Basic Science Concepts List

This is the updated list for the basic concepts posts that science bloggers have recently been doing. For another list organized and collected on different principles, see Wilkins's Evolving Thoughts.


'Science' understood as process of discovery

Prologue to Dating Techniques at "Afarensis"
How do you sequence a genome? at "Discovering Biology in a Digital World"
How do you sequence a genome, part II at "Discovering Biology in a Digital World"
How do you sequence a genome, Part III at "Discovering Biology in a Digital World"
How do you sequence a genome, Part IV at "Discovering Biology in a Digital World"
How do you sequence a genome, Part V at "Discovering Biology in a Digital World"
How do you sequence a genome, Part VI at "Discovering Biology in a Digital World"
Pottery in the Archaeological Record at "Hot Cup of Joe"


'Science' understood as content of discovery

Clade at "Evolving Thoughts"
Evolution at "Sandwalk"
Gene at "Pharyngula"
Fitness at "Evolving Thoughts"
The Central Dogma of Molecular Biology at "Sandwalk"
Biological Clock at "A Blog Around the Clock"
The Three Necessary and Sufficient Conditions of Natural Selection at "Greg Laden"
The Modes of Natural Selection at "Greg Laden"
Species at "Evolving Thoughts"
Linkage Disequilibrium at "Gene Expression"
Introduction to Microbiology and Infectious Diseases at "Aetiology"
What is a gene? at "Greg Laden"
What is a gene? at "Sandwalk"
Anisogamy at "Behavioral Ecology Blog"
Cell Migration at "Migrations"
Artifacts, Vectors at "Discovering Biology in a Digital World"
Hearing at "Retrospectacle"
Normal Flora at "Aetiology"
What is Ecology? at "The Voltage Gate"
Biomes at "The Voltage Gate"
The Real Genetic Code at "Sandwalk"
8th Grade Math at "Gene Expression"
Measuring Fitness at "The Questionable Authority"

Force at "Uncertain Principles"
Fields at "Uncertain Principles"
Energy at "Uncertain Principles"

Mean, Median, and Mode at "Good Math, Bad Math"
Normal Distributions at "Good Math, Bad Math"
Standard Deviation at "Good Math, Bad Math"
Margin of Error at "Good Math, Bad Math"
Natural Numbers and Integers at "Good Math, Bad Math"
Recursion and Induction at "Good Math, Bad Math"
Numbers at "Evolutionblog"
Infinity and Infinite Sums at "Evolutionblog"
Correlation at "Good Math, Bad Math"
Logic at "Good Math, Bad Math"
Syntax and Semantics at "Good Math, Bad Math"
Sets at "Good Math, Bad Math"
Turing Machine (with Interpreter) at "Good Math, Bad Math"
Modular Arithmetic at "Abstract Nonsense"
Real Numbers at "Good Math, Bad Math"
Real Numbers at "Good Math, Bad Math"
Halting Problem at "Good Math, Bad Math"
Multidimensional Numbers at "Good Math, Bad Math"


'Science' understood as object of discovery

Arguments at "Adventures in Ethics and Science"
What's a Feminist Theory of Science, Anyway? at "Thus Spake Zuska"
Falsifiable Claims at "Adventures in Ethics and Science"
Theory Testing at "Adventures in Ethics and Science"
Epistemology at "The World's Fair"


My original comments still seem to apply:

(1) Where is chemistry? (2) Most of the basics covered are theoretical. This really isn't surprising, but there are practical concepts too -- basic ideas used in experiments, practical applications, and so forth. (I'm thinking of things as diverse as dissection, force diagrams, cloud chambers, microscopes, and so forth.) Some of the posts do discuss concepts like these, but I, for one, would really like to see more posts that deal with basics of lab and field work on the list.

Also, don't forget the science blogging anthology.

Moreover, this is Just Science Week of Science for a number of science bloggers; the posts are being aggregated here. It's all science all the time.

Testimonial Bias

This is a repost, and I don't generally re-post things; but I'd forgotten that I'd written and thought it interesting enough to put it up again.

Hume, in his Essay on Miracles:

The wise lend a very academic faith to every report which favours the passion of the reporter; whether it magnifies his country, his family, or himself, or in any other way strikes in with his natural inclinations and propensities. But what greater temptation than to appear a missionary, a prophet, an ambassador from heaven? Who would not encounter many dangers and difficulties, in order to attain so sublime a character? Or if, by the help of vanity and a heated imagination, a man has first made a convert of himself, and entered seriously into the delusion; who ever scruples to make use of pious frauds, in support of so holy and meritorious a cause?

The problem with this argument is the first premise: "The wise lend a very academic faith to every report which favours the passion of the reporter." The problem with this, as was soon noted in responses to Hume, is that this, despite an initial plausibility, turns out to be untenable. Boswell records the following conversation with Samuel Johnson, which touches on the problem:

We talked of denying Christianity. He said it was easy to be on the negative side. "If a man were now to deny that there is salt upon the table, you could not reduce him to an absurdity. I deny that Canada is taken, and I can support my assertion with pretty good arguments. The French are a much more numerous people than we; and it is not likely that they would allow us to take it.--'But the Ministry tells us so.'--True. But the Ministry have put us to an enormous expense, and it is their interest to persuade us that we have got something for our money.--'But we are told so by thousands of men who were at the taking of it.'--Ay, but these men have still more interest in deceiving us. They don't want you should think they have gone a fool's errand; and they don't want you should think that the French have beat them, but that they have beat the French. Now suppose you should go over and see if it is so, that would only satisfy yourself; for when you come home, we will not believe you. We will say you have been bribed.--Yet, for all these plausible objections, we believe that Canada is really ours. Such is the weight of common testimony."

[Boswell's London Journal. Pottle, ed. McGraw-Hill (New York: 1950) 301-302.]

A similar line of thought forms part of Richard Whately's biting satire on Hume's arguments against miracles, Historical Doubts Relative to Napoleon.

And we can back their arguments up with an additional consideration. If you haven't recognized it yet, journalism is largely about testimony: reporters don't generally identify facts directly, but find a source that will give testimonial evidence for whatever is being put forward. Now, it has also been recognized that journalists have an infuriating habit of reporting crackpot testimony alongside respectable testimony. I think if you look closely at this practice, you will see that what lies behind it is Hume's principle. When scientists give testimony about what the best explanation of a phenomenon is, this testimony is in conformity with the passions and interests of the scientist themselves; when this is combined with Hume's principle, it follows that we must lend an 'academic faith' to the reports of scientists, because of the potential for bias. So journalists go off and find some other testimony with a countervailing potential for bias, so as not to prevent a one-sided view of a matter that is clearly conformable to the interests of those giving testimony.

Hume's principle, in other words, is, if taken strictly, the stuff of quackery and conspiracy theory.

Why then does it initially seem so plausible? The reason, I think, was rightly recognized by many of the early critics of Hume (Campbell, Shepherd, etc.): we do use something like Hume's principle, when we have independent reason for thinking the testimony in this particular case to be distorted by the passions of the reporter. In other words, Hume mistakenly treats as a general principle what in fact is a rule of thumb for particular cases that meet certain conditions. For Hume's principle to have merit, each case of testimony must be considered on its own. The reason is that there is very little testimony that is not in conformity with the passions and the interests of the reporter in some way; and, indeed, for all we can say a priori, the passions and interests of the reporters may in this case be helping them to give a more accurate testimony. We have to look and see whether there is any reason to think the testimony in this particular case is genuinely distorted.

St. Olaf Rolls a Lucky 13

This story came up in a thread at FQI. It's from the Heimskringla:

Thorstein Frode relates of this meeting, that there was an inhabited district in Hising which had sometimes belonged to Norway, and sometimes to Gautland. The kings came to the agreement between themselves that they would cast lots by the dice to determine who should have this property, and that he who threw the highest should have the district. The Swedish king threw two sixes, and said King Olaf need scarcely throw. He replied, while shaking the dice in his hand, "Although there be two sixes on the dice, it would be easy, sire, for God Almighty to let them turn up in my favour." Then he threw, and had sixes also. Now the Swedish king threw again, and had again two sixes. Olaf king of Norway then threw, and had six upon one dice, and the other split in two, so as to make seven eyes in all upon it; and the district was adjudged to the king of Norway. We have heard nothing else of any interest that took place at this meeting; and the kings separated the dearest of friends with each other.

The Nonconvergence Argument Against Moral Realism

While reading the SEP article on empirical approaches to moral psychology I came across the discussion of criticisms of moral realism related to Mackie's 'argument from relativity,' a.k.a., 'argument from difference', which is basically that the existence of fundamental moral disagreement undermines any claim that moral judgments are objectively true. In particular the argument discusses one variation on this, namely, that moral realism should imply that moral views converge through protracted argument, which they do not, therefore, etc.

But, of course, tha tricky point with this argument is that no other realism is committed to such an absurd claim. For instance, realism about evolution is not committed to the claim that protracted argument will lead to convergence on belief in the occurrence of evolution; evolutionary realists are not refuted by the existence of anti-evolutionists. And this is a much stronger opposition than we usually get in the case of moral disagreement, where the differences, although undeniably real and stubborn, tend to be much more subtle -- a difference of emphases. An example the authors of the article give that is supposed to be a problem for the realist is the tendency of those raised in southern states to have stronger physiological reactions to perceived affronts than those raised in northern states. But this is a pretty weak sort of opposition on which to base an anti-realist argument; it's as if you said an experiment suggesting that people from cities and those from farms notice different things in their environment would constitute evidence against the existence of the external world. Or, rather, from a moral realist perspective the parallel would be reasonably strong, although not perfect.

As moral realists have noted, convergence is not an issue unless the convergence in question is an idealization of an approximation over the long term; and it's a much harder sell to argue that there has been no such convergence on any moral point, e.g., the evil of slavery. Indeed, as I've pointed out before, the UNICEF charter, and the Universal Declaration of Human Rights following it, are based on such a convergence: while people disagreed about the right sort of arguments to use to justify certain rights, it was clear that they could often agree on particular rights. The interpretations of those rights would not be exactly the same across different cultures, but, again, the variation is far from being a rigorous opposition. And this is, I take it, the mistake the authors are making: assuming that variation is a sign of non-convergence, which is straightforwardly false. To use a physical analogy, if you and I are converging on a point that we won't, at our present trajectories, reach before the week is out, the fact that we are not in the same place at the end of the first day is not evidence against the claim that we are converging. (For that matter, if at the end of the week we are not standing on exactly the same place, but instead are right next to each other, this is not evidence against convergence, either.) Convergence is a process; in the case of ideas, when we are dealing with such a large population as the human race, it is a complicated and sometimes extremely long term one. Even in clearly factual matters, human beings do not all converge directly and immediately on the same facts, the mere fact of variation tells us nothing at all about whether they are converging or not, and even if it did, it wouldn't be enough, because what's relevant is whether they are able to converge rationally. (One of the problematic assumptions of the article is that realists would have to 'explain away' diversity; when in fact all realists of any field need is an explanation of how convergence is possible, which basically comes down to the questio of how we know moral truths. Attacking this point would be a far stronger argument against moral realism than the mere fact that people have various opinions on moral matters, and certainly a better argument than the fact that people have different physiological reactions in the same situation.)

The point is not a minor one, for what's really being attacked here is the potential for social progress, and the denial of such progress has serious consequences. After all, social progress is simply convergence on a better position; and even moral anti-realists don't usually want to deny that in moral terms the repudiation of slavery has been convergence on a better position, even if they disagree with moral realists about what 'in moral terms', or even 'better', implies.

Hippocleides Doesn't Care

We are told by Herodotus that Cleisthenes of Sikyon had a daughter named Agariste, and, having won the chariot race in the Olympic Games, he sent out a proclamation telling all those who thought themselves fit to be a son-in-low to the great Cleisthenes to come by the sixtieth day to Sikyon. All the potential suitors of all the noble Hellenic families came. One of the Greeks from Athens, Hippocleides, the son of Tisander, was far and away the most promising suitor, being extremely wealthy and handsome and of good family. For an entire year Cleisthenes feasted them and tested them to see if they truly were worthy. When it came to the day the announcement of the victor was to be made, Hippocleides was, we would say, far in the lead, and throughout the feast that day he was the star of the show.

At one point, however, he decided he would dance to the flute, and he did, to his great enjoyment. Cleisthenes, it is said, looked a bit doubtful at it. But Hippocleides was enjoying himself, and had a table brought in, so that he could dance on the table. Which he did, dancing now in one style, now in another, until finally he stood on his head and began dancing that way, gesticulating his legs wildly. Up to that point, Cleisthenes was merely annoyed that Hippocleides would be his son-in-law; but, apparently, the sight of the young man dancing on his head was too much, and he exclaimed, "You have danced away your marriage, son of Tisander!" To which Hippocleides replied, "Hippocleides doesn't care!" This passed into a proverb; and (largely through the influence of Herodotus) it's still a saying indicating indifference even to something major.

Of course, to get the full force of the story you have to remember that standing on your head is a bit more shocking if you are wearing the garb of ancient Greece than if you are wearing the sort of thing we wear today. They, after all, did not have pants. And I am told that there's usually thought to be a pun in the story based on this since the word Cleisthenes uses for 'dance' has a verbal similarity to the word for 'testicle'.

The Truth to Make Them True

My Lord, I find that nothing else will do,
But follow where thou goest, sit at thy feet,
And where I have thee not, still run to meet.
Roses are scentless, hopeless are the morns,
Rest is but weakness, laughter crackling thorns,
If thou, the Truth, do not make them the true:
Thou art my life, O Christ, and nothing else will do.

From George MacDonald's The Diary of an Old Soul, for February 4.

Edwin Abbott Abbott online

Re-reading Abbott's Flatland led me to look into which of Abbott's other works are available online. As a rule the other works of this polymathic schoolmaster tend to be hard to find, but thanks to the Internet Archive, you can find several.

Onesimus is an interesting little didactic novel in which the slave Onesimus comes into contact with the intellectual currents of the first century, including paganism, Epicureanism, Stoicism, and Christianity. Abbott was a classicist, so he does an excellent job of getting the Epicureanism and Stoicism more or less right (although he acknowledges that to do so he has to engage in a certain amount of anachronism, to bridge gaps in our knowledge) while at the same time keeping them accessible. The work can be seen as an argument for Christianity in the form of a historical novel. One of the things that makes it interesting is that Abbott was what has variously been called a Modernist or a Liberal: i.e., he accepts that Christ is human and divine, and that the basic outlines of Christianity are divine revelation, but denies that miracles have ever occurred. He is, in other words, someone who regards Christianity as 'morally true'; he argues, for instance, that the miracle stories encapsulate important moral truths, but that they are cases in which valuable metaphors for moral life have been mistaken for physical truths. He prefers to call this 'spiritual Christianity' or 'natural Christianity'. Onesimus is a fairly enjoyable introduction to his views on this subject.

The reasoning behind this form of Christian thought is developed rather ingeniously in his work The Kernel and the Husk, which, while little-read, is one of the great classics of religious epistemology, an interesting counterpoint to Newman's An Essay in Aid of a Grammar of Assent, which takes a very different sort of line. Abbott develops similar issues in the less interesting but more systematic The Spirit on the Waters, where he argues for a form of spiritual evolution. (It's interesting that he uses Flatland in both works in order to illustrate his claims that omnipotence, omniscience, and omnipresence are not distinctive features of the divine.)

Mentioning Newman and Abbott as a sort of antithesis is fitting. In his day Abbott was perhaps the foremost Anglican expert on what might be called the Problem of Newman. The Problem of Newman, roughly speaking, is this. Here we have an Anglican, Newman, who is well-known to be an anxious seeker for truth, who is often considered to be one of the Church of England's top-tier minds even by those who disagreed with his views, and who made a very close and profound study of the history of Christianity, who feels drawn -- compelled -- to leave the Church of England and become Catholic. It's hard for us to grasp how serious an issue this was for Anglicans at the time, but many Anglicans followed Newman's path, and the three qualifications Newman possessed were enough to give many Anglicans pause who had no interest at all in becoming Catholics. Abbott, who had flirted with some of the ideas of the Oxford movement when younger, and who studied Newman extensively, wrote several works addressing the Newman Problem from various perspectives. His Philomythus is an attack on Newman's book on Ecclesiastical Miracles; it's a mix of insightful discussion, rant, penetrating criticism, and missing the point. There is a tendency here to read Newman very uncharitably, I think; but it has to be admitted that some of his criticisms do strike close to home. He has an interesting, and very sarcastic, satirizing of Newman's reasoning toward the end of the work.

Another of his works on the Newman Problem is The Anglican Career of Cardinal Newman (Volume 2 here), a sort of critical -- very critical, in parts -- biography of Newman in his Anglican period. One of the features of this work, as with Philomythus, that is difficult to get used to is that the criticism is largely psychologizing: it's an attack not so much on Newman's arguments as on his state of mind, and involves considerable speculation about what features of his psychology led him astray. It's certainly flawed in that sense, although it has to be recognized that in some sense the Problem of Newman is precisely concerned with Newman's state of mind: it's the question of how an Anglican mind, truth-seeking, ingenious, and well-informed, could become Catholic, and for the Anglican it's a problem precisely because the Anglican must suppose that Newman went wrong somewhere. Thus these works on Newman are Abbott's attempt to pin down what went wrong. The hazards of such an undertaking, however, are obvious; and one wonders what a biographer would make of Abbott if they were given the room for close critical scrutiny and psychological speculation that Abbott allows himself with regard to Newman.

One of Abbott's major influences was Francis Bacon. He wrote a book on Bacon's life and works that makes for interesting reading. Bacon's life is a very complicated one and Abbott does an excellent job both in clarifying it and in avoiding oversimplifications. Again, there's probably too much interest in lesser details of Bacon's psychology to be quite healthy, but as Abbott is not as thoroughly and hotly critical of Bacon as he is of Newman, it's less noticeable in this work. And to some extent, perhaps, it's a nineteenth-century British thing; witness the heated disputes over Newton's character.