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.


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. 

My Thoughts on Free Will and Neuroscience

There have been a few articles written about neuroscience and its implications for free will in the last few days; here’s one in Salon, here in Scientific American, and here from Mind Hacks, which also links to an October article in the New York Times and August article from Nature

I’ve found that none of these reflect my own perspective, which is why I thought I’d add my thoughts to the mix just in case you wanted another opinion. Basically these articles portray a struggle over the definition of free will, and make it seem as if some people (namely neuroscientists) find free will soundly disproven while others (namely philosophers) think more evidence is needed. Philosophers argue that neuroscientists are seeing free will as something immaterial, a ghost in the machine, which is not how they see it – free will can coexist with a purely material brain.

My thought is that free will is irrelevant. Free will is an intuitive model for human thinking, a historical assumption. Now we have evidence for another model for human thinking, one based on physics via chemistry via biology. Is there any reason to continue to consider free will as a relevant way of thinking about thinking? I really don’t think so. It may be interesting to philosophers for the moment, but practically speaking what does it tell us? What reason is there for thinking it exists? Whether it exists by one or another definition is irrelevant if it’s a useless, unfalsifiable concept. 

The only point that’s brought up in these articles for the utility of free will is in courts, for assigning responsibility. However, we already acknowledge the flaws of free will in court, via the insanity plea. The idea is that insanity prevents a suspect from using their reason. I don’t think there’s any difference between that case and the case where reason prevents a suspect from using their insanity. There’s this common conception of a “normal” brain and a “defective” brain, instead of the more realistic acknowledgment that every brain is unique and has its own predispositions. Why would a brain we culturally consider defective not have free will, while an equally deterministic “normal” brain has free will? It doesn’t actually make any sense. 

So where does that leave us in terms of legal and moral responsibility? I think it leads us towards rehabilitation instead of pure punishment. The point of rehabilitation is to acknowledge and use determinism – change a convict’s circumstances, change their brain. We just have to realize that this applies to everyone, not just the people we currently don’t think have much free will, like children or the mentally ill.

I could probably ramble on, but I’ve probably made my point clear: free will is, as far as I can tell, a useless concept, and if anything it just obstructs a more effective justice system, as opposed to being the only thing between us and anarchy as some people would claim. I don’t think neuroscientists should be worrying about it at all, given what we know now, so I don’t. 

“Science can answer moral questions”

Here’s a TED talk in which Sam Harris argues that we don’t need to rely on conjecture or appeals to authority to find moral truths – we just need to look at the science. According to Wikipedia, “Sam Harris is an American author, philosopher, and neuroscientist, as well as the co-founder and current CEO of Project Reason.”

Unfortunately, I disagree with him, and I hope it’s obvious why I think he’s wrong. He immediately equates morality with human well-being, explains that through neuroscience and psychology we can measure well-being, and therefore through neuroscience and psychology we can dictate morality. If only it were that simple.

Not everyone equates morality with human well-being – in fact, I’d argue that few, if any, people do. There are at least two obvious alternatives to maximizing human well-being as the objective of morality – obeying a higher authority, or respecting human rights that appear self-evident. If someone finds a certain right to be self-evident and inviolable, for example, then whether or not it’s best for human well-being is absolutely irrelevant. One might assume that science could tell us how to maximize human well-being given the limitation of respecting human rights, but in any case that won’t result in everyone being able to agree on what’s moral or not. 

Sam Harris can claim that these alternative systems of values are wrong, but there’s simply no scientific basis for that, or for any system of values. He can use science to explain how best to get what we want, but not what to want – just like the chocolate or vanilla comparison he used, wrongly. 

This post of mine definitely seems to stray hard from science to philosophy, but I think it’s important to recognize the boundaries of what science can tell us. I think Sam Harris seriously misunderstands or misrepresents this. Science remains what it’s always been – our best tool for surviving and thriving – but how and if we use it is still up to us. 

Radiocarbon Dating

By request, I shall use my expertise to explain the magic that is carbon dating – what allows archaeologists to deduce the age of ancient artifacts.

Just kidding, I’ll link you to someone better: How Stuff Works has a 1 minute video that explains it pretty concisely. I wish I could embed it here, but WordPress is a jerk like that.

If for some reason that video didn’t do the subject justice for you, here’s the deal, in some more detail: Read more of this post

“What Do Organisms Mean?”

Finally we’re on to part 3/3 of this New Atlantis series I’ve been reading over the past two days (part 1, part 2), roughly about whether the mechanics of life are quantifiable; whether physics can fully explain biology. The series took a slide from scientific and agreeable to me to philosophical and disagreeable to me, but I stuck through it in the search of something convincing.

This third essay, “What Do Organisms Mean?”, basically expands on the arguments presented in the second one, and I feel the same way about them – his arguments are very god of the gaps-like, and he seems to give scientists’ pathetic fallacy significance that it doesn’t have.

A main thing that confuses me about his arguments is that he insists that he is not arguing for a non-material life force, while saying that physics cannot explain biology because there’s some greater organizing force at work in organisms. He addresses this discrepancy below; for context, his general argument is that there’s some sort of meaning inherent in living organisms, some overarching goal or thought process not encapsulated in its physical composition.

The accusation of vitalism seems inevitably to arise whenever someone points to the being of the organism as a maker of meaning. This is owing to a legacy of dualism that makes it almost impossible for people today to imagine idea, meaning, and thought as anything other than ghostly epiphenomena within human skulls. So the suggestion that ideas and meaning are “out there” in the world of cells and organisms immediately provokes the assumption that one is really talking about some special sort of physical causation rather than about a content of thought intrinsic to organic phenomena…

But ideas, meanings, and thoughts are not material things, and they are not forces. Nor need they be to have their place in the world. After all, when we discover ideal mathematical relationships “governing” phenomena, we do not worry about how mathematical concepts can knock billiard balls around. If we did, we would have made our equations into occult or vital causes. But instead we simply recognize that, whatever else we might say about them, physical processes exhibit a conceptual or thought-like character. And so, too: the meanings that give expression to the because of reason do not knock biomolecules around, but — like mathematical relations — are discovered in the patterns we see. The thought-relations we discover in the world, whether in the mathematical demonstrations of the physicist or the various living forms of the biologist, need to be genuinely and faithfully and reproducibly observed, but must not be turned into mystical forces.

From this I think I can succinctly state where I disagree with him: he claims that “physical processes exhibit a conceptual or thought-like character,” instead of recognizing that we assign conceptual or thought-like character to physical processes. To borrow my analogy from my previous post on this series, a protein that we call a master regulator isn’t analogous to a boss at work intrinsically; there’s nothing intrinsic about it that indicates that it relays orders or interprets feedback. That’s a purely human invention meant to explain a physical phenomenon through analogy, because we assign agency to things left, right and center.

Our unavoidable tendency to assign agency led people to create pantheons of gods in the past to explain the conscious motivations of nature, and leads us to anthropomorphize molecules now. The difference is that at this point we consciously acknowledge this fallacy, and embrace it as a part of human perception, not as part of reality. I think the author’s error is in failing to separate this feature of perception from the objective reality it tries to describe.

I think I’ve said about as much as I can about this series of essays; they are long and a bit dense, but I hope you’ll take a look at them too, to challenge how you think about biology and reality. I can’t capture all of it, but I’ll quote some of the meaty parts of this third essay below:  Read more of this post

Is a Whole Organism More Than the Sum of Its Parts?

Here is the second part of the essay series I started looking at yesterday, about the complexity of living things and ultimately pointing towards an argument for a new type of scientific explanation for life. The article is called The Unbearable Wholeness of Beings, and unfortunately it started being disagreeable to me from the get-go. If you’re interested in the idea that there may be more to life than chemical processes – whether in agreement, disagreement or uncertainty – you should check it out. 

(Update: here is my post on the third essay.)

This post is much longer than the norm – I had the “yelling at the TV” effect where I couldn’t help but disagree as I was reading along, so I thought I’d share my opinions along the way.

Animals and plants are a long way from rocks and clouds, and also from automobiles and computers. The need to point this out today is one of the startling aspects of the current scientific landscape. It is true that the concept of “vitalism” has been problematic in the history of biology, but no less so than “mechanism.” The two problems are in fact devilishly intertwined. We will never get straight about vitalism if we do not also get straight about mechanism. And until we sort through the associated confusions, we have little hope of meaningful conversation about many of the perplexities vexing biologists today…

Here, then, is my question: Are you and I machines? Are we analyzable without remainder into a collection of mechanisms whose operation can be fully explained by the causal operation of physical and chemical laws, starting from the parts and proceeding to the whole? It might seem so, judging from the insistent testimony of those whose work is to understand life.

The article goes on again into the depths of cell biology. The last article explained these complexities to show that the field of biology is not what it used to be, and that scientists have discovered that things are not as easily explained as they once thought. This article unfortunately seems to be making similar points but to the end of making a lower-level “god of the gaps” argument – not for religion, but for an explanation of life that doesn’t conform to modern science. 

The fact that I called it a god of the gaps argument shows chiefly what I think is wrong with it; it criticizes conventional explanations without offering any evidence for an alternative, and assumes that a current failure to fully comprehend something indicates a permanent failure. 

The author makes a few arguments, of which I’ll only excerpt a morsel: Read more of this post

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