This post is for my kids and anyone else who likes bugs (like me).
The other morning, in my Google news feed, I got an article about a recent fossil find that they are dubbing the world’s oldest bug. (Note for grandmas and anyone else who is not a kid, the blue underlined text means you can click on it and you'll go to a webpage which has more details about the topic. Also you can click on the images to magnify them or click to their source.) The article included a photo (above) of the proud owner of that “oldest bug” tag. Cute little thing isn’t it? Looks just like the millipedes you see crawling around under a rock or log that you turn over in your yard. Scientists estimated the age of the fossil at 425 million years old using zircon dating according to the article.
Those millipedes were not always such cute critters… one of the descendants or distant cousins of the little guy above became gargantuan and truly frightful. Something over 2 meters long and bigger than the average duuude, called Arthopleura, lived between 345-295 million years ago (during the Carboniferous period when the world was much warmer and moister and more oxygenated allowing gigantic bugs to rule the world). Check out the gray size comparison image in the lower right corner. At least they were vegetarian. We think.
And there is at least one arthropod that was even bigger than Arthropleura… a creature commonly called a sea scorpion whose biggest species was recently found and named Jaekelopterus rhenaniae. This monster is believed to have grown to a length of 2.5 meters. And this one was a predator.
I don’t know about you, but the first thing I notice about the little millipedes and all the other monsters below it (including us humans), is the segmented nature of the body plan – notice that the millipede looks like it is made up of repeated little rings, one after the other. I wrote about segmented body plans like ours in a previous post.
Here is what I said about segmentation:
… we humans share a basic developmental program with lizards, frogs, fish, lamprey, on down to segmented worms…. We all have a segmented developmental program - those segments are easy to see in things like worms and insects and other organisms which have - well - segments or repeated units making up their bodies (think of a lobster’s tail). Our own segmentation is harder to see - it is internal - and evidenced by our vertebra. When you fillet a fish, the beautiful segmented, repeating pattern becomes obviously clear. The gene, the protein molecule(s) that control the segmental development of everything from segmented worms to humans are called Hox genes. There is a similar high degree of evolutionary conservation in Hox genes as for Cdc25. Furthermore, humans and many vertebrates have multiple (four) clusters of Hox genes (Hox A, B, C and D), and each cluster is composed of a series (13) individual Hox genes (named in true Suessian fashion as HoxA1 through HoxA13, etc)…
There are even more primitive creatures with segmented body plans than millipedes, animals such as velvet worms, and as I mentioned in the previous post above, the phylum annelida which includes the familiar earth worm.
The earliest known fossil velvet worm dates back to about 500 million years, in the Burgess Shale formation of Canada. And the earliest known annelids date back about 518 million years ago. So we’re talking oooold…
Let’s put these dates into some kind of perspective. Say that the long horizontal line below represents 10 billion years, with the distance between each vertical marker representing 1 billion (or 1,000 million) years, and zero always being closest to us now, today. Anyways, along with the long bar for 10B years, I also have a short bar labeled “zoom” that we will magnify further down below – but ignore it for now. I have also labeled several key milestones in red letters, starting from the oldest (A) always to the farthest right, and younger events successively to the left.
Now 10B years ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (1B years each)
F E D C B A
|____|
zoom
Only for this blog, I’m going to use “B” as an abbreviation for billion, and the normal “M” for million (or mega) and “K” for thousand (or kilo). The formation of the universe began approximately 14B years ago (at A off to the right and about 4 units towards the edge of the page at our scale). The solar system including the earth (B) is believed to have formed about 4.5B years ago from a protoplanetary disk perhaps similar to those photographed by the Hubble telescope in the Orion Nebula. The earliest known evidence of liquid water (C) on the surface of the earth is about 4.3B years ago. The earliest known fossil evidence of life, probably bacteria (D), is about 3.5B years ago. The earliest known eukaryote (E, cells with a nucleus) is controversial but is somewhere around 2B years ago. The oldest known fossil of a fungus (F) is about 1B years old.
Now, let’s zoom into that 1 billion years closest to us in the above timeline, meaning that short bar labeled “zoom”. We are now going to magnify that short bar by 10X below, with each marker now representing 100 million years (above, each marker was 1000M years or 1B years). Ten of those units of 100M years sum up to 1B years as shown below:
Now 1B yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (100M yrs ea)
K J I H G F
|____|
zoom
About half way is where we believe annelids (G, segmented worms) and onychophoran (H, velvet worms) originated, and a to the left of that (4.25 million years ago) is where our oldest known millipede (I) sits. The oldest known lizard (J) is at about 240 million years ago. That is about when the first known dinosaur fossil (J) is also known from the fossil record. The first known mammal, Juramaia sinensis, (K) scurrying under the thundering feet of the dinosaurs was about 160 million years ago.
Let’s keep going and zoom into that first 100M years in the above timeline, expand that out again and now with each marker being 10M years – here you go:
Now 100M yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (10M yrs ea)
N M L
|____|
zoom
About half way is where dinosaurs (L) are believed to have died out due to a massive comet or asteroid impact known as the cretaceous-tertiary event, about 66M years ago. The earliest known primate fossil (M) is about 55M years old. The earliest fossil horse, eohippus (N), is about 50M years old.
If we zoom into that first 10M years, with each marker being 1M years, this is what we see:
Now 10M yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (1M yrs ea)
R Q P O
|____|
zoom
The earliest Australopithecus (O) is about 4M years ago. Homo habilis (P) was about 2.4M years ago. Homo erectus (Q) approximately 2M years ago. Homo antecessor (R) about 1.2M years ago. This is a very random selection of a few of the hominid fossils discovered over the past century. The evolutionary history of humans is far more complex than a simple climb up a ladder or even a tree - some have suggested a tangled shrub as a better visual representation of the human evolutionary past, and whether it goes through each of the species I have selected for this timeline is not certain by any means. We currently believe that there was tremendous overlap between species in time and place.
Zoom in again to that first 1M years (I can’t stop zooming!!):
Now 1M yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (100K yrs ea)
U T S
|____|
zoom
H. heidelbergensis (S) was from about 700K years ago. H. neanderthalensis (T) was from about 400K years ago. And finally, H. sapiens (U) emerged from Africa about 300K years ago.
That previous two blocks of time encompasses all of the known fossil record of hominid evolution. The next block will encompass all of the evolutionarily modern human record. So let's zoom in again to that first 100K years of the previous timeline:
Now 100K yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (10K yrs ea)
X W V
|____|
zoom
Colonization of Australia (V) by H. sapiens about 60K years ago. The famous Lascaux cave paintings (W) are estimated to have been done about 20K years ago. Earliest metallurgy and domestication of various animals (X) about 10K years ago.
Zoom in further to that first 10K years:
Now 10K yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (1K yrs ea)
Z Y
|____|
zoom
Earliest domestication of horses (Y) about 6K years ago. Earliest use of gunpowder (Z) about 1K years ago.
Zoom in again to that first 1K years:
Now 1K yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (100 yrs ea)
h g f e d c b a
|____|
zoom
Invention of the astronomical clock (a) about 900 yrs ago. First mechanical clock using an escapement mechanism (b) about 700 years ago. Black death and Renaissance (c) about 600 years ago. Circumnavigation of the world (d) about 500 years ago. Kepler measures the distance from the sun to various planets (e) about 400 years ago. Linnaeus catalogs organisms by genera and species (f) about 300 years ago. Fourier predicts greenhouse effects (g) about 200 years ago. Spanish flu pandemic kills ups to 100M (h) about 100 years ago.
Zoom in again to that first 100 years:
Now 100 yrs ago
|____|____|____|____|____|____|____|____|____|____|
0 1 2 3 4 5 6 7 8 9 10 (10 yrs ea)
q p o n m l k j i
|____|
zoom
Alexander Fleming discovered the first antibiotic, penicillin (i), about 90 years ago. World War II (j) started about 80 years ago. Bell Labs invented the transistor (k) about 70 years ago. Yuri Gagarin was the first astronaut in space (l) about 60 years ago. Hawking and Penrose proved that the universe began as a singularity (m) about 50 years ago. WHO used vaccination to eradicate small pox (n) about 40 years ago. The launch of the Hubble telescope and Voyager space craft photograph of the earth as a pale blue dot (o) were about 30 years ago. Wikipedia launched (p) about 20 years ago. The first replicating synthetic bacterial cell (q) was about 10 years ago.
For more fascinating milestones check out this website:
That last “zoom” bar represents 10 years – plus or minus a few years representing the approximate age of my kids – and we could populate that expanded 10-year timeline with milestones in their lives: when they were born, when they first said “dada” (that’s me) or “ball” (I think that was still me). When we first left them at the daycare, or when we moved to the new apartment or the new house…. I hope you get the idea. We casually throw around numbers like millions of years (or dollars, or whatever), but rarely do we have any sense of scale of what a million or a billion really are.
But there we have it – a zoomed in and zoomed out timeline which provides some form of context for the times we are talking about for these bugs. About 425 million years ago, we know millipedes were amongst the first land animals that walked the earth among some of the earliest land plants. One of those bugs died and was buried in a way that, by a one in a bazeeellion chance, managed to be preserved well enough that this soft-bodied creature is recognizable to us today. The earliest segmented worm (annelida) fossils date to about 518M years in age. Hopefully those zooming timelines gave you an idea of just how much time we are dealing with.
Over those half a billion years, things as simple as worms have evolved into things as complex as dinosaurs and humans. But… at the same time some of those ancient ancestral organisms have also passed that same simple body plan to a wide range of modern wormy descendants that live in an incredibly diverse range of environments.
Those animals today, from the annelid worms to the most complex vertebrate mammals (pick your favorite), all share the segmented body plan first evolutionarily devised by those simple worms and millipedes half a billion years ago. You just have to look at the fossilized remains of a gigantic sauropod like the Apatosaurus to the left and you can easily recognize the repeated segments of the vertebrae.
But here’s the even cooler thing. Over that same half a billion years, the information contained in certain genes within those cells, the genes that control the development of that segmented body plan, have also remained recognizably similar (at the same time that whole new genes with new functions have evolved to support things like a conscious brain that can plan and conceptualize and solve problems and paint and sing and choreograph a musical).
We’re talking about the Hox genes, which I mentioned in my previous post quoted above, that are seemingly frozen in time. But here’s the thing – the conservation of Hox genes is not preserved in the sequence of the DNA. That has been modified and changed enough that we can’t really recognize the sequence if we line them up side by side. But it is the sequence of the amino acids that the DNA encodes, which remains, recognizably similar (though again it is not from the sequence of amino acids, but the kinds of amino acids that are used).
How does all that work?
Well, you know that DNA contains the code for making proteins. And proteins are made of amino acids, right? And we know that DNA has four letters, A, G, C, and T, that make up the genetic code. The letters are an abbreviation for the name of the chemical that make up the chain of DNA: A = adenine, T = thymine, C = cytosine, and G = guanine. The DNA code is a long string of those four letters which effectively spells out the protein you are trying to make, say a Hox protein.
Also, there are 20 amino acids which are used to make proteins. Any given protein is a long chain of a very specific sequence of those 20 amino acids. And there are 20 letters, each letter representing one of the amino acids, such as M = methionine, etc.
So how does the DNA with only four letters encode a protein made of 20 amino acids?
It’s pretty cool – each three letters of DNA spells an amino acid. Here’s a chart from Wikipedia that translates the DNA triplet code into each amino acid.
What is especially important to our story is that the amino acids also fall into several categories of chemical properties – in this chart they highlight 4 properties and divide the amino acids into those four as different colors. There are 9 amino acids that have a nonpolar property (yellow). There are 7 amino acids which are polar (green). Four are basic (blue). And two are acidic (red).
So, here’s the thing. Over time, mutations occur that change the DNA. Those changes may or may not change the amino acid. For example, if you look at the chart, there are two DNA codons, TTT and TTC, which encode the amino acid Phenylalanine (abbreviated F). So if there was a mutation in a gene where a TTT was changed to a TTC, there would be no effect on the amino acid sequence, and therefore no change to the protein. That is called a silent mutation.
But – if that TTT were mutated into a TTA, then your amino acid F would be changed to a leucine (L). Depending on the protein, that may or may not have a big effect on the final protein – and the odds are somewhat with you since both F and L are non-polar amino acids (they have the same property).
Here's a second but – if that TTT were mutated and became TCT, you would change the amino acid from F to S (serine). Now not only have you changed the amino acid, but the property is also different, and instead of a non-polar amino acid, now you have a polar amino acid with very different properties than before.
So although the actual sequence of the protein's amino acid sequence is important, the properties of those amino acids may be even more important because those properties affect how the final protein functions.
Now let’s look at a part of the amino acid sequence for a bunch of proteins all lined up in horizontal rows so we can compare their sequences to each other. Each row of colored letters represents part of the amino acid sequence of a protein (the black letter/number code on the left is the database identifier for each protein from a certain species). Unlike the previous Wikipedia table, the color coding is slightly different in that green = polar amino acids, red is non-polar, blue = acidic, and pink = basic.
In the upper part of that chart you see parts of the proteins where the colors and often the letters of the amino acid sequences align pretty well, and down below where often neither the colors or the letters line up. These are short sections of the Hox protein's amino acid sequences from various species from worms to humans and all kinds of animals in between.
The part that lines up well among all the different genes is the most important functional part of the Hox genes called the Homeobox sequence – and the key function of that part of the protein is to bind to a certain sequence of DNA near a gene and to turn that gene on or off:
The other parts of the Hox genes that do not line up well do different things, as you expect a Hox gene for a worm to be somewhat different than the Hox gene for a human.
There you have it – the Hox gene is highly conserved despite half a billion years of evolution separating us from a worm – but we can see from the colors that there is a high degree of conservation in the Hox gene from one species to the other. By the way, the code for human HoxA6 protein is NP_076919.1 and for different Hox genes in a velvet worm the codes are CCK73376, 75 and 74.
I’ll let you find those and see where the amino acid sequences align well and where they don’t.
Looking at protein sequences is nowhere near as obvious as looking at a spinal column and recognizing a similarity between the vertebrae and the segments of a worm – this is a lot more subtle, but also more interesting.
Since segmented worms and humans and everything in between have Hox genes, we are confident that over half a billion years ago segmented worms burrowing in the mud on ocean bottoms also had Hox genes. We share a basic segmented architecture with millipedes and other creatures descended from those annelids, and we also share similar Hox genes that control that segmention like millipedes do today. Same with leeches and lampreys and fish and sharks and lizards and mice and apes… and us. We have preserved, in some slightly distorted but recognizable way, the fossilized remnants of those ancient Hox genes in each of our cells – a gift from our wormy ancestors many hundreds of millions of years ago.
So thank a bug today.
I hope you enjoyed the post today. If so, please pass it on. Also let me know what you enjoyed and what you didn't.
And stay safe and keep masking and distancing - we still have a ways to go with COVID-19 so be patient. Maybe write a blog to help you stay sane like I am. I'll read yours if you read mine. ;)
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