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.

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Sensationalism in Science News

Obesity Panacea at PLoS Blogs has a good article on something science journalists tend to do wrong, and how to fix it. For our purposes, we can take it as something journalists tend to do wrong, and to make sure to be aware of it and not misinterpret science news as a result.

All too frequently, newspapers portray individual studies as the definitive answer on a given topic.  This is a problem because most studies are not the definitive answer on anything. That is why researchers are constantly trying to replicate each  others’ work.

Just because one study finds a relationship between A and B, does not mean that other studies will be able to replicate that finding, or that it will extend to other situations. On the face of it, this seems like an incredibly obvious statement.  And yet it’s something that newspapers often forget, and which I think could have some very negative consqeuences.

… To be honest, all journalists really need to do is dial back the enthusiasm a bit, rather than painting every study as a GROUNDBREAKING NEW FINDING.

Journalists may also want to shift away from writing about individual studies, and look instead to systematic reviews. This is what researchers and policy-makers are doing already.  We know that many published findings turn out to be false (some have argued that most findings are false) and so when we want to know the definitive answer to a question, we look at systematic reviews rather than individual studies.

Trying to understand the health impact of any given behaviour (e.g. sedentary behaviour, physical activity, smoking, etc) is a bit like trying to make a map of a city by taking thousands of independent pictures using different angles, distances, and resolution, without knowing how all the pictures link together. Any one picture (or study) tells you relatively little about the city, and some pictures may seem to contradict (e.g. one picture may suggest the city is grassland, while another picture may suggest it is incredibly urban). But if you take enough pictures from enough angles, you start to get a pretty good sense of what the city looks like.

Systematic reviews are an attempt to bring order to that chaos by organizing the pictures, grouping types of pictures together, and placing more weight on the high quality pictures, while reducing the emphasis of low quality pictures, or simply throwing them out entirely.

If journalists focused more on systematic reviews rather than individual studies (and there are plenty of systematic reviews coming out these days), they’d be less likely to steer people in the wrong direction, and more likely to be spreading a message that will hold up over the long term.

The problem is that asking news outlets to be less sensational is probably not going to happen as long as sensationalism is what sells. The change should start, I think, with the readers – rewarding good science writing and complaining about the bad. We have to be mature enough to understand that studies can be important without being life-changing, and that studies can be interesting without being definitive. For that, I think we need a more scientifically literate public, so it’s all a rather circular problem. 

You may not need any more examples of this, but if you read the full article, the author, Travis Saunders, provides an example of how newspaper articles poorly representing science are dangerous, in this case in reporting on the relative health risks to inactive children of TV or video games or computer use. Science is our best tool for knowing how to take care of ourselves, so we have to be able to trust what we hear about current scientific progress, and this trust is shaken when media outlets continuously declare contradicting definitive results. 

So let’s do our part to fix this problem, and read (and discuss) more science!

Edit: A recent article at New Scientist discusses some shortcomings of science reporting more generally, and again how journalists can fix this issue. 

The Open Laboratory 2012

Every year the best writing from science blogs across the web  – 50 essays a year – is compiled and printed in a book called The Open Laboratory, organized by Bora Zivkovic at Scientific American. The final list of essays is up now at The Network Central – you should definitely go check it out. If you like anything that you’ve read here, well, you’re certainly bound to like the best science blogging out there.

I’ve also been meaning to subscribe to more blogs for more perspective on science news, as opposed to working just from press releases at ScienceDaily and PhysOrg, so the list at The Network Central was a nice compilation for me, and for you if you’re interested. More science!

Two New Elements Named, and Some Notes on the Periodic Table

In the thrilling sequel to the naming of darmstadtium, roentgenium and copernicum, two more of the heaviest elements in the periodic table have finally been named: give a warm periodic table welcome to flerovium and livermorium!

From LiveScience:

Element 114, previously known as ununquadium, has been named flerovium (Fl), after the Russian institute’s Flerov Laboratory of Nuclear Reactions founder, which similarly is named in honor of Georgiy Flerov (1913-1990), a Russian physicist. Flerov’s work and his writings to Joseph Stalin led to the development of the USSR’s atomic bomb project.

The researchers got their first glimpse at flerovium after firing calcium ions at a plutonium target.

Element 116, which was temporarily named ununhexium, almost ended up with the name moscovium in honor of the region (called an oblast, similar to a province or state) of Moscow, where the research labs are located. In the end, it seems the American researchers won out and the team settled on the name livermorium (Lv), after the national labs and the city of Livermore in which they are located. Livermorium was first observed in 2000, when the scientists created it by mashing together calcium and curium.

Textbooks are changing before our eyes! This same lab has also synthesized elements 113, 115, 117 and 118, but those have yet to be confirmed so they won’t be named just yet. That leaves the race to elements 119 and 120, which I discussed earlier.

According to different ideas there could be up to 137 or 173 physically possible elements, so element-hunters are eventually going to run out of real estate. Here’s what an extended periodic table might look like, via WikiMedia:

The 8th period (row) would introduce a new block, making the whole table much wider. These blocks represent the type of the highest-energy orbitals occupied by each element’s electrons. The types of orbitals are categorized by the shapes of the areas with the highest probability of an electron being inside. Weird, I know.

For example, pink elements’ most energetic electrons are in the s-orbital, which is shaped like a sphere. That means their outermost (from the nucleus), most energetic, electrons are most likely to be in that sphere (their exact paths are impossible to know due to the Heisenberg uncertainty principle). Each different colour in the periodic table above means that the outermost orbital is a particular shape, and elements over 120 are theorized to have a new orbital shape, which is why they get a new block.

That’s just a quick and dirty summary of course, but if you didn’t before, now you know why the periodic table is blocked off how it is. Those green elements in the extended periodic table above (the f-block) are usually shown separately below the periodic table, so that it’s not as wide. Here’s a standard table for reference, from Jefferson Lab:

In this table the yellow elements are gases at room temperature (ex. hydrogen, oxygen, nitrogen, helium), the greens are solid and the blues are liquid (only mercury and bromine). Notice that block I mentioned, the f-block, at the bottom, keeping the table nice and thin, although out of order. One technicality I have to note though is that elements 71 and 103 on the right end, lutetium and lawrencium, are actually part of the d-block, not f-block, but they’re still grouped with the bottom series, called the lanthanide and actinide series. 

Since I’m getting into the periodic table, I might as well explain why there is a periodic table in the first place: a scientist named Dmitri Mendeleev realized that if you organized atoms by their mass, they fell into a repeating pattern in terms of chemical properties, like helium, neon and argon having similar properties, for example. With what I’ve explained above, it should be easier to understand just why: the periodic table is effectively organized by the properties of the outermost electron orbital, which is generally what interacts in chemical reactions. Every element in a particular column has the same thing going on in its outermost electron orbital, so it’ll have similar chemical reactions compared to the elements above and below it.

Since you’re all up on your science news, you’ve probably heard of the idea of silicon- instead of carbon-based life, which makes sense when you see that silicon is directly below carbon in the periodic table. You may have also heard of the recent report on bacteria that possibly incorporated arsenic into their DNA instead of phosphorous (although that story should be taken with a pound of salt); arsenic is also directly below phosphorous in the table. The table is magic, is what I’m trying to tell you.

In summary: flerovium and livermorium, and I’m easily distracted, but I hope you learned (or at least remembered) something!

Lethal Underwater Briny Icicle

BBC has some phenomenal footage of an icicle forming from salty water in the Antarctic. It crawls down into the water (because the density of the saltwater makes it sink) and freezes everything around it, including the poor animals underneath.

That video was not posted by the BBC so hopefully it doesn’t get taken down too soon. Here’s the camera set-up they used:

I don't think my camera can do that

You should check out their article for the description of the brinicle. Very cool stuff. It feels like nature is just always up to random amazing things without us ever realizing it. 

Why Empty Space Isn’t Empty

New Scientist has a nice little video explaining that vacuums, empty space, aren’t really empty. You, my dear reader, already know that from reading about the big laser that will tear apart virtual particles, and the recent experiment that materialized virtual photons, but you should check this short video out if you’re interested (can’t embed the video here, sadly). 

They also link to a full-length article discussing how the theory of the vacuum has evolved over time, which it looks like you’ll have to register (for free) to read. I won’t go into all of it, but in essence it portrays a somewhat philosophical struggle over the millennia about how emptiness could be empty, which led to and away from the idea of a luminiferous aether filling everything, and finally to quantum mechanics.

Now we know that because of the quantum uncertainty involved at the smallest scales, there are always fluctuations of fields and particles in a vacuum, meaning that any vacuum does indeed have energy in it. There’s never nothing. Is that reassuring? I think a constantly fluctuating space is much more interesting than a giant, vast emptiness. 

What Casual Climate Science Deniers Don’t Understand About Science

I’m really averse to writing about the political controversy around climate science because it’s beaten to death in every kind of media already, and there are plenty of blogs revolving around it. Without it, though, I might not have started this blog in the first place, since that and the political controversy over evolution are the biggest symptoms of a society that doesn’t know enough about science.

You may have heard about what the media gleefully called “Climategate 2.0”, a release of more stolen emails from climate scientists. Here’s Scientific American and LiveScience discussing the leak, and Life’s Little Mysteries addressing the scientific complaints against anthropogenic climate change. 

In my opinion, the controversies over evolution and climate science stem largely from a sheer lack of understanding of how science works. As I see it there are a few main misunderstandings:

1) Nothing is 100% certain. Deniers demand 100% certainty in scientists’ claims, which is literally impossible. There is always room for error and misinterpretation, in every kind of science. Scientists know this and so they tend to talk about their findings cautiously. This doesn’t translate well in the public sphere; we’re used to people in everyday life making certain claims, especially when those claims are relevant to politics. What kind of politician would say “My plan is to do this, because such-and-such is probably the problem with our economy, and such-and-such will probably help”? That would be honest, but it wouldn’t sell, and that politician’s dishonest opponent would come off much more convincingly.

This creates a conflict when science is dragged kicking and screaming into politics. There’s pressure to put things into certain terms – it’s technically bad science, but good politics. From what little I’ve seen excerpted from the hacked emails, it looks like this is what these scientists are discussing – how to remain scientifically accurate while trying to get across an important public message. Does glossing over the science in this way make them liars or frauds? No, it makes them roughly as inaccurate as everyone else in the public sphere. It’s regrettable that science has to be dumbed down for public presentation, but the dumbing down is obviously not a conspiracy. 

2) There will always be internal disagreement between scientists on smaller issues. Deniers will point out any and every sign of disagreement between scientists when it comes to climate science or evolution, and use this to claim that the science isn’t settled. There will probably always be differing hypotheses when it comes to the details of the matter, but that has no bearing on whether the field as a whole is valid. There’s tons of uncertainty in climate science, and personally I don’t like it at all when bold predictions about 100 years into the future are made, because it seems obvious that those predictions are so error-prone as to be meaningless. However, there’s negligible uncertainty when it comes to the facts of the Earth gradually warming over the last century, and the human release of greenhouse gasses as a significant contributing factor.

Do we know how all of this will pan out? No, not at all. I summarized a New Scientist article earlier showing just how little we know about the magnitude of the problem. This kind of subtlety can be confusing to the public – if we don’t know, then why should we take such dramatic and costly steps to respond? Science doesn’t work strictly by knowing though, as should be clear by the fact that nothing is 100% certain. Everything is a matter of probability. If curbing greenhouse gas release is very likely to be beneficial, then it makes sense to do it, whether or not we can know for sure – which we really can’t, ever. Doing nothing is making an active choice to act on the much less probable future scenario, which doesn’t make any sense. 

3) Science is not an opaque, elite clubhouse. The fact that e-mails from a small group of scientists are being used to smear an entire field betrays a profound misunderstanding of, everything. Science is a global pursuit. Even if these fantasies about these emails being incriminating were true, it would have virtually no implications for climate science, since different groups of scientists have independently come to the same conclusions anyway. Individual scientists can’t just make things up or conspire with impunity. They’re accountable to everyone – anyone can debunk their claims, and if they’re caught forging data or being incredibly dishonest in any way, it’ll probably mean the end of their careers. Science is not like politics – you can’t just lie and move on. If you’re a bad scientist, you’re done, for the rest of your life. There’s no way one particular group of scientists would just decide to make enormous lies about something that’s being investigated all over the world. 

I think the faster-than-light neutrino story is a great example for understanding science better in this context. Were the CERN scientists shunned for going against the overwhelmingly dominant consensus theory? No, quite the opposite. Is there a possibility that the theory of relativity is incomplete? Yes, anyone will admit to that. Does that mean we should ignore all of the findings brought to us by assuming that relativity was completely correct for the last hundred years? No, that would be ridiculous. 

In sum: even the best of theories can be challenged, even the best of theories can be incomplete, but it makes sense to act on what information we have even if it’s not perfect (which, again, it never will be). This alone should be enough to finally move past this political misunderstanding.

All of that being said, another reason why I’m averse to writing about topics like this is because I get the impression that facts and reason are not what’s driving the discussion. I have no idea what will convince most deniers to jump on the modernity bandwagon and trust the global institution of science, but it’s probably not posts like this. 

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