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Thursday, March 31, 2016

Answering Quora - Does spirituality provide anything that science cannot provide?

MeditatingRecently on Quora, somebody posed the question, Does spirituality provide anything that science cannot provide? Below is my answer.


This question presents a false dilemma. Of course there are many, many aspects of our lives that science doesn't address, but why should we turn to spirituality to address those areas when there are other, better human endeavors to address those parts of our lives?

Science is great at what it does - answering objective questions. It's by far the best method humanity has developed for this purpose. But really, that's its only purpose. Science has nothing to say on right or wrong, beautiful or ugly, awe-inspiring or mundane. Surely, we may find wonder in some of the findings of science. Looking up at the night sky is so much more marvelous knowing what those stars actually are. And science can help inform our actions, using our morality that comes from elsewhere. We wouldn't even know about global warming nor its consequences without science. But our emotional reaction to the night sky, or deciding to do something about global warming, are not part of science itself. Science has only given us the objective information, and then we use other parts of our humanity to react.

The problem with 'spirituality' is that it's plagued by so many historical connotations and associations, that it's hard to know what people really even mean by the term. Just take a look at the Wikipedia entry, Spirituality, for how many different ways people use this term, from Christians ("A spiritual man is one who is Christian 'more abundantly and deeper than others' ") to Muslims to Buddhists to Hindus to New Agers and a whole bunch of others. The one thing that most of these definitions have in common is the mystical or supernatural. But if the mystical and supernatural aren't real, then those versions of spirituality aren't based on anything real. At best, they're noble human endeavors entangled with outdated superstition. So, why not just drop the superstition and focus on the noble parts? But once you do that, is 'spirituality' really the best term to describe it?

We're human beings. We have worries and passions and morality and wonder and all types of subjective concerns. We should spend time reflecting on and fostering these aspects of our lives. We should read literature, go to art museums, study philosophy and ethics, take time during the day to pause and reflect, or even meditate if you want to take that reflection further. But these can all be secular pursuits. There's no need to pretend there's anything mystical about them.

Image Source: Wikimedia with further editing by me

Monday, March 28, 2016

Pysanky Easter Eggs 2016

Well, we got out the Pysanky kit to decorate eggs again this year. Now that we've done it two years in a row, does it count as a tradition?

Once again, my daughter did the best by far, but this year, my wife's and my eggs were good enough to show here in public. Here are the four we all had finished up by Easter dinner. My daughter finished up one more last night, and got started on another one. Once she's all finished up with that, I may post an update with all of her eggs.

Pysanky Eggs

We didn't neglect the normal eggs, either. Here's our dozen normally decorated hard boiled eggs.

Regular Eggs


Related: Pysanky Easter Eggs (from last year)

Friday, March 18, 2016

Answering Quora - Why There Were No 'First' Humans

Human Family TreeIn what has become my modus operandi here recently, I'm going to recycle a Quora answer for this post. This time, the question was, 'would the parents of the first human grandchild have been siblings?'. My response is very similar to parts of a previous answer/post, Which Came First, the Chicken or the Egg? And a Discussion of the Fuzziness of Species, but I think I did a better job this time explaining the example. So, here's my answer, with a few minor edits, and some additional footnotes.


As many others have pointed out, there was no 'first human'. Evolution is a gradual process that occurs in populations. Trying to pinpoint the exact individual that was the first human is like trying to pinpoint the exact second when twilight becomes nighttime.

Some people have a bit of a hard time understanding this, even people who claim to accept evolution. They'll say that if we exist as humans now, while in the past there were no humans, there must be some individual that we can identify as the 'first human', even if it's an arbitrary distinction. But this still doesn't work.

For the sake of argument, let's say you want to arbitrarily define a certain set of genes as 'human', and any organism lacking those genes as not human*. It's just semantics, but let's see what would happen. Let's say that around 100,000 years ago, there was a population of hominids that was very, very close to fitting your definition of 'human', but lacking one last mutation that would give them the full set of genes to make them 'human'. And lo and behold, one day a couple has a child that acquired this last critical mutation, and now, by our semantic definition, it's fully 'human'**. How different will it look from its parents because of that one different gene? Once it grows up, how much of a problem will it have finding a mate among the rest of the population and producing children of its own. The answers are that it will look as much like its parents as any child, and it won't have a problem at all finding a mate and having children (at least, not because of that mutation). So, even though it fits our semantic definition of 'human', it's not a different species from its parents or the rest of the population using the biological species concept.

But let's take it further. Once this first 'human' finds a mate and has children, because its genes are being mixed with its mates, and because it likely only has one copy of this new gene, anyway, only around 1 in 2 of its children are going to contain this critical gene that makes them 'human', while the rest of its children are going to lack this critical mutation and be almost but not quite 'human'***. But those children will all grow up to have children of their own, and on and on. So at first, this particular gene was only present in one individual, so only one individual in the entire population was fully 'human'. Then in the next generation, the gene was present in roughly 50% of its children, so there were a handful more 'humans' in the population. Then, in the next generation, the gene was passed on to yet more children. And since we know in hindsight that this gene is necessary to be 'human', we know that the individuals with the gene will end up having slightly more surviving children than individuals without the gene, so that eventually, after many generations it will have spread throughout the entire population, and the entire population will be fully 'human'.

That's the problem with trying to define a 'first human'. Whatever genetic criteria you pick is going to be arbitrary. An individual with 99.9999% of the correct DNA wouldn't be human by this definition, but it would still be the same species and able to interbreed with an individual with 100% of the correct DNA. And at some point in time, there will be a population of organisms mixed between 99.9999% 'humans' and 100% 'humans', and a 100% 'human' could have a mix of human and non-quite-human children. But the only reason we'd be classifying these organisms any differently is because of hindsight, knowing that in their future, only one version of a specific gene is going to be dominant. In their own time, they'd look just like any other population with a mix of genetic diversity.

And even all that's using an arbitrary definition of exactly what genes are needed to be 'human'. In the example above, we could be tempted to say, alright, that 'almost-human' population of hominids is close enough - let's call them fully human. But now you've just shifted the same problem a few generations back. There will be a moment in time when their ancestral population was a mix of individuals with their same genes and very slightly different genes. Depending on which specific arbitrary traits are required for the definition of 'human', you could shift the first humans by tens or hundreds of thousands of years.

So, to answer the question, there never were only two individual parents that were the only ancestors of all of humanity. Our ancestors have always been members of large interbreeding populations. And because evolution is a gradual process, it's impossible to pinpoint any single individual as the 'first human'.

Image Source: Pinterest

* You'd probably be more focused on alleles than genes. Alleles are different variants of the same gene. But, since it's just a semantic definition, anyway, genes work for the discussion. It's also an over-simplified example. It's not as if the population was a bunch of genetic clones. Even among individuals in the population, there will be genetic diversity.

** Mutations happen regularly. Pretty much every person alive has at least some mutations differentiating them from their parents. Granted, a whole new gene is a much bigger change than just an allele, but it happens. More Info: Understanding Genetics - How new genes are made

***Remember that we have two copies of all of our genes. So, if this hypothetical individual had a mutation that created a new gene or new allele, it would have probably occurred on only one copy of the original gene, i.e. one strand of the double helix. Since reproduction involves random mixing of our genes for making sperm and eggs, since our individual only has one copy of this new gene, only around half of it's eggs/sperm will contain the new gene, while the other half will retain the old version.

Friday, March 4, 2016

Genetic Evidence for Evolution - Vitamin C Pseudogene

This entry is part of a collection on Understanding Evolution. For other entries in this collection, follow that link.

Histoire et culture des orangers, A. Risso et A. Poiteau. -- Paris Henri Plon, Editeur, 1872As I've been doing a lot recently, I'm going to recycle a Quora answer for this entry. The Quora question this time was What are 3 facts that prove the biologic evolution theory?. After a bit of preamble about science not being able to 'prove' anything (for example, see my essay, Confidence in Scientific Knowledge), I got down to the answer - genetics, and the specific example of the GLO pseudogene*. Here's an edited version of that portion of my Quora answer**.


I'm only going to look at one narrow piece of evidence for evolution in our DNA. But as an aside before getting to the meatier answer, just the general similarity in genes of all organisms is already a decent argument in support of common descent. Why else should organisms have common genes? If it was special creation, why even use DNA in all organisms, and not get a little more creative in how to store genetic material. But the similarity in DNA goes beyond just genes. It's also in the structure of our chromosomes, in regions in the DNA that don't code for genes (much of it quite frankly junk - Is Most of Our DNA Garbage?), and in regions that used to code for genes that have since become non-functional due to mutation (pseudogenes).

One particularly striking example is one of the genes involved in the synthesis of vitamin C, L-gulono-γ-lactone oxidase, or GLO. All but three lineages of mammals can synthesize their own vitamin C and don't need to get it from their diets like us. The three lineages that can't synthesize vitamin C are anthropoid primates (which includes us), guinea pigs, and bats. All three of those lineages contain a form of the GLO gene, but in each lineage, mutations to the gene have damaged it to the point of disabling vitamin C production. But the thing is, the specific mutations are different in each lineage, but common to all members of those lineages. In other words, the damage to the GLO gene is the same in all anthropoid apes, but different from the damage in either guinea pigs or bats. Similarly, all guinea pigs share the same damage, which is different from that in primates or bats. Ditto with bats.

When you think about that, that's hugely indicative of common descent. With similarities in functional genes, a creationist or Intelligent Design advocate can always say that common purpose means common design, and God (or the designer) simply used the same genes in different animals. And creationists can even sort of explain isolated pseudogenes as a result of The Fall, where mutations have damaged what was supposedly at one time a perfect creation. But having the same broken genes in closely related species, and broken in the same way, is a whole lot harder to understand from a creationist perspective. The chances of those same mutations occurring in the same manner in all of the anthropoid primates is simply too unlikely to be taken seriously (and that unlikelihood is only compounded by each of the other lineages with mutations to GLO). So, absent common descent, that would mean all those broken genes would have had to have been present in all anthropoid primates from the very beginning. Why would a god (or intelligent designer) have put broken genes into organisms in the first place, and why break them in the same way in all anthropoid primates, but then in a different way in guinea pigs and yet a different way in bats (and in yet more ways in non-mammals that I didn't discuss). From an evolutionary perspective, it makes perfect sense. The damage occurred once in the common ancestor of anthropoid primates through a particular set of mutations, and that broken gene was then passed on to all it's descendants. At another time in another place, damage of a different sort occurred in some ancestral guinea pig, which was then passed on to all the descendant guinea pigs. And the same thing for bats, and all the non-mammals that have damage to GLO.

And that's just one example of one pseudogene. There are other pseudogenes, genes, regulatory stretches of DNA, and regions of junk DNA that all make the genetic evidence for evolution one of the strongest lines of evidence there is. But it's hardly the only line. To echo something I wrote in yet another Quora answer, if you're willing to put in a little reading, there are some great books on the subject. My two favorite introductory books are Jerry Coyne's Why Evolution Is True, and Donald Prothero's Evolution: What the Fossils Say and Why It Matters, which cover topics like fossil evidence for evolution, vestigial organs, embryological evidence, evidence from poor 'design', and biogeographical evidence. Given the enormity of the evidence in support of evolution, a single book can't come close to being comprehensive, but both of those books present enough evidence to be very convincing. Why Evolution Is True is my favorite of the two, and is a little more broad in the types of evidence it covers, as well as covering a bit more of the theory and mechanisms, not just evidence. If you want to get even more on the mechanisms and theory of evolution, but still in a book aimed at non-biology majors, Carl Zimmer's The Tangled Bank: An Introduction to Evolution is very good (though a bit on the expensive side - you might look for it at a library).

The Genetics of Vitamin C Loss in Vertebrates

Image Source: Wikimedia Commons

* GLO had previously been mentioned briefly on this site before in Ein Sophistry's Genetic Evidence of Evolution.

** This Quora answer itself was adapted from a comment I left to another Quora answer, Niall Harman's answer to What is the evidence for biological evolution and what is the evidence supporting creationism?

Want to learn more about evolution? Find more at Understanding Evolution.

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