NOTE: Given the topic, you can consider this entire diary to be a "political aside" from the series focus of micro-agriculture.
As a scientist, it is quite scary to see the success that the anti-intellectual forces have had in creating, over thirty years, a sub-culture that successfully denies the most central fact of modern biology - evolution. This denial is not rooted in fact, but in political tactics and delusional thinking. As such, the denial is impervious to logic. That's because the denial is deep sociological engineering - getting people to hate education, demonizing all scientists as some kind of elitist, anti-religion monsters, and brainwashing children from the cradle to mistrust their own eyes and ears, and their very thoughts.
There are two kinds of evolution-deniers: outright lunatics, and mendacious power-grabbers.
Young-earthers/Biblical literalists
People who think the earth is less than 6,000 years old are insane. All anyone has to do to disprove these nutters is to go to Greenland and count (you know, 1, 2, 3, etc). the layers in an Ice Core. Scientists have counted back over 100,000 years in these cores, which reach up to 2 km. in depth. To believe the "young earth" lunacy, you would have to believe that the facts behind the Wikipedia entry on Ice Cores were authored by God as part of his grand conspiracy to fool us all.
Way too much time has been wasted trying to reason with these paranoid fanatics. God is not British Security Coordination, and the world is not some giant funkspiel he is playing on mankind. Let's move on to the merely mendacious.
Creationist/Intelligent Design weasels
The creationist line of bullshit has not really changed over the last 25 years. Its total lack of methodology and its fraudulent "controversy" rhetoric was debunked then, and time has only provided more evidence against them. In 2005, a conservative, W-appointed, Federal judge completely eviscerated a show trial case brought by the so-called Intelligent Design movement. The judge gave a lengthy ruling to the unmistakable effect that ID was nothing but repackaged creationism, not science. This was documented in a Nova TV program.
So, with decades of trials and articles on record, there is no need to write new words for this battle. All that is required is to repeat the old TRUE words until reality dawns on the targets of the ID propaganda campaign. Let's just go to the archive:
Evolutionists make no claim for perpetual truth, though creationists often do...In science, "fact" can only mean "confirmed to such a degree that it would be perverse to withhold provisional assent." I suppose that apples might start to rise tomorrow, but the possibility does not merit equal time in physics classrooms....
Scientists regard debates on fundamental issues of theory as a sign of intellectual health...Yet amidst all this turmoil no biologist has been led to doubt the fact that evolution occurred; we are debating how it happened...Creationists pervert and caricature this debate by conveniently neglecting the common conviction that underlies it, and by falsely suggesting that we now doubt the very phenomenon we are struggling to understand.
- Stephen Jay Gould, "Hen's Teeth and Horse's Toes" (1983)
I might add one bullet to the armory against these insincere hacks. I propose we name their stance "Evolution Denial" and their major speakers "Evolution Deniers", as in "Holocaust Denier".
Evolutionary imperfections are the "dog that did bark"
To deny the multi-layered evidence of evolution requires the whole corpus of evolutionary science to be thought of as some giant Potemkin Village.
Evolution lies exposed in the imperfections that record a history of descent. Why should a rat run, a bat fly, a porpoise swim, and I type with structures built of the same bones unless we all inherited them from a common ancestor? An engineer, starting from scratch, could design better limbs in each case.
- S. J. Gould, ibid.
Gould is talking in shorthand, for people who have studied enough to know what he is referring to: namely, it is the consistent interlocking of all of the facts about timelines and descent with variation at both the physiological and the molecular levels which gives the theory of evolution such a high likelihood of being correct.
A political analogy: Evolution denial is the equivalent to walking into the city of London, looking at the 1,000 year old tower, the 500 year old bridge, the 150 year old labyrinth of underground tunnels and railroad tracks, the 75 year old bunkers under Parliament for WW2, etc. and deciding that the city was built last Tuesday by a single construction company and that all these details are just an elaborate mind game meant to fool people.
Extending the analogy, it is like then walking into the London city planning office and digging through the carefully preserved old drawings and permits - which line up exactly with the structures you previously encountered on the ground - and still thinking this proves nothing.
Even sillier, it is like seeing the last of the old bomb and fire damage from the Blitz - seeing that part of this "built yesterday" city had been blasted and burned and then grown over with weeds and neglect and still insisting that its all an elaborate charade. Or seeing rundown districts of old, abandoned buildings and deciding they were just built, then run through some artificial accelerated delapidation process, with bits of debris deliberately scattered about for effect. The whole ludicrous scenario is utterly delusional. This is Occam's Rubber Razor.
The truth is that the genetic and physiological record of imperfect adaptation, of junk DNA, and of imperfect re-use of structures, is a vast testimonial to the timeline of evolution as well as the close inter-relatedness of all living creatures. So, lets start digging down through the layers of the real, non-Potemkin, village of evolution.
An archaeological dig through evolution
I already mentioned some of the interlocking layers of evolutionary fact in the first diary in this series. Let me quickly review them:
First there is the indisputable fact that all living creatures use the same genetic code; and that key genes are highly similar (if not identical) across all species. Another layer of this fact is the separate genetic code of mitochondria - again the same across species. This consistency argues for inheritance over special creation of species.
Second, there is the average mutation rate for DNA, which sets the molecular clock that allows us to measure evolutionary distance between species via the genome. The absorption of the mitochondrial DNA by nuclear DNA gives us yet another clock. These clocks match up with the fossil record and the physiological record.
A third layer of consistency is the limited set of protein folds - the shapes of the various machine tools and structural elements - which remain the same for all living creatures.
A fourth layer of cellular evolution is given by the endosymbiont hypothesis for organelles. This hypothesis has been nailed down by comparing the DNA sequence of mitochondrial and chloroplast DNA to the sequence of bacterial families suspected of being the "digestee" in the original endosymbiotic event.
Finally, there is the mechanism of gene duplication, which gives a mechanism for making spare copies of genes. These copies can be changed without damaging critical components of cell machinery. Newer genes can be traced back to origins as duplicates of older genes.
Now, let's add some more layers.
The size of genomes varies greatly; but there is an interesting chicken and egg relationship here. Genome size depends directly upon the fidelity of the copying. The British geneticist Mark Ridley (not to be confused with the British geneticist Matt Ridley) has written extensively about this. The important conclusion is that, if the mechanism for copying the DNA makes too many mistakes, there are no viable offspring; and the species dies. So, genomes reach a maximum size that depends upon the fidelity of copying machinery.
You might think that because viruses hijack the copying machinery of their host, their DNA wouldn't have a size limit. Not true. The DNA/RNA size for a virus is set by the size of the viral shell; its size determines how much DNA it can hold. For a fascinating detour into just how powerful evolutionary pressure can be, see how viruses have managed to evolve DNA which can be read in each of the three overlapping "reading frames", thereby tripling the effective size of its genome. Its like natural selection has learned to solve crossword puzzles!
The next step up the genome size ladder, bacteria, have a simple polymerase system whose fidelity maxes out at a few million bases of DNA - which, not coincidentally, is the size of bacterial genomes. When you get to eukaryotes, they have better polymerases and a proof-reading system. This allows them to get to the billions of bases in mammalian genomes. But, consistent with evolution, their systems are built upon the foundations of the earlier, more primitive systems.
The bottom line is that the DNA machinery itself has evolved to allow larger genomes. This leads to an interesting issue. One of the ongoing arguments among geneticists is whether or not the human species is at the limit of DNA copying error. That is, sexual reproduction is an error-correction technique. We get two copies of each gene, one from each parent. If one is bad, the other copy keeps the individual viable. But, we have so many genes and so many genetic syndromes that, as the saying goes, "we are all genetic lemons". We all have some minor genetic problem, e.g., migraines or bunions or near-sightedness.
Another layer of evolution is the deliberate generation of high mutation rates. Bacteria that come under stress (from antibiotics or radiation or other causes) turn on a system named the "SOS system". This system contains about 30 proteins whose job it is to clean up damage. What is interesting is that the SOS system shuts down the normal polymerase and deliberately uses a lower-fidelity polymerase - to generate mutations that might evade the stressor! Scientists have deliberately broken this system, and shown that SOS-impaired bacteria are much more likely to die under stress.
Finally, we come to "junk DNA" - the bomb craters of the genome. I will devote the fourth diary to this topic. But, for now, all I want to mention is that a significant chunk of the human genome is made up of very many copies of "selfish" jumping genes. Furthermore, the genetic history of various creatures allows us to pinpoint exactly when and where these random copies arose. The takeaway is that random things go on in the genome all the time. Hardly matches the fundamentalist picture of static species and miraculous one-time interventions.
In the sub-basement of the dig
The layers discussed above are all concerned with DNA-based life. But, scientists have pushed back even further. They were led to do this by some loose ends.
Scientists discovered that RNA was used for temporary copies of DNA information. That is, the nuclear DNA is copied onto "messenger RNA". The messenger RNA is sent out of the nucleus (hence, messenger) to machinery called the ribosome. The ribosome's job is to manufacture proteins to the specification given by the messenger RNA (mRNA). mRNA is less stable than DNA, and its natural decay is used by the cell to regulate how long a protein gets made. So far, its simple. RNA is just another genetic piece of paper.
But, then, it was noticed that critical components of the ribosomal machinery were not made from protein, but rather, were made from RNA. These components were called ribozymes (ribonucleotide-based enzymes); and they turned out to be incredibly ancient. Further study led to the realization that RNA could fold up into a great variety of catalytic structures, and that RNA could catalyze the cutting of other RNAs.
At this point, the hypothesis that early life was based on RNA molecules was proposed - the so-called "RNA world" hypothesis. RNA was both the information store and the enzymatic machinery. This hypothesis is widely accepted today, because of the increasing numbers of interesting ribozymes that have been discovered.
Of course, the RNA-world still begs the question of how DNA-world evolved from RNA-world. This question is still wide open. That is why evolution is still frontier science. It has fundamental unanswered questions. But...
Unanswered questions are not controversies
While creationism has no scientific methodology, it has a well-developed rhetorical methodology: "teach the controversy". Dr. Gould's formulation is still the best: Creationists spend most of their time twisting arguments about "how" evolution has happened into controversies about the fact that evolution has happened.
Political aside: "teaching the controversy" isn't science, it is the rawest form of political propaganda imaginable. To see TtC for what it really is, consider these examples:
Round-earth denier, circa 1500: "Since there is an argument about whether Columbus reached Asia or just discovered a New World, there is controversy over whether the world is round."
Holocaust denier, current: "There is no evidence for crematoria, concentration camps, or mass deportations. The Holocaust is nothing but Jewish propaganda."
To battle "evolution deniers" claims that controversy equals failure, you can't do better than the late Stephen Jay Gould for explaining how the neo-Darwinian synthesis of natural selection and Mendelian genetics doesn't explain everything. This is no more a failure of science than to say that Newtonian mechanics does not apply in situations that call for relativistic quantum physics.
In the next diary (The end of DNA dictatorship) I will discuss some of the legitimate and ongoing theoretical debates about how evolution happens, which are central to the scientific endeavor of evolutionary science. It is a cultural crime that the natural behavior of scientists is misrepresented to pretend that science is somehow in disarray.