Art in a Petri dish

Former microbiologist Zachary Copfer was mesmerized by what he was learning every day as an undergraduate seeking a degree in biology. However, shortly after graduation he found himself in a commercial lab setting and his romance with science began to wane. That’s when he turned to photograph:

Photography developed into my new method of inquiry. Everything that I had missed about science I rediscovered in photography. For me, the two seemingly disparate fields of study served the same purpose, a way to explore my connection to everything else around me. As a former microbiologist recently turned visual artist, I seek to create work that is less of an intersection of art and science and more of a genuine fusion of the two.

Here is some of what he has created:

Copfer explains the process:

The process is very similar to darkroom photography only the enlarger has been replaced by a radiation source and instead of photographic paper this process uses a petri dish coated with a living bacterial emulsion. I believe that great beauty and poetry reside within the theories woven by scientists. And that it is through the unification of art and science that these treasures can be fully explored and made accessible to the world at large.

He has a number of pieces of science-art on his website, including ones of a galactic nature. They are, of course, very nice, but I don’t think they are necessarily his best. However, I do really like the idea of them. He takes something like E. coli, part of a group of the smallest living things on Earth, and he uses them to emulate the grandest of scales:

It looks like most of the trivia of what Copfer is doing can be found by poking around his site, but for anyone wondering, Einstein is made from S. marcescens grown on nutrient agar. The other scientist plates look to be the same, but I don’t know what sort of media he used to grow the other pieces of art.

Hold your horses

People like fast things. Our amusement park rides zip on their tracks. We jump from planes for fun. Our video games have names like Need for Speed. We’re even willing to watch bad movies so long as they’re called Speed. But that doesn’t mean there isn’t value in taking things at a pace reminiscent of the olden days. Sometimes we like to slow things down. Sometimes we like to take the time to smell the roses. And sometimes bloggers will engage in hackneyed stock expressions, both in title and content, in order to slowly build up a contrast between quickness and slowness.

As I’ve explained in the past, Richard Lenski is running a 20+ year evolutionary experiment with E. coli. He has published some fantastic results (much to the chagrin of overwhelmed creationists), and now his lab has utilized his bacterial lineages to further probe how evolution works.

[Co-author Tim] Cooper and his colleagues looked at two Escherichia coli clone lineages, sampled after 500, 1,000 and 1,500 generations of evolution. They came from a long-term bacterial evolution experiment running in the lab.

By looking for the presence of five beneficial mutations, the researchers found that ‘hare’ bacteria had more advantageous genetic changes than ‘tortoises’ after 500 generations, suggesting they were more likely to go on to successfully survive and reproduce, and to eventually wipe out their competitors altogether.

The terms “hare” and “tortoise” refer to the speed with which each group experienced mutation. The more quickly mutating group would change so rapidly that it was unable to achieve the same beneficial mutations as the more slowly mutating group. Here’s how I like to think of it.

In the late 90’s, several children were treated with gene therapy for various diseases. This is when a virus is used as a vector for a gene that has the ability (hopefully) to correct whatever is wrong with the child. It’s how researchers cured color blindness in monkeys in 2009. Basically, a gene is missing, resulting in some malady. When the virus is inserted, so is the missing gene. This usually helps or fixes the given problem. However, in a number of the children from the 90’s, insertional mutagenesis occurred. This is where the inserted gene causes a mutation (for reasons we can skip). In these cases, it caused a downstream mutation. The result was leukemia years after the fact.

The reason I’m seemingly rambling is that it was a complex interaction of genes that caused the cancer. It happens often enough that one gene is mutated and it is the loss of function of that gene that causes cancer, but that wasn’t the case in the 90’s. Think of mosquito genocide. Ultimately it’s all such a complex question that the specific results cannot be known ahead of time.

The reason Lenski’s lab found that the slower mutating group of E. coli out-competed the faster group was because the faster group had too many changes. The high number of mutations prevented it from obtaining other certain mutations. A change in one location can have long-reaching implications for future change in another location, in a way superficially similar to that of children from the 90’s, it turns out; it isn’t the case that just any gene can jump into a genome or population and be beneficial, or even work.

This research is important because it is generally assumed that high mutational rate means high evolvability. And that is still going to remain the assumption. But this gives factual credence to the idea that genetic background matters in a very deep way. In fact, Lenski’s earlier work with the same E. coli demonstrated that mutations themselves can be very much contingent. What this all means is that life doesn’t proceed with a single ‘strategy’. High mutation rates have their advantages, but just the same so do lower rates. It’s like driving through the city versus walking through the city. Plenty can be seen and much ground can be covered by car, sure, but a stroll by foot reveals doors and windows and alleys and other things that otherwise could have gone unnoticed.

Are humans “more advanced” than other organisms?

I recently had a discussion with a friend where he asserted that he was more advanced than, say, a plant. By the common connotations that come from the word “advanced”, we would have to agree that his statement was true. But it asks an interesting question: What do we really mean when we say we’re advanced?

To put the discussion in a proper framework, think in evolutionary terms. That means we can’t compare Albert Einstein to Sarah Palin and say, “Why, yes, he was more intellectually advanced than she is.” Of course that is true, but if we’re going to discuss evolution and what it means to be advanced, we’re necessarily comparing species, not individuals. That is what makes my friend’s initial comparison to plants a reasonable starting point.

But it is only a starting point. Because what are we comparing exactly? In terms of brain development, yes, he beats that plant handily. But what about in terms of ability to photosynthesize? Well, the plant just got a knockout in that round. Clearly there is a difficulty in making useful (and, in my view for this discussion, any) comparisons between species. Maybe we need to find a species that is closer in relation to humans. (It certainly would help for it to have a brain in the first place.) The animal I chose for the discussion and the one I am choosing for this discussion is the skunk. Jerry Coyne is the inspiration.

It does not always [evolutionarily] pay to be smarter, either. For some years I had a pet skunk, who was lovable but dim. I mentioned this to my vet, who put me in my place: “Stupid? Hell, he’s perfectly adapted for being a skunk!” Intelligence comes with a cost: you need to produce and to carry that extra brain matter, and to crank up your metabolism to support it. And sometimes this cost exceeds the genetic payoff. A smarter skunk might not be a fitter skunk.

A skunk is vastly more well adapted to life as a skunk than any human ever could be. All the things it takes to be a skunk? A skunk has them nailed down pretty well. The counter to this point was to say that if humans decided to destroy all skunks, we could. True enough. But does that make us more advanced? Of course our intelligence allows us to wipe out many other species, but the whole point of bringing up a skunk and its adaptation is to say that a comparison of intelligence is not valid for purposes of this discussion in the first place! (As always, you know I mean it when I use the lazy-man’s exclamation point.)

When we choose to compare intelligence in order to define what it means to be advanced, we have two massive assumptions going on. First, we’re assuming that intelligence is better than toothiness or having sharp claws or any other characteristic we see in nature. This assumption is untenable because some environments might call for all or any of those characteristics over intelligence. To put things in perspective, try thinking on an evolutionary timescale. So far I have only been comparing humans to other extant organisms (plants and skunks). But what if we go back 100 million years? 200 million? 500? 600? Any human put into an ancient enough environment would die. We know this because the right foods would not be available or because there would be no proper shelter or because the atmosphere would be poisonous or because our immune systems would not be evolved to cope with the bacteria and viruses present at the time or because…and so on. The assumption that intelligence is better than anything else is clearly wrong once we recognize that evolution and the ability of a species to survive depends largely upon environment.

The second assumption in this whole discussion is that we can even say something in evolution is “advanced”. We can say more complex or better suited to a particular environment, but “advanced”? That implies evolution is on the march towards some goal, to some end. That is not true. Science has demonstrated this again and again by showing what a contingent process evolution is. Take the Lenski experiments, for example. (I’m rather disappointed I never wrote about them here.) Richard Lenski and his researchers followed several lineages of E. coli for 20 years (in fact, they’re still following them). They would freeze samples every 500 generations so they could go back and re-run the tape of evolution should some fundamental change occur. And, eventually, such change did occur. Some E. coli were able to consume a natural by-product of their environment after nearly 30,000 generations. Lenski et al. unfroze the old generations to see just what enabled the bacteria to obtain their new found skill. As it turned out, they had to go back many thousands of generations; it wasn’t just one mutation, but at least three. The first two were effectively random. But they were necessary in order to get to the third mutation – the one that opened up a new food product for the colonies. But in the re-running of the tape, not all lineages re-evolved the new mutations. The chance involved in the process was too great to be inevitable; evolution is contingent.

So my answer to the question, Are humans “more advanced” than other organisms?, is to say it is an inappropriate question in the first place. There are several things we should not be assuming:

  • Intelligence is the best trait (whether to this point or in terms of possibility)
  • Evolution is goal oriented
  • The ability to destroy other species and still survive is a mark of advancement

I mentioned the argument for point three, but I have yet to address it. This one is pretty straight-forward, I think: We may be able to destroy many species, but that really only applies for large organisms. The vast majority of life is microbial. Since we would never be able to destroy it all (or even a minute fraction of it), does that mean it is more advanced than we are? What about all the bacteria we need to keep us alive? We certainly could not destroy all the mitochondria of the world and still survive.

Evolution is a contingent process that has no march towards any end. It is about the ability to survive. Our genes are interested in propagating themselves and that is why we are here. Life may mostly (though not entirely) be more complex since it first sprung forth nearly 4 billion years ago, but it always depends upon its environment – and that makes some characteristics more valuable than others. Sometimes.

Lac Operon

The lac operon of E. coli is the classic example for describing inducible prokaryotic gene expression. One excellent video description of it can be found here.

The jist is this. Not all genes are turned on all the time. There are ones which are needed constantly, others which are only needed in specific types of cells, and then others which are ‘turned on’ in specific situations. It is on this last point which I will focus.

In order for a gene to be ‘turned on’, it must be ‘off’ in the first place. All this means is that an organism’s (relevant) DNA is not being transcribed, thus preventing translation and the manifestation of proteins. The way this occurs in E. coli by means of the lac operon is that the lac repressor is bound to a DNA sequence.

A repressor is itself a protein. It binds to an organism’s DNA, thus preventing RNA polymerase from transcribing anything. This is a physical blockade; the repressor prevents the RNA polymerase from physically attaching and running along a specific sequence of DNA. This is the default position for an inducible repressor.

The way the repressor is removed is simple to understand. It has a specific shape to it which enables it to bind to the DNA sequence. However, this shape can be changed if lactose is present. The lactose will bind to the repressor, thus causing an allosteric change in shape. This means the repressor is no longer the specific shape needed to attach to the DNA, so it releases its ‘grip’.

This release allows the RNA polymerase to continue with transcription. This, eventually, turns to translation. In this stage, enzymes are created, two of which are β-galactoside permease and β-galactosidase (there is a third which can be ignored here). The former of the two is membrane-bound. This means it becomes embedded in the cell membrane. This quickens the transport of lactose from outside to inside the cell. Think of it like a tunnel through which only specific shapes can fit.

Once these specific shapes (lactose molecules) pass into the cell, ß-galactosidase breaks them into their constituents, one of which is glucose. This is used as a key source of energy in many organisms, including E. coli.

Once concentration falls, lactose molecules are no longer bound to the repressor, making it free to resume its normal duties attached to DNA.

Misleading Science Articles

French, German and Hungarian physicists have taken another step in supporting Einstein’s theory of special relativity.

A brainpower consortium led by Laurent Lellouch of France’s Centre for Theoretical Physics, using some of the world’s mightiest supercomputers, have set down the calculations for estimating the mass of protons and neutrons, the particles at the nucleus of atoms.

According to the conventional model of particle physics, protons and neutrons comprise smaller particles known as quarks, which in turn are bound by gluons.

The odd thing is this: the mass of gluons is zero and the mass of quarks is only five percent. Where, therefore, is the missing 95 percent?

The answer, according to the study published in the US journal Science on Thursday, comes from the energy from the movements and interactions of quarks and gluons.

In other words, energy and mass are equivalent, as Einstein proposed in his Special Theory of Relativity in 1905.

All that is fine. What is misleading is the title of the article:

    e=mc2: 103 years later, Einstein’s proven right

Nothing here has been proven. Science never does that. What is seeks to do is disprove. The hypothesis here is that energy and mass are equivalent. In order to discover this, scientists attempted an experiment that, if falsified, would weaken Einstein’s great discovery. That isn’t what happened. It turns out that energy and mass are equivalent – in this instance. That doesn’t mean that in every instance that that will be the case. We cannot possibly know for certain that if the experiment is run again or a new experiment is created that the results will be the same. This is precisely what occurs in all of science. Evolution is not proven in the scientific sense of the word. Gravity has never been proven. We could find a slew of rabbits and sharks in the pre-Cambrian whose fossils fall up tomorrow, disproving both theories, at the very least disproving them in part.

Of course, it should be noted that we know these events to be vanishingly unlikely because of the strength of both theories; neither (modern) one has been disproven in any way meaningful to their overall statements. Despite the constant attempts of scientists to show these (now) theories to be incorrect, they have failed. These constant failures – which manifest themselves as monumentally beautiful and elegant discoveries, quite unlike anything we should normally call “failures” – are what make hypotheses into theories; they are what enable us to refer to so many worthwhile ideas as facts, even if they are tentative by their very nature. They are the core of science – a way of knowing that never seeks to prove anything.