Science & Nature Archive

Friday, October 13, 2017

Understanding Evolution - The Big Picture of Geologic Time

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


Geological Time SpiralThe Earth is old. Very old. You may have heard that it's 4.5 billion years old. But 4.5 may not sound like a huge number. The United States federal budget is nearly $4,000 billion. That's a bigger number than 4.5 billion, and it's something the government deals with on a yearly basis. So how old can 4.5 billion years really be?

This is the problem. Us humans aren't very good at dealing with really big or really small numbers. We're good at dealing with things on a human scale, whether it's size or age. When it gets to things that fall outside that range, we have a hard time wrapping our heads around it.

One of the better analogies I've seen is to imagine compressing 4.5 billion years down into one year, and then looking at how long things would take at that time scale. (It's not a big difference, but let's use a 365 day year, not a leap year.)

Let's start off by calibrating ourselves to something we're used to. Count to 1 second. That's 150 years - twice an average lifetime. If you're close to 40 like me, you only need to count to a third of a second to account for your entire life. Learning to walk, ride a bike, drive, my first job, my wedding day, watching my daughter grow up and graduate from high school. That all fits into 0.3 seconds in our compressed timescale.

For a slightly longer calibration point, let's go back to a big milestone - 1 AD. Well, maybe that's only a big milestone in hindsight since nobody at the time was actually changing their calendars, but it's still a number we can relate to - 2016 years ago. In our compressed calendar, that would have been a mere 14.13 seconds ago.

Keep those numbers in mind - 0.3 seconds for 40 years, 1 second for 150 years, or 14 seconds for 2000 years.

Okay, so now let's start going through the calendar. Keep in mind that a lot of these time periods and dates aren't known exactly, so in our 4.5 billion year year, they may have really been a few days or even weeks earlier or later.


Days 1 - 41, January 1 - Febrauary 10 (4.5 - 4.0 BYA)
Protoplanetary DiscFor the first 40 days or so, there wasn't much recognizable as the Earth as we know it. The cloud of dust and debris around the sun would have coalesced into the protoplanetary disc, with clumps forming and sticking together, until eventually some of the clumps got big enough to be early planets. Some time during this period, when the 'Earth' wasn't quite as big as it is now, it collided with another early planet about the size of Mars. This was a gargantuan impact, throwing out huge amounts of debris, some which coalesced to form the moon.


Days 41 - 57, February 11 - February 26 (4.0 - 3.8 BYA)
There were still a lot of asteroids out there at this point, so for roughly another two weeks, the Earth continued to get pummeled by these bodies, in what's known as the Late Heavy Bombardment.

Some time during those two weeks, the very first life got started. It would have been comparatively very simple, and certainly single celled. It would have been the type of life now known as prokaryotes - the archaea and bacteria. For the next 5 months or so, until August 3rd, these archaea and bacteria will reign supreme as the only type of life on the planet. Of course, they were evolving - replicating, mutating, and adapting, but they remained prokaryotes.

By the way, there was no oxygen in the atmosphere, yet. All the bacteria and archaea alive at this point are anaerobic.


Day 122, May 2 (3.0 BYA)

CyanobateriaCyanobacteria evolved. Forms of photosynthesis had evolved much earlier, but cyanobacteria evolved a new, more efficient method that created oxygen as a byproduct. Since oxygen is so reactive, at first any oxygen these cyanobacteria created would have reacted with iron to make rust. There was a lot of iron for the oxygen to react with, so for a while yet, there still wouldn't be much oxygen in the atmosphere. Until...


Day 163, June 12 (2.5 BYA)

The Great Oxygenation Event. Once all the free iron on Earth had reacted with the oxygen that cyanobacteria were making, there was nothing left to capture that oxygen, and it built up in the atmosphere very rapidly. But because oxygen is so reactive, it was actually poisonous to many organisms that hadn't evolved to handle it (antioxidants are still important even for us oxygen breathers - we don't want extra, unaccounted for oxygen running amock in our cells). This probably caused the first mass extinction on Earth (though it doesn't get as much press as other mass extinction events since no multi-cellular life was involved).


Day 215, August 3 (1.85 BYA)

YeastEukaryotes evolved. Okay, if you don't read about biology as much as me (or actual biologists), you may not know what a eukaryote is. They're the types of organisms that have a nucleus in their cells, and store all their DNA in chromosomes in that nucleus. They also have 'organelles', specialized little parts inside their cells with specific functions. One of the most famous is mitochondria, so often referred to as 'cellular powerhouses' for making the ATP that powers the rest of the cell. Amazingly, the most likely way this happened was symbiosis - a type of bacteria that would eventually become the mitochondria living alongside/inside some other species.

By the way, we're eukaryotes ourselves, but it will still be a while before we appear in this calendar.


Day 301, October 28 (800 MYA)

The first multicellular life appeared. Colonies of eukaryotes (and prokaryotes) would have been around before this, but these were the first eukaryotes to nudge past the distinction between a colony of clones and a group of clones considered a single organism.


Day 318 - 325, November 14 - November 21 (580 - 505 MYA)

Cambrian ExplosionThis was the famed Cambrian 'Explosion'. But it barely counts as an explosion even in our compressed calendar. Remember that in reality, this period lasted some 75 million years. It was during this time that complex multicellular life evolved, and branched out into many of the major groups that are still around. Granted, most of these organisms would have looked fairly primitive, but there at least would have been organisms big enough for a person to see with their naked eye (assuming you had a time machine), and recognizable as animals.


Day 326, November 22 (485 MYA)

Early FishThe first vertebrates with actual bones evolved, the jawless fishes. These jawless fish would eventually give rise to all the vertebrates alive today.


Day 330, November 26 (434 MYA)

The first land plants evolved. These first plants wouldn't have been particularly impressive, probably looking more like lichens. But over the coming ages, they would evolve more and more traits that benefitted their terrestrial lives.


Day 336, December 2 (363 MYA)

CarboniferousWell, it's the second day of the last month of our Earth history year. And by now, the Earth finally looks fairly recognizable. There are sharks and other fish swimming in the ocean, insects crawling around on land, feeding on plants with stems and leaves. It's round about this time that the first tetrapods took to the land. Sure, there are many types of plants and animals that haven't yet appeared, but if you went back in a time machine, you wouldn't feel like you were on a completely alien world.


Day 340, December 6 (320 MYA)
This was when some species of animals split into two, one of whose descendants would go on to become the synapsids (which includes us), and one of which would go on to become the sauropsids, which includes lizards and birds. But at the time, those two sister species would still have looked practically identical.


Day 343, December 9 (280 MYA)
The first seed-bearing plants evolved.


Day 347, December 13 (225 MYA)
The first dinosaurs evolved sometime around now, and just a few million years later (no more than a day or two in this compressed calendar), the first mammals also evolved. For the time being, both remained rather minor groups of animals, with therapsids and non-dinosaur archosaurs being the most dominant land animals for now.


Day 349, December 15 (200 MYA)
A mass extinction occurred, killing off most of the synapsids. After today, the dinosaurs would diversify and come to dominate the planet. Mammals still remained small.


Day 353, December 19 (155 MYA)
Archaeopteryx - Berlin SpecimenThis may not be the most significant event in the history of the planet, but it's one I'm interested in personally - Archaeopteryx evolved. And since Archaeopteryx was either one of the first birds, or a very close relative of the first birds, it was right around this time that birds evolved.


Day 355, December 21 (130 MYA)
Flowers evolved. Just think about that. We're two thirds of the way through December, and the first flowers are just now appearing.


Day 360, December 26 (65 MYA)
K-Pg Impact EventA gigantic asteroid collided with the Earth, causing a massive explosion and cataclysmic devastation on the planet. With only a few exceptions, no land animals over 50 lbs survived. All of the non-bird dinosaurs went extinct, though plenty of bird species were wiped out, as well. In fact, species from pretty much every major branch of life went extinct - mammals, marine reptiles, insects, plants, fish, all the pterosaurs, etc. In the wake of this devastation, the remaining mammals would diversify to become the dominant large animals on land.


Day 365, December 31, 12:00 noon (6 MYA)
ProconsulOn noon of the last day of our compressed year, an ancient species of ape split into two species. The descendants of one of those species would remain in the forests, and eventually give rise to chimpanzees and bonobos. The descendants of the other would gradually move out to the savannahs, eventually giving rising to us - but not for a little while, yet.


Day 365, December 31, 11:48 pm (100,000 YA)
Modern humans appeared about a quarter of an hour till midnight. This gets a little into semantics on which of our ancestors you're willing to say are 'human' vs. 'pre-human', so give or take a few minutes here to allow for the fuzziness of this transition.


Day 365, December 31, 11:58:50 pm (10,000 YA)
The first human civilizations started some time around now.


Day 365, December 31, 11:59:25 pm (5,000 YA)
Early WritingThe famous ball in times square is about halfway through its drop, and humans have just developed writing.


Day 365, December 31, 11:59:46 pm (2,016 YA)
The year 1 AD.


Day 366, January 1, 12:00 midnight (Now)
And now, at the stroke of midnight, we've reached the present day.


So, it may seem like things really started accelerating there towards the end of the year, but that's mostly due to our own bias of being more interested in those particular events, and the bias of the geologic record in containing more younger fossils and artifacts than older ones. Just as much was happening 100 million years ago as a few thousand years ago, just without us humans around to see it.

And even if it seems like a lot was happening in a few mere days, recall what these time scales really mean. On this condensed calendar, a human lifespan is less than a second. The last two millenia were a mere 13 seconds, and all of humanity's time on Earth is no more than a few minutes*. Start counting out seconds, trying to imagine entire generations passing with each count, to get an idea of just how vast these timescales are. Then, try to imagine continuing that count for a whole day, and just how much time that really represents. And then, think back to what you were doing a year ago, and how many seconds have passed since that moment, and maybe you'll start to get an idea of how long 4.5 billion years really is.

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*To be fair, most species haven't been around very long on a geologic scale, even if humanity is a bit on the young side. Species last maybe a million years or so before either going extinct, or evolving into something else. Life is constantly changing and adapting.

Image Sources:


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

Monday, August 21, 2017

Eclipse Watching

I was all set to break out my daughter's Astroscan telescope with the sun viewing screen for the eclipse. But when I went to go grab the sun viewing screen last night, it wasn't where I thought it was. And for a variety of home improvement & other reasons, our house is a bit of a mess right now, so further searching for the screen proved fruitless. But, at least I still had the telescope itself and the lenses. And I happened to come across a creative idea on Google this morning - a homemade sun funnel (directions from NASA). So I took a bit of an early lunch break, ran to Walmart, and bought everything I'd need to make it, then came back, and with the help of a co-worker (I have a broken foot right now and didn't want to go tramping around the shop), got it all put together just in time for the eclipse. Here are a few photos of what we saw here in Wichita Falls - the first showing our setup, the second at the max obscuration, and the third a little later, but with my camera's brightness adjusted to make the sun spots more clear.

Eclipse Viewing Setup
Eclipse at Max Obscuration for Wichita Falls
Eclipse Viewing Setup
(Click on images to embiggen.)

Since we're engineers, we also couldn't resist taking measurements. We pulled out a tape measure, and took the following measurements from the image projected on the screen:

Eclipse 2017 Measurements in Wichita Falls

Assuming the same diameter for the moon and sun, those measurements correspond to a max obscuration of 82.5%. According to NASA, max obscuration where we were watching was 77.44% - not too bad for our less than precise methods.

Anyway, it was a nice little diversion today at work, going out every half hour or so to check on the eclipse's progress. One guy's wife and son even showed up to take a look. And the homemade sun funnel worked great - though I already have ideas for minor improvements before the next eclipse.

Friday, June 16, 2017

Evolution in Action - Visualizing Bacteria Evolving Antibiotic Resistance

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


e. coliNot too long ago, I came across a question on Quora, Evolutionary biologists usually say that organisms adapt to their environment. Does this not contradict Darwinism?. It seemed like a good opportunity to explain how natural selection adapts organisms to their environments, and especially to use a recent experiment involving e. coli. Here's what I wrote, with some very minor edits.

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I'm going to assume that by 'Darwinism', you mean natural selection. Organisms adapting to their environments is pretty much textbook natural selection, but let's go through an example to see what this means.

There was a very interesting experiment/demonstration last year involving bacteria and antibiotics. A team of researchers from Harvard Medical School and Technion - Israel Institute of Technology made in effect a giant petri dish - a rectangle 2 ft x 4 ft. The unique aspect of this petri dish, besides its size, was that it was divided into regions with varying concentrations of an antibiotic. Either end of the rectangle was free of antibiotic. The next region in had the minimum concentration to kill the e. coli bacteria that were the subject of the experiment. Each subsequent region moving in increased the concentration ten fold, until the center region, which had a concentration 1000 times higher than what would normally kill e. coli.

e. coli experiment setup
Image Source: Screen Capture from Video Shown Below
(Click to embiggen)


So, the researchers seeded the antibiotic free ends with e. coli, and then let them grow, taking periodic photos of the petri dish, and combinging them all into a time lapse movie. I'd really recommend watching the whole thing. It's really very interesting, with more explanation than what I've provided here, and only 2 minutes long.


So, let's take a closer look at one instant to see what exactly is going on. At one point, the tray looked like this:

e. coli experiment screenshot 1
Image Source: Screen Capture from Video Shown Above
(Click to embiggen)


So, the antibiotic free ends are completely colonized by bacteria. The two regions with the lowest concentration of antibiotic have just begun to be colonized. There are several small resistant colonies, and you can see where each one of those colonies got their starts. What happened was that the original e. coli, with no antibiotic resistance spread across the agar until they hit the antibiotic. Since they weren't resistant, that was as far as they could go without dying. But those e. coli kept on living and reproducing, with mutations appearing throughout the population. In bacteria that just happened to be at the boundary of the antibiotic, who also happened to acquire just the right mutations to make them resistant to the antibiotic, they now had a whole new environment opened up to them and their descendants.

Notice that there's really no pattern to where those colonies got their starts. It was basically random, because mutations are random. No bacteria were trying to evolve. No bacteria were attempting to figure out a strategy to survive the antibiotic. Bacteria don't even have brains to try to do any of that. It was just whatever bacteria happened to be lucky enough to acquire the appropriate mutations by chance, an error at the chemical level when copying DNA.

Once those first resistant bacteria entered this new region, they spread. Then, once they hit the region with 10x the antibiotic concentration, they were contained again, until a few more bacteria happened to acquire the proper mutations by luck, and had a new environment opened up to them and their descendants. This repeated, until the bacteria were eventually colonizing the region with 1000x the concentration of antibiotic that would have killed the original e. coli that seeded the plate:

e. coli experiment screenshot 2
Image Source: Screen Capture from Video Shown Above
(Click to embiggen)


So, these e. coli were adapting to their environment. However, it wasn't any conscious intent, or Lamarckian type of use and disuse. It was random mutations creating variation in the e. coli populations. Whichever e. coli happened to be lucky enough to have mutations to survive the antibiotic were the ones that thrived. Any e. coli that weren't lucky enough to have those mutations were limited to their existing environments.

This experiment had a pretty strong selection pressure with the antibiotic, but the same principles are at work in nature with other selection pressures. Whatever individuals happen to be lucky enough to acquire by chance the mutations best suited to an environment will be the ones that have the most offspring, increasing the frequency of whatever mutation that benefited them. Multiply this over generations, with natural selection 'ratcheting' additional mutations, so that the population becomes better and better suited to the environment. That is what is meant by saying that organisms adapt to their environment.

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More info on the e. coli experiment:

Image source: Wikimedia Commons


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

Wednesday, April 5, 2017

How Bad are Unpronouncable Chemical Ingredients in Food?

I ran across a new line of frozen lunches the other day, SmartMade by SmartOnes. One of the key selling points on the box is 'Made with real ingredients you can pronounce'. This seems to be a common attitude among people who don't understand chemistry as well as they could. But how bad for you are foods made up of all these strange sounding chemicals?

For example, here are the ingredients to a treat I eat nearly every weekend:

Ingredients for Weekend Treat


And here are the ingredients to an energy drink I drink nearly every day:

Ingredients for Energy Drink


Should I be worried about all those chemicals?

.
.
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Okay, it was a trick question. I cropped those images to hide what types of food they were. Here are the original, uncropped images, made by James Kennedy, showing what the foods were (click to go to source):

Egg Ingredients


Coffee Ingredients


Mr. Kennedy has a whole series of these types of images (as well as posters of them for download and for sale).

The whole point is that everything we eat is made up of chemicals. Living things, especially, are this whole complicated cocktail of chemicals. And most of those chemical names sound very foreign to those of us who don't study them on a regular basis. But that doesn't make them dangerous.

When certain chemicals are added to processed foods, it's done in a very controlled way. Instead of the cocktail of chemicals you get from natural foods, they're adding very specific ingredients, in tightly controlled quantities. There's nothing inherently dangerous about not being able to pronounce those chemicals, unless you think we should be avoiding eggs because they contain arginine and eicosatetraenoic acid.

Tuesday, March 28, 2017

Recommended Reading - Evolution

Tree of LifeI write quite a bit about evolution, but if you're new to this site or the subject of evolution, it might be a little overwhelming to just browse through the site and read the articles at random. So, this page offers some recommendations on entries to start off with, to give you a good foundation before moving on. I very strongly recommend reading the first four essays in the Foundation section. And if you happen to doubt evolution for religious reasons, and have seen presentations or read material from some of the more prominent creationists (e.g. Answers in Genesis, Kent Hovind, Discovery Institute, etc.), then I'd also recommended the entries from the 'Responses to Misunderstandings and Creationist Arguments' section.


The Foundation


Exploring Other Evolutionary Concepts


Responses to Misunderstandings and Creationist Arguments

The first two of these are probably the most informative. They're also rather long. I took the time to respond in decent detail to a myriad of misunderstandings and misconceptions about evolution. The third is offered as a kind of example of the bad arguments many creationists use.


Further Reading, This Site

I've written quite a bit more about evolution and creationism. You can find most of it in the following archives.

  • Science & Nature Archive
    Evolution will be mixed in here along with a variety of other science topics. These entries tend to be more straight science.
     
  • Skepticism, Religion Archive
    These tend to be focused on skepticism, so the evolution related articles mixed in here will be more in response to creationists.
     
  • My Quora Profile
    Okay, this isn't exactly this site, but I do write a bit about evolution on Quora, and only adapt some of those answers for this blog. Evolution related answers will be mixed in with all my other Quor answers.
     


Further Reading, Other Sources

I'm actually going to link to a Quora answer I wrote with those types of sources. You can also see what others suggested.

Image Source: DavidPratt.info

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