Why, specifically, does each generation, on average, improve upon the design of the species rather than degrade it?

Question

In every non-life example I can envision, a copy of a copy is always a degraded or less pure version of the original unless some outside influence acts to correct the copy back toward the ideal represented by the original. Photocopies get blurrier with each generation. Casts from a mold are distorted from the original from which the mold was made. In fact, each cast degrades the mold itself. When data is copied on computers or across networks, parity checks verify that no mistakes were made, but even then, every long once in a while, combinations of errors can cause a false positive in a parity check. So given enough time, the copies would degrade.

In eukaryotes, new individual organisms always begin as a zygote, so in all kingdoms, reproduction boils down to the genesis of a single cell. This involves correctly building the DNA as well as all of the other complex architecture of the cell. Why doesn't this cell degrade like every other example I can think of? In fact, cells are capable of such perfect reproduction that the system generally supports the introduction of additional randomness in order to promote the possibility of productive change. I can think of some probable contributing factors that make this work, but I must be missing something. I can't imagine that this model would actually work the way it does - so well in fact that the design actually improves over time. What am I missing or underestimating?

Contributing Factors (I guess):

Perfect Building Blocks: Cellular development follows a pattern at every level, and ultimately operates all the way down to the molecular level. At that level, nearly all building blocks are identical. Life is built of stable atoms, not something like plutonium, and in the rare event that an atom does change, the result is simply a different kind of atom, which still tends toward a stable form in the long term. Because the structures of life are ultimately made of stable components that are plentiful everywhere in the environment, the essential structures being copied are precise and can be copied precisely. Photocopies and casts are not precise to the molecular level, so copying them is more approximate by nature. Digital data propagation, however, is a very similar process. Bits are also theoretically perfect building blocks.

Fitness Correction: When mistakes do degrade the reproduction process, rather than maintaining or randomly improving upon it, there is a correction mechanism that removes the defects from the process. Those defects do not survive to reproduce. This evolutionary process acts to keep the reproductive pattern focused back upon a theoretical ideal which is independent of a specific physical form to be copied. This seems like the most essential element of the explanation, because it is ultimately only through progression that digression can be avoided, but it is also the part that seems the most dubious. Astronomical quantities of defects would have to be produced before developing just one advantageous feature. I would expect living creatures to be 99% defective with only 1% surviving to breed. I would expect 99.9% of zygotes to expire without being born or sprouting from seed. I would expect all sexual organs (ovaries, testes, stamen, etc.), if not the majority of the whole body, to be mostly dead cells, with just a few successes surviving to fertilization. I would expect 99.9% of the genome to be experimental, almost completely unusable liability to the species. Essentially, I would expect premature death to far outweigh successful life everywhere and at all times. And even so, I would still expect evolution to be even slower than it has been.

Mutation Management Mechanisms: I understand that there are mechanisms in reproduction that decrease the likelihood of mutation in more established and stable parts of the genome compared with sections that are more open for discussion - epigenetic structures, HOX genes, etc. Portions of all genomes have been established and functional for hundreds of millions of years, so I gather that there are mechanisms for protecting them (I suspect probably far more than we have yet discovered).

Note: The numbers I present are fuzzy and are based not on calculations but on general impressions I get of the magnitude of the numbers involved and the relative rareness of useful mutations. Is there any place where this kind of calculation has been performed with more realistic approximations of probabilities?

Answer 1

You have clearly given this a lot of thought. Unfortunately, as @adam.r said, you are laboring under certain misapprehensions. The quick answer is that each generation does not "improve" on the last. That is a common misconception. In a bit more detail:

1. First of all, your copying metaphor is a bad one. There was no "perfect original", I expand on this theme at length in my answer here but, briefly, all species are constantly changing. They are not moving away from a platonic ideal of the perfect species (or towards it for that matter), they are simply changing in response to the world around them. What's 'good' today is not necessarily 'good' tomorrow.

2. Your copy machine metaphor does hold for changes from one generation to the next though. Copying DNA is fraught with errors. There is a huge cellular machinery in place whose only job is to catch and correct those errors. Nevertheless, many get through and result in diversity that can then be selected for or against through the process of natural selection. So, the copies do actually degrade. That, in fact, is the very basis of how evolution works.

3. Another important point is that most changes are neutral. They have absolutely no effect one way or the other. There are many reasons for this but the main ones are

   1. The vast majority of DNA does not actually code for protein. What it does do is an area of active research but minor changes in sequences that don't code for protein are extremely unlikely to cause a change in phenotype.

      Almost all of the information necessary to produce a viable organism is in the genes, and genes represent a very small (~5% in human for example) percentage of the genome. Changes that affect the fitness of an individual are almost invariably found in the coding sequences of genes. This means that of the ~30 billion possible sites for mutation in any given cell, 95% of them (even less actually since only exons count and they're ~2%) will not cause a phenotypic effect.

   2. The genetic code is redundant. Basically, DNA is "read" in "words" of three "letters", the codons. Since there are 4 bases in the genome (A,C,T and G) this means there are 64 possible codons. Each codon specifies a particular amino acid (the building blocks of proteins) and a given sequence of codons will result in a specific sequence of amino acids. However, there are only 22 amino acids, many of which are specified by the same codon:

      

      As you can see in the image above, in most cases, changing the third letter of the codon does not affect the amino acid that will be specified. This means that even for those mutations (changes) that occur in the coding region of genes, the chances are relatively high that they won't actually result in any phenotypic change. If you change the genetic code but the changed codon still codes for the same amino acid there will be no change in phenotype.

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As for your contributing factors:

1. Perfect Building Blocks: Nope, sorry this one is wrong. First of all there is no such thing as a minor change that involves changing an atom. Any change that happens at the atomic level is huge by definition. That kind of thing happens a the hearts of stars and in nuclear reactors. The chemical reactions in our body involve changing molecules not atoms.

   There is no such thing as a minor change really, if you replace one atom in a molecule by another, you are significantly changing the properties of that molecule (this is less true for large, complex macromolecules where some changes can indeed be minor). If you were to change, for example, a single atom in normal table salt ($NaCl$) from sodium to hydrogen, you would get $HCl$, hydrochloric acid and not something you want to put in your soup.

   There are no perfect building blocks, in biology nothing is perfect, that only happens in math.

   Also, the organism does not follow the same pattern from the organismal to the cellular to the molecular (never mind atomic) level. In fact, there are very different organizational principles at play at the different levels and the way that cells are organized (see here for example) has nothing to do with the way that a cell's contents are organized.

   Stability is overrated. In fact, our bodies contain loads of unstable (reactive) chemicals, oxygen being chief among them. By definition, chemical reactions involve changing molecules (not atoms, but we don't deal with that level, biological effects tend to be at the molecular, not atomic level). All reactions that go on in the factory that is your body involve the changing of one molecule into another.

2. Fitness Correction: Actually, at the cellular level, the corrections try to faithfully reproduce the template they are copying from. When a cell copies itself, it will also copy its DNA. It does so by using its own DNA as a template. There is no "theoretical ideal", the cell has no information about the genome of its parent, only its own. As I mentioned above, there are various corrective mechanisms whose job it is to spot errors and correct them. They have no way of knowing whether a given change will be beneficial or harmful to the individual, as far as these processes are concerned, any change is bad and should be corrected. The only thing they do is try to make a daughter cell's genome identical to the parent cell's.

   When a change makes it past the cellular level, then it can be selected for or against based on whether it makes the individual carrying it more or less likely to reproduce. This, however, is not a directed process. It just happens. If a mutation makes a male blue whale stronger, it is more likely to be the one that catches up with the racing female and so more likely to reproduce. There is no direction other than the selective process itself. There is no one around comparing new individuals to an ideal and selecting accordingly. If you're better at reproducing than your peers, your genes will be selected.

   Actually, many many gametes are discarded. Many cells die. You just don't know about it because they die before you can see them. So deleterious (very bad) changes do occur.

   "I would expect 99.9% of the genome to be experimental, almost completely unusable liability to the species." In a way this is true. Despite recent findings, 98% of the human genome does not directly affect the phenotype. It is only the 2% that represents the protein coding parts of genes that has a direct effect on fitness. In fact, in the human genome specifically, there is a short sequence that does not code for any protein and does not (directly, though there are various theories about this) affect our phenotype, that has been making copies of itself and propagating in our genome for generations. Today, this sequence (Alu) represents ~10% of the human genome, that's twice as much as all our genes together!

3. Mutation Management Mechanisms: The basic protection mechanism you mention in your question is quite simply death. Mutations that render housekeeping genes (like the HOX cluster) inactive kill the organism that carries them. That does not mean they don't occur, it simply means that when they occur, we don't see them because the individual carrying the mutation is dead (see point 3).

Answer 2

I’ll add a slightly different perspective, although terdon’s answer already contains the relevant facts.

The thing that makes DNA endure in the face of imperfect copying is that, like computer storage, it’s digital. The relevant property of digital data here is that individual pieces of information aren’t given on a scale, they’re drawn from a strongly limited number of possible alternative values. That property allows error correction to take place: if possible values were continuous, error correction fundamentally wouldn’t work.

This gives the appearance of error-less copying. In reality it’s anything but, same as with computer storage and data transfer. Nevertheless, as you’ve noted, errors will accumulate, even with an error correction mechanism in place. And even though most of these errors have no influence on the outcome (due to downstream effects like the degeneracy of the genetic code), many more are detrimental than are positive. In direct contradiction of this we can see that species (but not individuals!) improve their adaptation in each generation.

Why? Because evolution. More specifically, because natural selection acts in a purifying manner to rid the gene pool of defects. This is a fundamental part of Darwin’s and Wallace’s argument. Less adapted individuals have an (ever so slightly) reduced chance at reproducing, and therefore prevent detrimental changes in the gene pool from accumulating.