Science & Nature Archive

Saturday, July 7, 2012

Arguing on a Website - Explaining Evolution

Evolutionary TreeI didn't write much on the blog this week because I spent a few lunch breaks getting caught up in a discussion in the comments section of an article in the local paper. So, I'll do what I often do in these situations, and copy my comments here. It's a bit repetitious of other things I've written before, but due too the nature of comments, a bit briefer.

You should read the Letter to the Editor that kicked off the conversation first. Be warned that much of the discussion in the comments section degraded into name calling, triggered by the second letter at that link.

Here's my first comment.

Although I agree with much of the sentiment of Jim Edwards, I did see a few places where what he wrote is in need of correction, or where I might add a litte more information.

"First of all man did not evolve from apes."

Granted, this is a semantic issue, but it's one of my pet peeves. Humans did not evolve from any of the other extant apes, true. We didn't evolve from chimps or bonobos (they didn't evolve from us, either). We all three species share a common ancestor. Further back still, we share a common ancestor with gorillas, and even further back with orangutans. But if you were to get in a time machine and travel back to any of those common ancestors, whatever species they might be, they would still be referred to as apes. It would be like arguing that crows didn't evolve from birds, but only share a common ancestor with birds.

Regarding the time of the split, the current best estimate is around 6 million years between us and chimps & bonobos. The other apes split off from our lineage earlier than that. You have to go back around 20 million years for the split between old world monkeys and us apes, and back around 30 million years for the split with new world monkeys.

If you're really interested in the family tree, just google "primate phylogeny".

Regarding 'missing links', I'm not sure what people expect them to look like, but there are plenty of transitional fossils that have been found. To give just two examples, tiktaalik roseae is a great example of the transition from fish to tetrapods, and ambulocetus is a great example of the transition from terrestrial mammal to whale. But keep in mind that these examples don't rest solely on their own. You have to look at them in context of other fossils. For example, animals like Eustheopteron and Panderichthys are similar to Tiktaalik, but more fish like, while animals like Acanthostega and Ichtyostega are also similar, but more tetrapod like. On the human side, just google "talk origins hominid skulls", and you'll find a page showing skulls grading gradually from earlier hominid ancestors into us modern humans.

And my second:

tdgriffin wrote:

"I have no doubt that the DNA of apes and humans are similar. I wouldn't be surprised if doves and pigeons have similar DNA. They resemble each other. It doesn't prove they came from the same ancestor."

Why would our DNA be so very similar to that of a chimp's if not for common ancestry? Let me use an example. Most animals can make their own vitamin C. They don't need to eat foods high in the vitamin because their bodies simply synthesize it from the other molecules of the food they eat. Scientists have found the gene responsible for this, the L-gulano-γ-lactone oxidase gene. They've found a broken copy of this gene in humans. So the first question is, why would we have a broken copy of a gene, unless we inherited it from an ancestor with a functioning copy? Now, I know some creationists might say that maybe Adam and Eve did have functioning copies of this gene, and mutation crippled it. But guess what, scientists have also found this gene in chimps, macaques, and other primates, and it's broken in the same location as the human copy. So now you have to accept that this gene either just happened to mutate in the same location in all of these different animals, or that a creator intentionally put the same broken, non-functioning gene in all these animals, when it just makes so much more sense to assume that it mutated in a common ancestor of all these animals, which passed it on to all of its descendants.

(As to why a broken gene could have persisted in successful animals, if you're eating a diet rich in fruits and vegetables, it really won't hurt you if you can't make Vitamin C, so there's no selection pressure for those individuals with a working copy vs those with a broken copy.)

And L-gulano-γ-lactone oxidase isn't the only example. We share other pseudogenes with the great apes, and similarities in 'junk' DNA also match the pattern predicted by common ancestry.

And then my third and final comment:

in response to tdgriffin:
So, I take it you disagree with me? Oh well. But I still wonder why we, in our never ending quest for the perfect species, would hang onto a broken copy of an unnecessary gene over millions of years, since we and the apes decided to go our separate ways. When I break a cd, I chunk that bugger.

Another thing I wonder about, when I hear it mentioned: Just how many generations would it take for a black family living in New York to become white, or a white family living in South Africa to become black?

Natural selection only acts on beneficial or harmful traits. Beneficial traits allow an organism to have more offspring, so that trait becomes more common in a population. Harmful traits cause an organism to have less offspring, so that trait becomes less common in the population. Neutral traits aren't acted on by natural selection, and can persist (although, in the long run, neutral traits tend to deteriorate or drift just because there's no pressure from natural selection to maintain them). Also keep in mind, that there's no mechanism in our cells to do what you propose - cut out bad sections of DNA. Our cells just copy the DNA, making a few mistakes here and there in mutations. And of course, there's no conscious intent. You can't will your cells to cut out your broken L-gulano-γ-lactone oxidase gene in the sperm or eggs that you'll provide to your children.

So, some of our distant ancestors lived in an environment where they ate lots of fruit and vegetables, and got plenty of Vitamin C from their diet. When some mutation occurred that crippled Vitamin C synthesis, it didn't help or hurt that individual. Even if a mechanism existed to do it, cutting out the broken gene wouldn't have been noticeably beneficial. It was a neutral mutation. So, it didn't hurt that individual's chances of having offspring, and the broken gene began to spread.

But now there is an interesting question - if the broken gene wasn't beneficial, how did it become so widespread as to become fixed in the entire population? Here's where it's good to remember that populations are composed of individuals, and that sometimes a little bit of chance comes into play. From time to time, there will be population bottlenecks. This may be due to hard times that kill off most of a population, or from a small group becoming isolated and then developing into a new species. So when you get down to those small population sizes, chance plays a big role in which versions of genes are present and, and consequently which will persist in that population. (You can read more about this on Wikipedia under 'Founder Effect':

As to the question of skin color, I honestly don't know, but I suspect that in modern times, it might not happen at all. Remember that in evolutionary terms, 'fitness' merely means successfully leaving offspring. And for natural selection to act on a trait, it has to result in individuals having either more or less children than other individuals with different traits. In modern day New York City or modern day South Africa, where much of people's lives are spent indoors, and where dietary supplements are readily available for those with Vitamin D deficiencies, I doubt there's any strong selection pressure on skin pigment.

Thursday, June 7, 2012

Venus Transit

Other people got much better photos of the Venus transit than I did (see Bad Astronomy or Why Evolution is True for a few), but this is my blog, so I'm going to post mine. I used my daughter's Astroscan telescope, with a sun viewing screen to project the image onto. So, here's the transit, taken with my iPhone. It's a little skewed because the camera was off to the side.

Venus Transit

And just to show the telescope setup, here are a couple photos of that.

Venus Transit

Venus Transit

I also installed a Barlow lens to get even more magnification - the sun wouldn't even fit on the screen. At that size, there was a very noticeable shimmering around the edges of Venus (I think due to a phenomenon known as astronomical seeing). I tried to take some video of that, but none of the videos turned out well at all.

Wednesday, May 23, 2012

Theistic Evolution vs. Intelligent Design

Theistic EvolutionI must be getting old - I'm becoming forgetful. Jerry Coyne recently wrote a post titled Does theistic evolution differ from Intelligent Design?. I left a comment on his site, and had already started to write a blog entry expanding on that, when I came across an old entry of mine that said almost exactly what I was planning to write, Difference Between ID Proponents and Theistic Evolutionists. Oh well, since I already have some of this written, I might as well go ahead and post it so as not to waste the effort.

Coyne stated his position right in the introductory paragraph.

My answer is that these two brands of bad science elide seamlessly into one another, with no sharp line to demarcate them. Nevertheless, I don't call people like Francis Collins advocates of ID simply because that term conflates them with the hard-core, get-in-your-school adherents of ID who populate the Discovery Institute. But let us remember that this is a quantitative and not a qualitative difference.

He went on to write in his penultimate paragraph:

If you think that an intelligent god intervened in the process of evolution, especially to ensure the appearance of human beings made in that god's image, then you're advocating intelligent design. If you accept even a little bit of divine tinkering in the evolutionary process, you're not standing on some inclusive middle ground--you are, as P.Z. Myers said, halfway to crazy town.

I understand that both concepts are related, and maybe there is a grey area in between them. But I think there is an important difference between the two positions. To a proponent of theistic evolution (TE), if you take away God, evolution continues to work, you just may not end up with humans. To a proponent of Intelligent Design (ID), if you take away God, evolution is vastly different, without any complex structures. In other words, a TEist accepts all the evidence for evolution, but adds in an extra mechanism on top of it to accommodate their religious belief. An IDist rejects all the evidence for evolution, and invents a mechanism to replace it.

Part of the problem is that ID is so poorly defined. But even someone like Michael Behe, who accepts a bit more of the evidence for evolution, still accepts irreducible complexity, and believes that some features of organisms just couldn't have come about without divine intervention (or alien intervention, if the less honest press releases from the Discovery Institute are to be believed). And if you look at something like the ID textbook, Of Pandas and People, it reads like straight up creationism. Here's a passage from page 22 of that book that I've quoted twice before on this blog.

Instead, fossil types are fully formed and functional when they first appear in the fossil record. For example, we don't find creatures that are partly fish and partly something else, leading gradually, in the dozens of characteristics which they exhibit, to today's fish. Instead, fish have all the characteristics of today's fish from the earliest known fish fossils, reptiles in the record have all the characteristics of present-day reptiles, and so on.

And here's another one from page 25.

There is, however, another possibility science leaves open to us, one based on sound inferences from the experience of our senses. It is the possibility that an intelligent cause made fully-formed and functional creatures, which later left their traces in the rocks.

And as I pointed out in that previous post of mine, what else can you expect of a theist? They see God's intervention in everything, from the weather to diseases to coin tosses. Why would they leave evolution out?

I also disagree with Coyne implying that because the two positions "elide seamlessly into one another, with no sharp line to demarcate them", that they shouldn't be considered as different. The same argument can be made for many things, from colors, to night and day. I'm especially surprised at an evolutionary biologist using this argument*. If you could get in a time machine and see every individual in the lineage from one of our ancestors from 6 million years ago to today, you'd never be able to pick out just exactly when one species transitioned into another. But I don't think anybody would try to argue with the fact that we're a different species than that 6 million year old primate.

So, while TE and ID may be related in that they both see the hand of God influencing the history of life on the planet, there is enough of a distinction between the two positions to merit separate labels.

*Don't take this as an attack on Coyne. I have great respect for the man, read his blog website almost daily, and think his book, Why Evolution Is True, is possibly the best introduction to evolution for people who don't know much about it.

Tuesday, April 10, 2012

A 3D Model of the Solar System

Solar System 3D Model Isometric ViewSpace is big. I've written about it before, but that was about distant galaxies. But even when you look in what's supposed to be our own 'neighborhood', the solar system, the distances involved are staggering. I don't think most people have a sense of scale of the solar system, such as how big the Sun is compared to the Earth, or how far it is between the planets. So, I did what any nerd with access to a 3D drafting program would do - I modeled it. And once I had it modeled, I figured other people might find it interesting, so I'm sharing it.

To explain the model a bit, I went to Wikipedia and looked up the diameters of each of the planets (all 8 of them - sorry Kuiper Belt objects), and their distances from the Sun. I averaged out their distances so that I could draw the orbits as circles instead of ellipses - not perfectly accurate, but it still gives a good idea of the sense of scale. I put all that into a spreadsheet, and then divided everything by 1,000,000, to get it in sizes that would work in Solidworks. And keep in mind that Solidworks deals in inches by default. So for example, instead of drawing the Sun at 864,900 miles in diameter, I drew it at 0.8649 inches in diameter. The Earth, instead of being 92,956,050 miles from the Sun, was drawn at 92.956 inches from the Sun. And the biggest distance, Neptune's distance from the sun, instead of being 2,798,310,157 miles from the sun, was drawn at 2798.31 inches from the Sun.

Actually, just stop and think about those numbers. If the Sun was less than an inch in diameter, the Earth would be almost 8 ft away (the standard height from floor to ceiling) and only .008" in diameter, while the most distant planet, Neptune, would be 233 ft away (23 stories).

Anyway, here's the model, in two different formats, along with that Excel file that I mentioned.

That first format is Solidworks. It's the better of the two 3D formats, but you need the right software to view it, and Solidworks isn't cheap (a couple thousand dollars a license - so not really for home use). The second format is an eDrawing. There's a free viewer that you can download. The third file is the Excel file. It has a few more ways of scaling that just what I discussed above, which should be pretty obvious from the text.

Here are a few images taken from the model. Each image has been scaled to fit on the blog. If you click on it, you'll get the full size version.

This first picture is the Sun and all of the planets - Mercury, Venus, Earth, Mars, Jupiter, Saturn, Uranus, and Neptune. It's tough to see the inner planets (Mercury through Mars) because they're so tiny. They look like little more than a smudge in the image below, but they're a bit easier to make out if you click on the full size version. The vertical line just to the left of the terrestrial planets is the center of the Sun. In the model, all of the planets are aligned. The image below was made by first looking straight down all of the planets, then rotating the model just 0.04º so that you could see each planet without it being obstructed by any other planet. Another way to think of this is that it shows the planet sizes to scale, and shows the distances properly relative to one another.


This next one is the same view as above, except zoomed in on the terrestrial planets. Again, the tick mark on the left shows the center of the Sun. You can see the Moon in front of the Earth (our Moon is the only moon I modeled).


The next three images are a kind of series. They're looking 'down' at the solar system from outside the ecliptic plane. To me, these really gets across sense of distance. The first is zoomed in to just the Sun and Mercury's orbit. The second one zooms out a bit to show the orbits of all the terrestrial planets. The third zooms out to show the orbits of all the 8 planets.

So first, here's the Sun and Mercury. Mercury's so small that it gets lost in the curve showing its orbit.


Next, here's the Sun and the terrestrial planets. You can still make out the Sun as a sphere and not just a point. The little tick mark at the Earth is because Solidworks shows tick marks at the center of all circles, and I drew a circle there to show the orbit of the Moon around the Earth. But even that orbit's too small to see at this scale.


Third, here's the Sun and all the planets. Zoomed this far out, even the Sun becomes just a point. You can really see just how far away the outer planets really are.


And finally, here's our own backyard - the Earth and the Moon. It kind of gives a sense of scale of just how far the Appollo astronauts went.


To me, this does help to put into perspective just how big the Solar System is. When you look at the farthest humans have ever traveled - to the Moon and back - and then see how even that distance gets lost in the immensity of the Solar System, it makes you feel tiny. And then when you consider the vast distances between stars and across galaxies - I just can't even wrap my head around it.

Anyway, have fun playing with the model.

Friday, March 9, 2012

Science and Engineering Indicators 2012

NSB LogoEvery two years, the National Science Foundation comes out with a report on Science and Engineering Indicators, detailing the state of science and engineering in this country, including public perception and understanding. The latest report is out at Science and Engineering Indicators 2012. Since 2004, I've written a short blog entry each time on that public understanding part (2004, 2006, 2008, & 2010). I'd always known that people didn't understand science well, but I was amazed at just how ignorant the population is.

Per my usual approach, I've reproduced some of the data from the section on public understanding of science. This year, however, I'm presenting the tables using an image format (I'm tired of fighting the formatting to make an HTML version fit). If you want an actual HTML version, you can find them here: Tables in HTML Format

This first table shows the U.S. compared to other nations. Honestly, the U.S. doesn't stack up so bad. Other than the questions that contradict a literal interpretation of Genesis, the scientific understanding of U.S. citizens is on par with those of other countries.

It's worth noting that the questions are organized a bit differently this year (separated between the physical sciences and the biological sciences). There was also a new question on cloning that hadn't been asked in years past. And two questions that were dropped a couple years ago to some attendant controversy have been brought back - the questions on the big bang and human evolution.

Science and Engineering Indicators Comparison Between Nations

This next table is something that had been included in previous years' reports, but I couldn't seem to find it this year. So, I made it on my own. Below that is a graph of that same data, making it a bit easier to see the trends. All in all, nothing much has changed since they started doing these surveys. The only two questions that have shown significant variation over the years are 'The universe began with a huge explosion' and 'Antibiotics kill viruses as well as bacteria'. The big bang question only appears to have changed significantly due to an exceptionally high number of correct answers for the first year for which data is provided (54%). Since then, it's held steady at about 1 in 3 people getting it right. The antibiotics question showed a trend of significant improvement for many years, but seems to have plateaued in 2006 at 56% - the next two reports after that show a slight decrease.

Science and Engineering Indicators U.S. Trends

Science and Engineering Indicators U.S. Trends

Since nothing much has changed, I'm just going to quote my conclusion from two years ago, instead of trying to think of something new.

"Just look at those results - around a quarter of Americans think that the Sun goes around the Earth, half don't realize that electrons are smaller than atoms, and half don't know that it takes a year for the Earth to go around the Sun! Keep that in mind whenever you hear people citing public opinion polls on the validity of concepts like global warming or evolution.

"It's always a bit depressing to see those numbers. It's hard to believe that the people of our nation are so ignorant. If there's one lesson to take away from these results, it's that we need to vastly improve our education system."


Selling Out