Monday, August 26, 2013

Evolution For Dummies - Part 4

Welcome back to Evolution for Dummies, a multi-part series on the sometimes thorny topic of The Theory of Evolution.

What I’ve told you about so far (in Part 1, Part 2 and Part 3), is that you can use family trees to follow lines of inheritance - or lines of gene transfer - from offspring, back through time to the common ancestors that gave rise to groups of relatives, or groups of animals. I've told you that populations are immensely important and that they arise quite rapidly - even in species such as the human, in which the individuals don’t produce large numbers of offspring very quickly (humans have what we refer to as a long generation interval). And that it is in populations that genetic changes occur, and those genetic changes provide for diversity in characteristics such as morphology – shape, size, muscularity, skin color, eye colour, male-pattern baldness, etc., etc. I’ve also given you a primer on how to interpret phylogenetic trees to identify the interrelationships between animals and to trace the common ancestors of entire groups of animals.

So moving on. In this Part, we'll try to answer the big question. Why is this important? Why do we care?

So what??!! 

To get at this question, I'm going to introduce you to animal models. 

First, though, I should explain that there is a subtle difference between what my youngest daughter might think is meant by animal models - shown below - and what biologists mean by animal models.

Model animals. Not very useful in biology.

In the context of biology, when we talk about animal models, what we generally mean is, rather than performing our experiments on actual human beings, we use some other appropriate animal - such as laboratory mice, for example. These are used as surrogates on which we can perform our experiments to study biological processes, and then from those experiments we can make inferences about how those biological processes may occur in humans. I already mentioned the laboratory mouse, but there are many model species you might hear about in the news, including, but not limited to, pigs, rats, frogs, zebrafish, worms, and even fruit flies. 

Now, there are some very valid ethical considerations when using animal models for biological experiments. The welfare of animals used in research is extremely important and, in addition to ethical reasons, there are good scientific, legal and economic reasons for making sure that animals are looked after properly and used minimally. I won't go into the reasons here, but I will say that scientists, in general, are very aware of these considerations and, in fact, must jump through all kinds of hoops to justify the use of animal models in every single experiment they propose. Every scientist in The USA (or, indeed, in most of the world) is aware of the principle of "The 3 R's" - and it is worth laying those out as they are the foundation of good scientific endeavor:

1. Replace the use of animals with alternative techniques, or avoid the use of animals altogether.
2. Reduce the number of animals used to a minimum, to obtain information from fewer animals or more information from the same number of animals.
3. Refine the way experiments are carried out, to make sure animals suffer as little as possible. This includes better housing and improvements to procedures which minimize pain and suffering and/or improve animal welfare.

So, with that out of the way, in the context of this series of posts, what I want to stress is that the study of evolution validates our ability to study model animals to understand many aspects of human biology. Things such as how we are made, how the processes that determine how we are made can go wrong to cause birth defects and disease, and how we respond to our environment and to various stressors such as drugs and poisons. And this word "validates" is important. 

This is because, actually, for centuries, man has been carving up animals and noticing the similarities and differences between them and/or the differences and similarities between those animals and us humans. An ancient greek hunter, for example, might have noticed how a deer heart looked similar to the heart of a duck. This sort of observation would have been the beginning of what we now know as comparative anatomy - "this looks the same, this looks different".

The hearts of a deer (left) and a duck. Even an ancient Greek hunter would have recognized the similarities
In fact, without delving too deeply into the history of the study of evolution, even ancient Greek philosophers were trying to work out the interrelationships between animals, and it was Aristotle – back some two and a half thousand years ago -  who came up with the idea of "The Great Chain Of Being", which, although imperfect by modern standards, set the stage for many other thinkers who followed. He also identified the heart as the most important organ of the body, the first to form according to his observations of chickens in their eggs. He described the heart as being the seat of intelligence, motion, and sensation. Perhaps a little overstated, but there is no arguing the importance of the heart! 

Another Greek, a man called Claudius Galen, lived back in the second century AD and was (among other things) a physician to gladiators! He advanced the field of comparative anatomy by performing dissections on animals such as monkeys and pigs. This looks the same, this looks different. Interestingly, even though Galen's work was ultimately shown to be - shall we say - naive, it was so convincing that it remained effectively unchallenged until well into the Renaissance, over 1,000 years later!

Galen's famous (and not quite accurate) sketch of the heart

Leonardo da Vinci (1542 - 1519 ) was famed for his drawings of comparative anatomy. This looks the same, this looks different:

Leonardo da Vinci's legs (actually, they are the legs of a dog and a man)

But now we have entered an era of fascinating discoveries about the molecules of life. We can look at - and study - DNA, proteins, and the interactions occurring within and between individual cells, and now we understand the interrelationships between animals based on these minutiae, rather than on just "this looks the same, this looks different". So we now know that the reason an ancient Greek hunter might have noticed how a deer heart looked similar to the heart of a duck was because, actually, they are constructed throughout embryonic development in very much the same way, using very much the same genetic programs. We see high levels of conservation (meaning the percentage of genes that are identical, or the degree of 'identicality' between genes of different animals) in those genes that are utilized in the embryonic development of a human and of many other species.

To illustrate this point, I have another question for you. Would you think that this creature - the lowly fruit fly, the annoying little pest that buzzes around your overripe bananas in the summer - would be useful as an animal model to inform us about the embryonic development of a human heart, for example?
The fruit fly (Drosophila melanogaster)

Well, in fact, many of the genes that are known to be important for the proper development of a human heart were first identified in a fruit fly! A gene called Tinman, for example, was discovered in the fruit fly and if this is rendered non-functional in the fly then it doesn't develop a heart and dies. Hence the name Tinman, who was the character in the Wizard of Oz who didn’t have a heart. If the equivalent gene is rendered non-functional in humans, the result is also serious cardiac defects.

To give another illustration of genetic conservation, below is a photograph of a chicken heart taken at a stage of embryonic development just before hatching. What is important is that it is colored by two highly specific reagents - for the purposes of this post, let's just call them "dyes" - to color one type of muscle red and another type of muscle green. Actually, these dyes are highly specific biological molecules called antibodies that recognize a minute portion of a protein expressed inside the individual cells that form chicken muscle. The muscle "dyed" red is the beating heart muscle - called myocardium - and the muscle "dyed" yellowy-green is the vascular smooth muscle in the arteries.

Earlier in development, the chicken heart looks like this, 

but we can still see that the muscle is dyed by these highly specific chicken muscle markers demonstrating that the proteins are already being expressed in the heart.

Now when I use these exquisitely specific chicken muscle dye molecules, these antibodies, on the heart of a shark, we see that they bind to exactly the same compartments of the heart. They dye the shark myocardium red and the shark vascular smooth muscle yellowy green.
Shark heart

What this means is that minute portion of a protein that exists within the cells of the chicken heart also exists within the cells of the shark heart. And perhaps you will already know (but I'll explain anyway), proteins are the product of genes, so this is a very effective demonstration of genetic conservation. It shows that in spite of the millions of years that separate sharks and birds - you would actually have to travel back in time about 400 million years to find the common ancestor of sharks and chickens - these two species, that now lie as contemporaries at the tips of the tree of life, use very much the same gene program to construct a heart. And it also suggests that the common ancestor of sharks and birds had a heart constructed by very much the same genes and passed those genes on down those lines of gene transfer - those lines of inheritance - to both populations derived from its offspring. Populations that gradually gave rise to sharks and birds.

And, in fact, these same highly specific chicken muscle labels work in the zebra fish - this is a zebrafish heart. 

Zebrafish heart

And, these same highly specific chicken muscle markers work in a mammalian model, the mouse.

Mouse heart

And, while I don't actually have an image to show you, I can tell you that experiments with biopsies have shown that these same highly specific chicken muscle dyes work in the human heart, too - again suggesting that the common ancestor of sharks, fish, birds, mice and even humans possessed a heart constructed of very much the same genes and proteins, driven by very much the same genetic program.

To labor the point about why this might be an important observation, I'm going to show you a very particular region of the heart. The region of the heart where these two colors meet - the region where the beating myocardium (dyed red) connects to the smooth muscle of the arteries (dyed green) - is known as the cardiac outflow tract. It is a kind of obvious term, as this is where the blood flows out of the heart - hence "outflow tract". This is where the blood leaves the heart and flows out into the vascular system. And - importantly - in humans it is the region of the heart that is most commonly affected by congenital heart defects.

I can show you this region in a little more detail by taking an idealized drawing of a heart - and cutting it open

Idealized cartoon of the heart

I know this picture is in 2 dimensions, but just imagine it is in 3D and I am going to take a machete and slice the heart right down the middle - down the plane of the screen - and then remove the front half. Like this:

The heart - cut in half

Then, by making another cut just a few fractions of a millimeter behind this first cut and removing the back of the heart, we get what is called a section. It is an extremely thin slice of the heart, often only a few thousandths of a millimeter thick.

"section" of the heart

The outflow tract of the heart is shown below, highlighted by the superimposed circle, first in a full section, and then in a zoomed-in, detailed image just below it.

The circle highlights the outflow tract of the heart

I can now dye that section of the heart with those highly specific chicken muscle dyes again. What you can see is an overlap between the beating myocardium and the smooth muscle of the arteries - where these two types of muscle form a junction:

The outflow tract of the heart - now in pretty colors
In 3D, this would be like the connection of two pipes, or the connection between a hose pipe and a spigot, where one fits snugly just inside the other. The red myocardium effectively forms a collar around the green "pipe" of the artery.

Well, this dude I know - while doing his post-doctoral research - was able to show in 48 different species, including representative species of sharks, fishes, lungfishes, amphibians, reptiles, birds and mammals, that this portion of the heart has extremely high levels of genetic conservation in the way it is constructed through embryonic development. This means that we can effectively study the development of the heart and the way the outflow tract is constructed in any one of possibly thousands of species. And by identifying any subtle differences in the way these various species connect the heart to the arteries, we may be better equipped to recognize and address the possible ways by which the human gene pool may occasionally get things wrong and produce a defective heart.

Evolution has allowed this, because the interrelationships between animals means that we don't have to redesign the wheel every time we investigate a new animal species. We humans have known about these similarities for many centuries, but only in the last few decades have we been able to work out why these similarities exist. Evolution has validated much of that previous work and now validates the much more effective application of the "Three R's". We can certainly Replace the use of fluffy animals with alternative, less sentient animals, such as zebrafish, for example. We can thus Reduce the number of fluffy animals used to a minimum and Refine the way experiments are carried out, by utilizing frogs, or snakes, for example.

I'd like to finish this post by introducing you to a truly amazing person whose work inspired me to go on and learn more about evolution and embryonic development.

Helen Brooke Taussig

This is Helen Brooke Taussig, who pretty much on her own began the scientific discipline now known as pediatric cardiology. At Johns Hopkins hospital in Baltimore, she pioneered surgical interventions that have saved the lives of countless children born with a condition known as blue baby syndrome and she was very influential in the drive to have the drug thalidomide taken off the shelves. Sadly, she died in a car accident in 1986, just short of her 88th birthday, but she was still performing research even in retirement - trying to better understand the impact of genes and genetic defects on the way a baby’s heart grows during embryonic life. She had a profound understanding about how evolution has fashioned the human heart and how the study of the heart in other species can help us better understand the way a human heart is formed and how that can go wrong to cause conditions such as blue baby syndrome. After her death, two highly regarded cardiologists, Edward Clark and John Opitz, wrote that she understood how:

everything that develops has evolved; that nothing can occur in development, whether normal or abnormal, that has not been made possible by evolution; and that all analysis of birth defects is the study of evolution in the clinic or at the bedside”.

And I should stress here that the word “develops” here refers to embryonic development – the way an embryo grows from a single cell through to an independent, fully formed animal.

So - in summary - what I hope I have impressed upon you in this series is that common ancestry or common descent is a central theme of evolution and is applied by tracing back lines of inheritance or gene transfer through often millions of generations to infer the interrelationships between animals. You can't draw a straight line between any two populations of animals or any two modern species - you have to trace the lines back through the parents, the grandparents, the great grandparents, and so on, until you find the common ancestor.

I've told you that although there are some cases of rapid evolution, as we humans have managed with domesticated dogs, more usually natural selection works over eons - millions of years - and occurs as a result of genetic diversity within populations.

You should now be more familiar with family trees and how phylogenetic trees are constructed by assessing characteristics such as morphology and the similarities and differences in genetic information.

And, using embryonic development of the heart as an example, I have shown you how animal models are being used in biology and how evolution validates that endeavor.

Thanks very much for reading. Please feel free to comment or to share with others.