no barriers for freedom of inquiry. There is no place for dogma in science. The scientist is free, and must be free to ask any question, to doubt any assertion, to seek for any evidence, to correct any errors.” – J. Robert Oppenheimer

So I ask again, what do you think science is? Does it mean anything to you? How has it affected your philosophies?

Last night I was cooking enchiladas. The packet of corn tortillas, which was inside a box, said “contains wheat”. I checked the box and couldn’t find any sign saying the corn tortillas contained wheat and I thought it was a shame because there could have been someone allergic to gluten who had hoped to eat those tortillas. [Although, if someone really was allergic to gluten they would probably have a better idea than me of which foods to buy at the supermarket.] “What does this have to do with GM foods?” You might be asking. Well, nothing, but it got me thinking about labelling foods, which led me to the topic of genetically modified (GM) foods.

How do you feel about the prospect of eating food from genetically modified sources? Do you know what it means that something is genetically modified?

What is GM?

It seems to me that there is a lot of who-haa about GM foods and GM organisms, but much of the opposition comes from misunderstanding. People are afraid of GM and they don’t even know what it is (they’re probably afraid because they don’t know)!

For centuries farmers have selectively bred plants and animals that have desirable features. Plants have been cross bred to mix different characteristics together, with no concept of what else – other than the traits they want – they’re getting. Now they have the ability to choose what they want and to insert it.

Genetic modification doesn’t involve dealing with disgusting chemicals. It also doesn’t mean that you will be modified when you eat it. When you eat something you break it apart into its little molecules. Some molecules you will use whole, like vitamins, and some you will break down even further so that you can use them to make other things. The things that your body doesn’t want tend to get disposed of, things don’t become incorporated into your person, the DNA in Flavr Savr Tomatoes doesn’t combine with yours to stop your skin from getting droopy. Not everybody has the means to breakdown everything and some things can cause an immune response before they get broken down (e.g. people with coeliac disease, lactose intolerance, nut allergies). That doesn’t make gluten, lactose or nuts inherently bad.

There are legitimate concerns with GMs such as the containment or spread of introduced genetic traits. Whether other beneficial traits are lost in the process of introducing genes. Whether introductions of pesticides or antibiotic resistance is harmful to us. However, I find these concerns rarely addressed and rather the general fear of misunderstanding drives arguments on this topic.

More pressing dangers

There are many things that have been done in the past that you would never know about, chemicals that have permeated our lives and are continually increasing in concentrations in our bodies. For example, I knew a guy who worked with microbes to produce proteins for face care products (moisturisers etc). By law they were allowed to bombard these microbes with chemicals to make them over-produce proteins, but they couldn’t just make a little change to the genetics to do the same thing. Admittedly there would probably be little harm to the consumer because the proteins are extracted and wind up very far away from those chemicals. However, while everyone’s afraid of GM, the lab workers still have to work with stinky and harmful chemicals in processes that are more time consuming and less effective than GM.

For decades it was common practice for industrial sites to dump waste in near-by waters and to bury industrial waste in the ground, where it can leach into ground waters and surrounding areas. Many industrial chemicals accumulate in bodies and accumulate up the food chain. In the past, residential buildings have surrounded factories because factories are a good source of work, but then those factories spout heavy metal dust all over the houses.

As a result of industrial waste in Sydney waters it’s now illegal to fish in Sydney Harbour because the fish contain an unreasonable amount of dioxins and PCBs.
Many doctors recommend that pregnant women don’t eat crustaceans while they’re pregnant. I originally thought that the reason was for their tendency to attract dangerous microbes and to go off quickly. I thought the suggestion was odd due to our ability to refrigerate and adequately cook foods, reducing the risks of infection. I realise now that it’s also due to their ability to accumulate toxins that break down extremely slowly. In reality the recommendation should probably go to all women who might have children and breast-feed, which is a great way to pass on accumulated substances.

What I’m saying is that we should try to understand technologies and our current environment before boycotting something that may be useful. Driving a car, eating fish, breathing the air in old buildings can be just as dangerous, maybe even more so, as eating GM foods.

Extended reading

• Genetically Modified Food: Harmful of Helpful? – Has a good, simple overview of most of the issues, including the different types of GMs (e.g. pesticides nutrition, cold/heat tolerance).
• 50 Harmful Effects of Genetically Modified Foods – a good example of fear leading the discussion. I think most of the points are either taken out of context or don’t come under the banner of genetic modification.
• Food Standards website
• Genetically Modified Rice F.A.Q. (Poole Remix) – Intelligent discussion on Golden Rice and GM issues.

Would you be happy buying GM foods at the supermarket? Would you be happy to know that you’d bought and eaten GM foods that weren’t labelled as such? Do you think any genetic modification they perform and deem safe to sell is worse than the pesticides and other chemicals they’ve already fed you?

Today’s XKCD comic reveals a marvelous truth about science.

It’s the same in biology. Put a PCR on, or something that needs to digest or wash for an hour or two and then do something interesting. :P

This article reported that the Venter Institute managed to transplant the genome of one species of bacteria into another. The recipient bacteria appeared to become the donor, but they’re not sure quite how it got rid of the recipient’s original DNA. Venter said that they’re not reporting on synthetic life, but this could be a significant step to creating artificial life.

Things like this, while exciting, start to push on my comfort zone. It’s impossible to foretell how quickly technology might advance and how far things will go. Would we end up in a Gattaca, Bladerunner or The Island type world? Thankfully there is an enormous difference between manipulating bacteria and manipulating more complex cells.

The Institute wants to patent the processes involved. Trying to do that seems to go against the spirit of science. Surely science pursues knowledge, which is shared and built upon. Discoveries are also reported, such that the findings can be reproduced and shown to be true. If all the methods involved are owned and monopolised then they’re not really able to be tested against other scientific knowledge and methods. They may even evade testing by common morals and ethics since what is known about them may be limited to certain people. Perhaps it’s all about money, people can measure the findings to their heart’s content, only restricted by their wallet.