The Genes Don't Have the Last Word: Epigenetics Comes to Town

 

From DNA to Epigenetics

 For many years, scientists thought that the discovery of the DNA double helix provided the solution to the code of life. Whatever the DNA code says, the organism does, they said. But the thought occurred to many that every cell has the same DNA in it and yet cells in different locations know that they should turn into part of a fingernail or part of a kneecap, and not part of the spinal chord.

 These considerations led to the conclusion that DNA is only an instruction book, waiting for decoding and implementation on request. But how does this work? A different set of biological systems is necessary to read and act on the instructions in the DNA library. And here we enter the realm of epigenetics.

 Epigenetics refers to the change in gene functions not relating to changes in the gene sequencing or changes in the gene itself. Dictonary.com defines it more clearly: Epigenetics is “the study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself” (Dictionary.com). In other words, the very same unmutated gene could cause the beaks of some birds to grow shorter and thicker during one year and then the next year cause the birds to grow longer and thinner beaks.

 (I’d like to know if anyone has investigated the Galapagos finch beak changes with this in mind. Is the birds’ DNA actually changed by mutation and selection as the traditional story goes, or are the different beaks simple different expressions of exactly the same DNA, influenced by external factors, such as rain, temperature, wind conditions, and so on?)

 

Example: Epigenetics and the environmental adaptability of a plant.

 One year my brother and I put up a hot house in the back yard for growing cactus. On a whim we planted some radish seeds, all from the same packet, inside on the dirt floor and a few outside on the ground. Same seed packet, same soil. All environmental variables were held the same, except for the temperature, and humidity (in the hot house, warmer temperature and high  humidity.

 In this case, there is no argument for a mutation causing larger leaves because of a warm, humid environment or smaller leaves because of a hot, sunny, low humidity environment: When the radishes grew, the seeds planted outside the hothouse produced leaves about two inches wide by six inches long. The radish plants inside the hot house grew leaves six inches wide and fourteen inches long.  The plant evidently possesses a built-in flexibility allowing it at each germination to respond to various environmental factors. Different environment, (such as  different climate) produces a different plant, no new DNA required. The plant cannot “pre-package” an environmental response in its DNA; it can only offer the instructions necessary to produce any of a range of expressions, each readily available as an immediate response to current environmental conditions.

 

Getting from Warm, Rainy Weather to Nice Big Radishes

Let’s think about this.

 Question 1: If the epigenetic process is to work, what is necessary in order for a radish seed and plant to respond to environmental factors such as those described above, so that the seed can alter its outputs, sometimes dramatically, after only  few day’s exposure to the surrounding climate?

 1. To respond to the environment accurately, the epigenetic process must rely on a  set of inputs about its surrounding climate. This suggests the need for a set of sensors that can detect and measure

·         air temperature, night and day

·      humidity
·      soil moisture
·         soil richness (a nutrient measure)
·         soil acidity (PH)
·         sunlight intensity and duration
·         and possibly
o    soil temperature

o   soil hardness

 2. A set of transducers to convert the information gathered by the sensors into useful input signals.

 3. A processing capability that can receive the data delivered by the transducers over a period of time, and by appropriate processing, predict what the environmental factors will be during the growth and reproductive cycle of the plant.

 4. An implementation mechanism that will apply the resulting answers to turning on and off certain genes to make the plant grow according to the analytical output of the processor.

 5. At the minimum, a series of logic gates that will allow the data to be applied to the various processes working on gene activation.

 6. But logic gates still leave open the questions of 

• What mechanism or environmental event causes each sensor to be put online and sampled (trigger event)?

·         How often are the sensors sampled?
·         What mechanism selects, channels, interprets, and applies the data and processes it into information?
·         How is this information used to control the gene expressions?

·         What is the process or event  or turning the various genes off?

One known mechanism for turning a gene on off:

·         methyltransferases attach methyl groups to cytosine bases in DNA

·         protein complexes are “recruited” to methylated DNA, where they remove acetyl groups, thereby repressing transcription

 Questions:

1. What are these implementation mechanisms and what controls them? What are the algorithms that “run” their programs? For example, what is the process or mechanism that “recruits” protein complexes?

 2. How did this “detect and adjust” system come to be constructed in the first place? And if it evolved over time, how did an accumulation of random, non-guided, non-purposeful mutations produce such a system? And how did a similar adaptability system come to be in many if not most plants?

 3. Like a computer-controlled machine, a fully complete and operational system is needed:

Sensors, transducers, data transmission, data processors, implementation mechanisms.

 The Big Questions

In many plants and animals, a range of change is possible depending on the external, environmental influences acting on the life form. Fruit flies grow an extra pair of non-functional wings, house flies develop an immunity to DDT, the beaks of finches adapt to tougher seed pods. These events are usually all explained as evidence of “microevolution,” and held up as evidence for the correctness of the grand synthesis (neo-Darwinism).

A first rebuttal to the microevolution claim has been that the changes are temporary changes in gene frequency, which  disappear when the environmental influence disappears. For example, in a state of undisturbed nature, every population of house flies has a few members that are naturally resistant to DDT. When the population is sprayed with DDT,  most of the non-resistant flies die, and the resistant flies take over and reproduce. The flies are now said to have developed a resistance to  DDT. But what happened is merely that the non-resistant flies were eliminated and the resistant ones took over. Now, such a collection of events like this might be claimed to be a powerful example of “evolution in action,” when, in fact, this change in the percentage of flies with the resistant DNA is only temporary, and when the spraying of DDT is stopped, the population soon reverts to the previous state, with only a few flies resistant. From this it is argued that a built-in flexibility in the gene allows for a limited range of variance.

(An example of this limited range of variance comes from botany. A rose grower wanted to  develop some new styles and colors of roses, so he irradiated rose seeds.  He got red roses,  yellow  roses, white roses, roses without thorns, roses with big thorns, and so on, but he never got any hibiscus plants.)

 However, the “change in gene frequency,” or the “micromutation” idea might not be the  true answer. What appear to be examples of plants and animals reflecting a newly mutated gene might be only a built-in set of gene expressions, controlled by epigenetic mechanisms.  Thee genes themselves can remain exactly as they were.