Let’s start with a simple question. What are the main kinds of living things on our planet?
You may think of what you see around you and say, “plants and animals”. Plants are usually green but don’t move. Animals are usually not green and they move. This is a useful dichotomy.
It is simple like the Scala Naturae, or natural ladder that Aristotle proposed nearly 2500 years ago. The mineral world is at the bottom, followed by plants, and then animals. Aristotle considered humans to be separate from animals, and the highest form of all living beings so the actually had three categories of life. Aristotle’s anthropocentric view sat well through most of human history and was well liked by Medieval European theologians as well.
If you’re not too traumatized, you may remember plant cells and animal cells that you had to label in school. And then you may pause and say, “Wait. There’s one more. Microorganisms like bacteria that are very small, too small to see with the naked eye”. If you remember more, you may recall bacteria are prokaryotes that don’t have a nucleus, and plants and animals are eukaryotes with cells, each with a nucleus. Aristotle didn’t know about bacteria, of course. They were not discovered until around 2000 years later.
Before I move on, I just have to share a fact that will blow your mind. I certainly have been picking up grey matter from the floor after reading more about this. More than a quarter of all known animals are beetles. There are 400,000 different kinds of beetles. And those are just the identified ones. Bear in mind, that in comparison, there is only one living species of humans- us. Other creepy-crawlies with a large number of different species include wasps and worms. To all the kids out there who like bugs and mud: follow your heart. You may end up getting to discover and name dozens of new animals. In comparison, it is rare for paleontologists to make new dinosaur discoveries.
Where was I, then? Oh, yes. We were discussing how many kinds of life are there, very broadly speaking.
Before I went into this, I wanted to see what the kids were learning. Trigger warning: I am going to lambast our education system for a bit, but in order to do that I need to share some evidence from a school textbook. It’s OK to find school biology traumatizing. I’m a professionally-trained biologist with decades of relevant experience and just looking at this stuff gives me flashbacks of all-nighters committing information to memory (which I have never since needed or used) before exams.
The NCERT textbook has a chapter on biological classification for XI standard high-school students in India that is wrong!
Let’s look at what India’s gold-standard biology textbook is force-feeding our kids.
Chapter 2 of the NCERT Biology textbook starts off by talking of Carolus Linnaeus’ two-kingdom classification into plants and animals (basically unchanged from Aristotle). And then it goes into a five kingdom classification (I promise this will be short).
Before I was born, in the year immortalized by a Brian Adams song (i.e. 1969), R.H. Whittaker proposed a system of classifying animals into five separate kingdoms. Setting aside the navratan korma mélange of information in the table which can cause nervous twitches of “do-I-need-to-remember-this”, this system of classification was in vogue for exactly eight years. Until 1977. And it’s been wrong ever since.
But before I get into what cataclysmic event happened in 1977, I need to set the stage.
We didn’t really learn modern biology in high school.
I want to stress that biology is a very modern science. There are very few theories or observations that extend back more than 200 years. When most people think about biology, they think about scientists who study and categorize plants and animals, mainly based on morphology, or the large structures of organisms.
And it's thought of essentially as a field science with zoologists categorizing animals based on structural features such as limbs, and botanists looking at plant flowers. When people hear that you’re a biologist they tend to make small talk by telling you they were good at drawing and labelling plants or dissecting small animals in zoology class. Extending from morphology is phylogeny which tries to figure out relationships by comparing organs and sometimes embryonic development. The idea here is that embryonic forms of life capture some of the natural history of the organism.
Indeed, for much of history, this would’ve been a correct assessment because biology was a descriptive science. Naturalists like Charles Darwin constructed field-changing theories based on the various forms of life on display. And Darwin’s theory of evolution by natural selection has impacted not only biology but has also resulted in seismic changes to geology (see what I did there?).
Palaeontologists break up the history of life on earth based on fossils found in the ground. But not all animals and plants fossilize, and this is acutely a problem for soft-bodied animals, small plants, and microscopic organisms which precede modern life.
Darwin himself knew that fossils appeared suddenly, and he was perplexed by it. Life didn’t arise 542 million years ago as the fossil records suggested at the time. But Darwin has been vindicated because there are traces that go back to early life at least billions of years before that. I’ll get to that shortly, but suffice it to say advances that are less than 100 years old have revolutionized geology and biology- and these include the ability to date the age of rocks and compare lineages based on molecular information.
This is really what I want to talk about. Modern biology is not just the biology that you and I learned in high school. It is a quantifiable science with many of the attributes of mathematics, physics, and chemistry. From what Nobel Laureate Theodosius Dobzhansky would call organismic biology, it has branched out into molecular biology. As you might expect, much of this was done by people who made significant contributions to biology after training in other disciplines.
From the middle of the 20th century biology has included basic principles for life based on physical, chemical, and mathematical ideas. This has been possible because we’ve learned that all the diverse forms of life are related and can be reduced to certain categories of molecules including carbohydrates, lipids, proteins, and nucleic acids. And finding out that DNA was the genetic material changed everything. In 1953, using Rosalind Franklin’s experimental data (without her awareness or permission), Francis Crick and Jim Watson deduced the simple structure of DNA, which is the genetic material in all cellular life. In doing so, they beat out another Nobel laureate, Linus Pauling (who was arguably the greatest chemist of all time). The era of molecular biology had begun.
Why is this important in order to categorize life? I thought you’d never ask.
When plants and animals deviate from one another due to mutations, they can form new species. By tracking the changes in molecules that all living things possess, we can find out relationships and construct a universal tree of life. In a landmark paper in 1965, Pauling along with another scientist proposed just this idea: that biological molecules could serve as “molecular clocks”. Changes in organisms would be more or less the same over evolutionary time. And for the first time there was a quantitative way to look at biological relationships. This went hand in hand with the ability to sequence DNA from various organisms. Molecular palaeontology was born.
We have to know how living things are related to one another.
The five kingdom system of classification of life is wrong because it does not consider actual relationships between organisms based on their quantifiable molecular properties.
So how are organisms related? To answer this, I have to introduce the greatest disruptor of evolutionary biology since Charles Darwin. A man named Carl Woese. In 2018, New York Times ran a long magazine article about Woese entitled “The Scientist Who Scrambled Darwin’s Tree of Life”. This is a good essay to learn more about him, but I’ll summarize for those who don’t have time.
In 1977, Woese along with scientist George Fox proposed that all of life was categorized on the basis of molecular evolution (they looked at a particular type of nucleic acid) into three main domains of life. Woese called these Bacteria and Eukarya, and also a third domain of life consisting of single-cellular forms of life that often lived in unusual environments such as thermal vents on the bottom of the ocean floor and the can often stand conditions of high temperature, high salinity, and no oxygen. Woese called this third domain of life Archaea.
Woese’s main conceptual contribution was not only the third domain of life, Archaea, but figuring out that it was radically different and shared properties of Bacteria and Eukarya (which includes us). Woese kept pushing this radical idea, which took over a decade to gain traction.
In 1990, he published a paper with a revised tree of life. This is a figure from the paper:
We (and by that, I mean all animals) branch out from 14. All green plants are 16. Fungi at 17. The point is that all of macroscopic life (that we can see) is more closely related than most unicellular organisms which are the most diverse forms of life on the planet.
And I’ve highlighted one particular node in yellow. That is the conceptual Last Universal Common Ancestor or LUCA. All subsequent life on earth for billions of years, and including every single form of life we see on the planet is descended from LUCA. After LUCA, life began to diversify, but all of us from humans to methane-producing microorganisms, to confers, to mushrooms, to the bacterium causing syphilis are all descendants of LUCA.
Here’s another version of the tree of life. The two things to remember are - the two single-celled microscopic domains of life (Bacteria and Archaea) represent most of the diversity of life. And we are closer to plants than many bacteria are to one another!
Where did we all come from?
As you can imagine, a lot has happened since Woese’s landmark paper forty years ago. I’m going to mention some very exciting developments in the last few years to get you up to speed on the history of life.
Scientists have looked for early traces of life in some of the earliest rocks on the planet. Some of these sedimentary rocks mixed with volcanic flows date from 3.8 billion years ago and are found in Greenland. The amount of a carbon isotope in some of these rocks is similar to that found in marine microbes, but the evidence from these rocks is not definitive. So, were not sure that this is the earliest form of life.
In 2016, scientists claimed to have found structures called stromatolites in an outcrop of rocks in Greenland. This was published with much fanfare in Nature. Stromatolites are domes consisting of sheets of microbial mats that build up over time. They’re made up of single-celled organisms that make their own food through photosynthesis and they’re usually formed in warm, shallow water. Unfortunately, just two years later another group published another paper in Nature challenging that assertion. They said these are just natural geological shapes where rocks squished against one another.
But some stromatolites may be the oldest forms of life that we know of so far. Strong evidence seems to exist for stromatolites that are 3.5 billion years ago that have been found in Australia. As of 2020, that seems to be the oldest form of life that we can trace.
But that might not the oldest form of life in existence. Scientists look for microfossils in rocks as evidence of past life, but as we go further into the past the quality of evidence diminishes.
A group of scientists think that the first common ancestors originated in an extreme environment such as a hydrothermal vent at the bottom of the ocean. A paper in Nature Microbiology published in 2016 seems to back the assertion that we all came from a kind of microorganism for which oxygen was poisonous.
We evolved from freakish microorganisms.
I started this long newsletter by telling you what you and I learned in high school in India, and what your kids are learning right now is obsolete (more than 50 years old) and wrong.
From there we did a nosebleed survey of some of the major developments in biology in the last century. I’m going to tie it all together by telling you that there really were only two major forms of life on the early planet. For the last decade or so, biologists have found evidence that the Last Universal Common Ancestor split up life into Bacteria and Archaea… and we (all of Eukarya) are mainly descended from the freakish Archaea much later, around 1.8 billion years ago. This dropped as a bombshell and in 2017, scientists published a paper in Nature that traced a type of Archaea that might’ve been a progenitor.
But wait. There’s more! Ancestral cells also engulfed a kind of bacteria as well that became mitochondria. So, we’re sort of hybrids of two of the earliest forms of life.
This is what the most accurate current tree of life looks like.
This isn’t the last word, of course. And new information will build on or negate what we already know. But that’s how science works in the real world.
The link for the hardcover “COVID-19: Separating Fact from Fiction” is now available on Amazon’s Indian site.
Thanks so much for sticking around on this long journey. This topic was picked through a poll and it took a bit of effort to write.
I didn’t talk at all about how life might’ve actually emerged for the first time, how life made a transition from water to land, or the evolution of multicellular organisms (like us). Perhaps, that is something to pick up on another day.
Please comment to let me know if you found it interesting.
And please also share with others if you did.
Awesome. Its a fallacy to see science in silos. Loved the simple connection to geology, evolution and microbes. That's what it is. With climate change and the perma frost reveals, more information may to light that may shift our understanding ever so slightly.
Super write up as always. Thanks for doing this. Also, I have always wondered about the exact nature of life forms. I know this may sound weird (or stupid) to an expert like you, but why do we assume certain things about life forms? For example, I keep hearing that certain planets are not suitable to sustain life forms (very cold, very hot, no carbon, no oxygen and so on). But why do we assume that these are not suitable? I mean, for all we know, there might be life forms who thrive in nitrogen or helium rich environment and are not carbon based. They might be giving out absolutely different signals than what we are looking for. Is it too far fetched?