this gastrulated human embryo develops distinct types of tissue: its cells lose their pluripotency and start to specialize. The innermost layer, which will form the lining of the gut, is called the endoderm (“inner skin”). The outer layer, or ectoderm, generates the surface layer of the skin as well as the brain and nervous system. Between these layers is the mesoderm (“middle skin”), which is the primal fabric of the inner organs and tissues: the heart, kidneys, bone, muscles, ligaments and also the blood. At this stage, some of the embryonic stem cells are also set aside to become the germ cells: the precursors to the gametes (eggs and sperm).
Gastrulation of the human embryo and formation of the primitive streak.
And there you have it: the schematic human body, its cells launched on their road to specialization. The rest is refinement. For example, some neural cells in the head region develop (around week five of gestation) not into neurons but into the retinal cells of the eye. Some cells don’t differentiate where they first sit, but actively migrate through the embryo to where they need to be – we saw that the primordial germ cells do this. The sex organs develop identically at first in both sexes, becoming female organs unless triggered into the structures of the male if the cells have a Y chromosome instead of a second X. On the Y chromosome sits a gene denoted SRY, which controls other genes needed to develop male characteristics.
All of this refinement happens through cell dialogue. Molecular messages pass from cell to cell, each at the proper stage of development, so that cells get assigned their roles in collaboration with their neighbours. “The parts of each organ help the other parts to form,” explains cell biologist Scott Gilbert. It is because organoids like my mini-brain lack this information from surrounding tissues that their development – their morphology – is imperfect. To make a body or even a mature organ, cells need community.
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The idea that genes involved in development interact and control one another via diffusing morphogens is only a part of the story of how embryos take on their form. The distinctions between cell types initiated by such signals become permanently imprinted on the cells as they develop into different tissues.
How can that be, if they still all share the same genome?
That problem was recognized by Thomas Hunt Morgan and others in the early days of molecular genetics, but no one really knew how to address it. So it was largely put to one side. The discovery of DNA’s genetic code in the 1950s and ’60s all but eclipsed the question, seeming as it did to promise an underlying simplicity in the way cells function. Already in 1941, Morgan’s former student George Beadle, along with biochemist Edward Tatum, had shown that genes (whatever they were – it wasn’t yet clear) encode protein enzymes. This became understood to mean that each gene has a unique corresponding protein. The key question was then how a gene made a protein. Crick and Watson’s double helix, zipped together with information-bearing nucleotide bases, seemed to deliver the answer: DNA carries the coded plan, and RNA and ribosomes are the machinery that does the translation.
But how do you get from a protein to the phenotypic effect of a gene on the unfolding organism? That wasn’t at all obvious. By the 1960s, the general idea was that genes act in some vague way to dictate the developmental programme, which was then envisaged merely as “an unfolding of pre-existing instructions encoded in the nucleotide sequences of DNA”, as American biologist-cum-historian-cum-philosopher Evelyn Fox Keller has put it. According to the French biochemist Jacques Monod, as far as gene action is concerned, “what’s true for [the bacterium] E. coli is true for the elephant.” What seemed to matter was establishing the common basis by which gene becomes protein. Somehow the rest – meaning the living organism itself – followed. Which would be all very well, if E. coli looked like an elephant.
In this picture, then, the answer to the question of development must reside in the gene sequence, and the ultimate goal of biology becomes the decoding of that sequence. This picture has been burnished for a remarkably long time, culminating in the Human Genome Project, which began in the 1990s and announced the almost complete sequencing of the human genome between 2001 and 2003.12 The objective was simply to get the code, which took on the status of the “fundamental” information directing all biological activity. Meanwhile, genetics more broadly looked for correlations between genes and phenotypic outcomes. Exactly how and why genes exert their effects was a question long bundled up in the vague concept of “gene action” that, as Keller says, allowed scientists “to get on with their work despite almost complete ignorance of what that ‘action’ consisted of.” There was an implied hierarchy of causation in which genes were paramount, as reflected in Nobel laureate David Baltimore’s comment that the development of an organism involved the “greasy machines” of the cell directed by the “executive suite” of the genome. (Engineers are very familiar with this kind of prejudice.)
The resulting view was that development was a kind of painting by numbers of the plan in the genome. For a complex organism like us, that left an awful lot of instructions to be packed into the genes. As the Human Genome Project got underway, biologists estimated the number of genes the project would find as being somewhere between 140,000 and a lower limit, proposed by a few bold souls, of 26,000. Most put the figure at around fifty to seventy thousand.
The answer turned out to be 23,000.
This is often presented as a sobering example of how experts can get things wrong. It’s certainly that, but rarely does anyone identify the real moral: that the genome doesn’t work the way it was thought to.
Zoologist Fred Nijhout is one of the few to have come properly to terms with the implications. “A more balanced and useful view of the role of genes in development,” he says, “is that they act as suppliers of the material needs of development and … as context-dependent catalysts of cellular changes … they simply provide efficient ways of ensuring that the required materials are supplied at the right time and place.” They are less like Baltimore’s executive directors, and more like stewards guiding a crowd. It’s no coincidence that Nijhout sees things this way, because he is an expert on the genetics of butterfly wing patterns, where it is clear that just a few genes, creating interacting fields of influence through the diffusion and spreading of morphogens, can generate a startlingly diverse array of patterns and forms, dictated by the details of how the genes are expressed in time and space. It’s somewhat meaningless, in such a situation, to say what a gene does (beyond “encode a class of proteins”) without specifying where and when it acts.
The view now emerging is that a relatively small number of genes is able to generate the complexity of the human form, with its many different tissue types so precisely arranged and coordinated, because they act in networks that produce distinct patterns of gene expression varying over time. With 23,000 genes, the number of possible networks of influence is astronomical.
How do genes acquire and change their patterns of behaviour? The control, activation and silencing of genes in different cell types and at different stages of development is called epigenetics. The word literally implies something additional to genetics, but what it really connotes is that the observable outcome of genetic activity – the phenotype, such as the tissue type of a cell – isn’t determined by the genotype (that is, which genes are present), but by the question of which genes are active. Epigenetics is all about how genes become modified to alter whether, or how much, they are expressed.
There are several ways in which this can happen. One is by the attachment of molecular “tags” to the respective genes, which might act as markers that deter the machinery of transcription, suppressing gene expression. Some genes can be switched off, for example, by proteins that stick a so-called methyl group – a carbon atom with three hydrogen atoms attached – onto DNA bases in the gene, which forms a sort of “shield”
