The Meaning of Life

The word, not the phenomenon – that’s a story for another blog. Carl Zimmer has an article at Txchnologist on the ongoing disagreements of how to scientifically define life. It seems intuitive that we know what life is – it’s… you know… living stuff. The reality is much less settled:

When NASA says it wants to find out if Mars was ever suitable for life, they use a very circumscribed version of the word. They are looking for signs of liquid water, which all living things on Earth need. They are looking for organic carbon, which life on Earth produces and, in some cases, can feed on to survive. In other words, they’re looking on Mars for the sorts of conditions that support life on Earth.

But there’s no good reason to assume that all life has to be like the life we’re familiar with. In 2007, a board of scientists appointed by the National Academies of Science decided they couldn’t rule out the possibility that life might be able to exist without water or carbon. If such weird life on Mars exists, Curiosity will probably miss it.

Defining life poses a challenge that’s downright philosophical. There’s no ambiguity in looking for water, because we have a clear definition of it. That definition is the same whether you’re on Earth, on Mars, or in intergalactic space. It is the same whether you’re dealing with water as ice, liquid, or vapor. But there is no definition of life that’s universally agreed upon. When Portland State University biologist Radu Popa was working on a book about defining life, he decided to count up all the definitions that scientists have published in books and scientific journals. Some scientists define life as something capable of metabolism. Others make the capacity to evolve the key distinction. Popa gave up counting after about 300 definitions…

[Edward Trifanov, biologist at the University of Haifa] analyzed the linguistic structure of 150 definitions of life, grouping similar words into categories. He found that he could sum up what they all have in common in three words. Life, Trifonov declares, is simply self-reproduction with variations…

A number of the scientists who responded to Trifonov felt that his definition was missing one key feature or another, such as metabolism, a cell, or information. Eugene Koonin, a biologist at the National Center for Biotechnology Information, thinks that Trifonov’s definition is missing error correction. He argues that “self-reproduction with variation” is redundant, since the laws of thermodynamics ensure that error-free replication is impossible. “The problem is the exact opposite,” Koonin observes: if life replicates with too many errors, it stops replicating. He offers up an alternative: life requires “replications with an error rate below the sustainability threshold.”

Jack Szostak, a Nobel-prize winning Harvard biologist, simply rejects the search for any definition of life. “Attempts to define life are irrelevant to scientific efforts to understand the origin of life,” he writes…

It’s conceivable that Mars has Earth-like life, either because one planet infected the other, or because chemistry became biology along the same path on both of them. In either case, Curiosity may be able to do some good science when it arrives at Mars this summer. But if it’s something fundamentally different, even the most sophisticated machines may not be able to help us until we come to a decision about what we’re looking for in the first place.

I have to agree with Szostak; the definition of life is, at least from science’s perspective, irrelevant. However, there is a standard set of criteria used by biology, as far as I learned in school and Wikipedia has to say:

  • Homeostasis: Regulation of the internal environment to maintain a constant state; for example, electrolyte concentration or sweating to reduce temperature.
  • Organization: Being structurally composed of one or more cells, which are the basic units of life.
  • Metabolism: Transformation of energy by converting chemicals and energy into cellular components (anabolism) and decomposing organic matter (catabolism). Living things require energy to maintain internal organization (homeostasis) and to produce the other phenomena associated with life.
  • Growth: Maintenance of a higher rate of anabolism than catabolism. A growing organism increases in size in all of its parts, rather than simply accumulating matter.
  • Adaptation: The ability to change over a period of time in response to the environment. This ability is fundamental to the process of evolution and is determined by the organism’s heredity as well as the composition of metabolized substances, and external factors present.
  • Response to stimuli: A response can take many forms, from the contraction of a unicellular organism to external chemicals, to complex reactions involving all the senses of multicellular organisms. A response is often expressed by motion, for example, the leaves of a plant turning toward the sun (phototropism) and by chemotaxis.
  • Reproduction: The ability to produce new individual organisms, either asexually from a single parent organism, or sexually from two parent organisms.

Seems like pretty basic, inclusive criteria. Homeostasis is a word you don’t hear often, but it’s important; it’s basically what keeps organisms being themselves. It’s an organism’s negative feedback mechanisms, always adjusting to changes and trying to keep its state in the ideal place – ideal temperature, ideal CO2 level, ideal blood sugar, anything and everything. Also note that viruses aren’t considered to meet this definition of life; they can’t reproduce themselves per se, they’re not composed of cells, and they don’t grow, as far as I’m aware. 

Carl Zimmer posted a response to his article from an evolutionary biologist named David Hillis that I found interesting and insightful:

Like all historical entities (including other biological taxa), it is only sensible to “define” Life ostensively (by pointing to it, noting when and where it began, and following its lineages from there) rather than intensionally (using a list of characteristics). This applies to the taxon we call Life (hence capitalized, as a formal name). You could define a class concept called life (not a formal taxon), but then that concept would clearly differ from person to person (whereas it is much less problematic to note examples of the taxon Life). So, I’d say that I can point to and circumscribe Life, and that it the appropriate way to “define” any biological taxon. A list of its unique characteristics is then a diagnosis, rather than a definition. So, I’d argue that any intensional definition of Life is illogical (does not recognize the nature of Life), no matter how many words are used.

Defining Life (the taxon) is like defining other particular historical entities. We don’t “define” Carl Zimmer or the United States of America by listing out their attributes. Instead, we point to their origin and history. The same should be true for Life. If we ever discover a Life2, we’ll have a new origin and history to point to…

So that is another way of looking at it that I had never heard before, and it seems like the reasonable way to think about life. I don’t know if we’ll find any revolutionary kind of life in my lifetime, but if we do it’ll be pretty interesting to see different fields struggle with the implications. I hopefully will not be too worried about that – I’ll just want to pick its brains.


The Basic Human Tastes

Our society has traditionally recognized four tastes: sweet, salty, bitter and sour. In modern times however we’re better able to get to the root of taste, seeing what molecules are detected by our taste buds, and it has become apparent that there are more basic tastes than we once thought. The most well known one is umami, a savory taste, but LiveScience brings us some other candidates for basic tastes, excerpted below:

1. Calcium

The element calcium is critical in our bodies for muscle contraction, cellular communication and bone growth. Being able to sense it in our chow, therefore, would seem like a handy tool for survival.

Mice seem to have it figured out, kind of. Recent research has revealed that the rodents’ tongues have two taste receptors for calcium. One of those receptors has been found on the human tongue, though its role in directly tasting calcium is not yet settled, said Tordoff.

Calcium clearly has a taste, however, and counterintuitively most mice (and humans) don’t like it. People have described it as sort of bitter and chalky – even at very low concentrations. Tordoff thinks our calcium taste might actually exist to avoid consuming too much of it…

2. Kokumi

That calcium receptor might also have something to do with an unrelated sixth-taste candidate called kokumi, which translates as “mouthfulness” and “heartiness.” Kokumi has been promulgated by researchers from the same Japanese food company, Ajinomoto, who helped convince the taste world of the fifth basic taste, umami, a decade ago.

Ajinomoto scientists published a paper in early 2010 suggesting that certain compounds, including the amino acid L-histidine, glutathione in yeast extract and protamine in fish sperm, or milt – which, yes, they do eat in Japan, and elsewhere – interact with our tongue’s calcium receptors.

The result: an enhancement of flavors already in the mouth, or perhaps a certain richness. Braised, aged or slow-cooked foods supposedly contain greater levels of kokumi…

3. Piquance

Spicy-food lovers delight in that burn they feel on their tongues from peppers. Some Asian cultures consider this sensation a basic taste, known in English as piquance (from a French word). Historically, however, food scientists have not classified this undeniable oral sensation as a taste.

That’s because certain piquant compounds, such as capsaicin from peppers, directly activate our tongue’s touch, rather than taste-bud, receptors. The key piquancy receptor is called TRPV1, and it acts as a “molecular thermometer,” said John E. Hayes, a professor of food science at Penn State….

4. Coolness

At the opposite end of taste sensation from piquance’s peppers is that minty and fresh sensation from peppermint or menthol. The same trick of sensory perception is at work here – activated touch receptors, called TPRM8 in this case, fool the brain into sensing coldness at normal oral temperatures, said Hayes.

As touch sensations, both piquance and coolness are transmitted to the brain via the trigeminal nerve, rather than the three classical nerves for taste. “The set of nerves that carry the burn and cooling sensation are different than from taste sensation,” said Hayes.

Still, there is an argument that temperature sensation, both in the genuine sense and in the confused-brain phenomenon of piquance and coolness, deserves to be in the pantheon of basic tastes. Interestingly, Germanic people dating back to 1500 had considered heat sensation as a taste, Hayes said, and the modern debate over temperature’s status is far from over.

5. Metallicity

… Some Asian cultures place gold and silver leaf, as it’s called, atop curry dishes and candies, while Europeans fancy a bit of these metallic foils on pastries…

Although usually tasteless, such garnishes are sometimes reported as having a distinctive flavor. Researchers have shown that this sensation might have something to do with electrical conductivity, in effect giving the tongue a little zap…

Lab tests have failed to turn up a metallic-taste receptor, Lawless said, and it remains unclear if electrical conductivity or something more is going on for those shiny culinary embellishments. “We’re leaving the door open,” Lawless said.

6. Fat

The jury is still out on whether our tongues can taste fat, or just feel its creamy texture…

Mice can taste fat, research has shown, and it looks like humans can too, according to a 2010 study in the British Journal of Nutrition. The study revealed varying taste thresholds for fatty acids – the long chains that along with glycerol comprise fats, or lipids – in participants.

Intriguingly, the subjects with the higher sensitivities to fat ate fewer fatty menu items and were less likely to be overweight than those with low sensitivity…

7. Carbon Dioxide

Yet another strong sixth taste candidate: carbon dioxide (CO2). When dissolved in liquids, this gas gives soda, beer, champagne and other carbonated beverages their zingy fizz.

That familiar tingling was thought to result from bubbles bursting on the tongue, and had therefore been consigned to the touch category. “It’s tricky because CO2 was always considered a trigeminal stimulus,” said Tordoff.

Researchers presented a strong case for dedicated, taste bud-based carbon dioxide sensors in a Science paper in 2009. They found that an enzyme called carbonic anhydrase 4, which appears on sour taste-sensing cells, specifically detects carbon dioxide in mice…

Pretty interesting stuff. This is another scientific topic where it pays not to get emotionally attached to convention – the fact that there aren’t 5 senses or 9 planets or 4 tastes should be exciting new developments, not scary challenges to our worldview.

It’ll be interesting to see when our culture catches up to these realities; we already acknowledge foods as spicy or minty, but how long will it be before advertisers say their food is more umami or kokumi than their rivals’? 

The Science of Cloning

LiveScience has a good FAQ article on the basics of how animals are cloned. Cloning is only going to get more prominent in the future, so it wouldn’t hurt to have an idea of what it is and how it’s done. I won’t summarize it here, since it’s already explained briefly and nicely. The last paragraph mentions the recent successful cloning of a human embryo for harvesting embryonic stem cells, which I discussed a while ago along with some background on stem cells.

As always, feel free to let me know if you’d like any aspect explained in more detail.

Mental Time Travel in Birds

Mental time travel is a term for recalling past events and planning for the future, in terms of animal behaviour. This was originally thought to be a uniquely human ability, but research is gradually showing that other species are indeed capable of impressive acts of planning. This article from Science Daily discusses research on tropical birds that eat insects flushed out of hiding by army ant raids. They show that birds check on ant nests at the end of the day – when they’re not hungry – presumably using this information to plan their hunting for the next day.

Army ants have regular alternating periods of high and low raiding activity, and birds visit the ants’ temporary nest sites (bivouacs) to determine which colonies are raiding on a given day.

The new findings published October 14 in the journal Behavioural Ecology, suggest that bivouac checking allows birds to keep track of multiple army ant colonies, keeping account of which colonies are in periods of high-raiding activity while avoiding colonies with low-raiding activity.

Recent research has discovered that birds check army ant bivouacs at the end of the day, after they have fed at the raid. They may use the information about the army ant nest location the next day to find the ants again, thus accessing a past memory (the nest location) to fulfil a future need (bird will be hungry tomorrow), also known as ‘mental time-travel’…

Mental time-travel consists of two elements: the ability to remember past events and the ability to anticipate and plan for future events. It has traditionally been considered a quality unique to humans. However, ever since Nicola Clayton of the University of Cambridge discovered that scrub jays (a species of large-brained crow) can remember the past and plan for the future, there have been a suite of studies showing evidence of this ability in other species as well. We now know that corvids (birds in the crow family), some primates, and possibly rats have all shown the ability to remember the past and plan for the future.

Corina Logan, said: “We suspect that future planning could be involved in bivouac-checking bird behaviour because the birds were checking bivouacs when they were not hungry, a behaviour that does not make sense until the next morning upon return to the bivouac when the bird finds the ants raiding again and encounters its next meal — a delayed benefit.”

It’s unclear how confident they are that these birds are in fact planning ahead, but I thought this article was interesting anyway as an insight to bird intelligence. Western scrub jays, mentioned in the article, are pretty intelligent, possibly “among the most intelligent of animals”, according to Wikipedia. And they’re always watching you…

A Microbe Census Deep in the Earth

There are lots of microorganisms out there; we’ve only identified a fraction of them. Just as the deep dark oceans represent a huge question mark in terms of the incredible amount of undiscovered species, the subterranean offers a daunting opportunity to discover new forms of life. A new census, called the Census of Deep Life, is determined to find and categorize microorganisms living 10 to 100 kilometres below the Earth’s crust. 

A microbe, or microorganism, is just an organism that you can only see under a microscope. They’re usually unicellular. Bacteria are the most prominent example, but there are others across the spectrum, like algae (various kingdoms), slime molds (protist), yeast (fungus), dust mites (animal), and even single-celled plants

From LiveScience:

Little research has been done to identify the unicellular denizens of the Earth’s inhospitable depths. An ocean microbe census indicated that as many as a billion kinds of microorganisms live in the planet’s seas, but the deep Earth is more difficult to access, and microbial populations are more sparsely distributed.

Yet the data that are available on crust-dwelling species suggest that as many as several million categories of bacteria and their unicellular relations could live in the planet’s deeps…

For the census-takers of microbes, it’s a huge challenge to identify distinct species.

“Microbiologists have tried to do so the way traditional biologists have, but they’re frustrated by this because microorganisms tend to trade DNA,” Colwell said. In fact, microbes can swap DNA by merely engaging in what amounts to hand-holding.

Such a cavalier exchange of genetic material makes it difficult to unequivocally differentiate one group of microorganisms from another.

However, the microbe census is focused on getting samples from deep, isolated communities that have been left to their own evolutionary devices for long periods of time, and may have distinctive genetic characteristics.

The project receives rock and fluid samples retrieved from diverse environments such as caves, mines, and drill projects on land, and from projects in the ocean that have drilled deep beneath the seafloor.

Finding very unique species would be awesome. For example, a very important protein used in labs for DNA replication was taken from bacteria that were discovered in hot springs at 70°C. The protein is useful because of its resistance to heat, and is key to conducting modern molecular biology research. Who knows how discovering novel kinds of life could change science in the future?

On a separate note, I probably won’t be posting anything tomorrow (unless I really need a break) because I have my GRE biochemistry test on Saturday morning, and I have a marathon of cramming to do before then. Afterwards I’ll make up for it with some extra posts though, for your and my entertainment – provided this test doesn’t turn me off of science entirely. 

“World’s First Cloned Human Embryonic Stem Cells”

From New Scientist: For the first time, scientists have successfully put human adult somatic cell DNA into an unfertilized egg, induced that egg to divide and develop into a blastocyst – a first step towards a fetus – and harvested embryonic stem cells from those blastocysts, containing the adult’s DNA. There was a problem though: they could only accomplish this if they left in the egg’s DNA, so the stem cells have too many chromosomes (humans have 46; these cells have 69). Nevertheless, it’s a first step towards having real embryonic stem cells (as opposed to IPS cells) with adult DNA, which is a big boon for medical research.

If the above didn’t quite make sense to you, here’s some background:

Stem Cells To Date

You may have heard that there are two main types of “stem cells” in play in the research world: firstly, there are embryonic stem cells, which are cells derived from embryos that can potentially differentiate into any type of body cell. As they divide, their daughter cells will have more and more specific functions and more restricted potential, until they give rise to very specific cell types – a particular type of neuron, or a particular type of blood cell, for example. These cells will have varying limitations; for example, a neuron can’t divide – that’s about as limited as a cell can get. An embryonic stem cell has the most potential of any cell type – it can divide into anything. 

This is useful because it means researchers can grow any kind of cell they want in the lab. They can study how everything develops, and they can study, well, anything. There’s also the potential for stem cell therapy – injecting young, healthy cells into an injury to replace injured cells that the body wouldn’t normally be able to – like neurons, which I mentioned above can’t replicate. 

More recently scientists created induced pluripotent stem cells, or IPS cells. Basically they figured out ways of dedifferentiating adult, specialized cells, making them less specialized, less limited. This meant that they could make embryonic stem cell-like cells that would have the DNA of a particular person. In relation to the uses of stem cells mentioned above, this offers the benefits that you can study the progression of a particular disease, for instance; you could take cells from an adult with a known disease, grow their IPS cells in a lab and see where they go wrong, to put it broadly. In terms of stem cell therapy, you could have better odds of injecting cells into a person without having their immune system reject these cells, since they’d be their own body’s cells.

Perhaps most importantly to a lot of people, you can create IPS cells without destroying human blastocysts in the process, which has been and still is a huge source of political controversy regarding embryonic stem cell research. Contrary to what many morality-based advocates of IPS cell research would have you believe though, IPS cells are not the same as embryonic stem cells. They may be very similar and behave in largely the same way, but they are most certainly not the same thing, and there’s no way to possibly prove that they’re exactly the same, even if it were likely. There’s a lasting place for both of them in research; both will prove useful in understanding everything about human life. 

New Stem Cells

Whew, okay. That’s a very, very brief and simplified overview of stem cells-to-date. This new research took a different approach (typically used in cloning): they took the DNA from an adult, specialized cell, and put it into an egg; they then grew that egg into a blastocyst. From the blastocyst, they could extract embryonic stem cells. This method has the benefits of harvesting actual embryonic stem cells, while also having cells with the DNA of a particular adult, meaning they could be used for specialized stem cell therapy and whatnot. 

But not yet. They weren’t able to get the egg to form a blastocyst when they tried to remove the egg’s own DNA; they had to leave it in there for it to develop into stem cells, meaning that with the egg’s DNA and the adult donor DNA, these stem cells had too many chromosomes – they’re not an accurate model of human cells. Of course, now they’re working on figuring out how to get the egg to develop after they take out its DNA; I’m sure we’ll hear about this in the near future, and it’ll be big news.

Once they can make a viable blastocyst with just the adult DNA, it’s not a far leap to actual human cloning: they just have to implant it into a woman and bring it to term. Of course that entails who-knows-how-many years of troubleshooting, but it’s closer now than it’s ever been before. I call dibs on being cloned. 

Reimagining the Light Microscope

I worked in a lab that used cells grown in vitro, on a glass plate. You have to put them in an incubator for them to survive and thrive, but you often have to take them out of the incubator to put them under a microscope and examine them, often for extended periods of time. This can be problematic in terms of maintaing their temperature, not to mention time-consuming. 

So it gives me personal satisfaction to read this, from PhysOrg: CalTech engineers have built a petri dish (the main type of dish for growing cells) with a built-in light and image sensor that can wire into a computer outside of the incubator, meaning you can examine cells at your leisure and perhaps with better imaging techniques. 

As the image sensor takes pictures of the culture, that information is sent out to the laptop, enabling the researchers to acquire and save images of the cells as they are growing in real time…

“It radically reconceives the whole idea of what a light microscope is,” says Elowitz, a professor of biology and bioengineering at Caltech and a Howard Hughes Medical Institute investigator. “Instead of a large, heavy instrument full of delicate lenses, Yang and his team have invented a compact lightweight microscope with no lens at all, yet one that can still produce high-resolution images of living cells. Not only that, it can do so dynamically, following events over time in live cells, and across a wide range of spatial scales from the subcellular to the macroscopic.”

Elowitz says the technology can capture things that would otherwise be difficult or impossible — even with state-of-the-art light microscopes that are both much more complicated and much more expensive.

“With ePetri, you can survey the entire field at once, but still maintain the ability to ‘zoom in’ to any cells of interest,” he says. “In this regard, perhaps it’s a bit like an episode of CSI where they zoom in on what would otherwise be unresolvable details in a photograph.”

Microscopes are hugely important and used a lot, so any breakthrough in their use in research will be very far-reaching. I can’t tell if this system is actually practical yet – I imagine they’ll at least have to get rid of the wire first before it’s widely implemented – but it’s a step towards a new paradigm in cell imaging, which is huge. Science takes a long, long time to do; anything that cuts that time down will mean great things for scientific advancement. 

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