Should we promote tolerant religion?

There's an interesting essay at Positive Liberty: While Europe Slept, by Jonathan Rowe. It made me stop and think. I'm an advocate for peaceful co-existence with religion; and have debated this up and down the blogs in recent times along with lots of other opinionated folks with diverse notions of how we relate to religion and to religious believers. The author of the above essay also advocates the gentle conciliatory approach, but with a bit of a twist.

You may want to read Jonathan's essay first, and then come back here to see what wisdom I can add. Because -- despite being a milk and mildness atheist myself -- I can see scope for my more hardline "new" atheist colleagues to use the same evidence Jonathan submits to argue for a negative effect of mild tolerance.

Jonathan adds a wrinkle to the notion of tolerance. He proposes that the founding fathers of the USA had a conciliatory approach to religion in which they deliberately promoted a notion of "authentic" religion that was consistent with their own secular ideals of liberality and tolerance. No matter that the actual divines of the time were still burning heretics and seeking to promote their notion of "right" religion with all the possible force available... the founding fathers deliberately chose to single out and promote forms of religion that were "compatible with liberal democratic, secular, pluralistic norms".

Jonathan proposes that we should be doing the same thing right now, with Islam. That is, in talking about Islam we should at every opportunity emphasize that "authentic" Islam is a religion of peace. As he says in the essay:

Whenever I criticize the more extreme elements of Islam, I always stress that most Muslims say this doesn’t represent the authentic version of their faith. Now, in truth, I have no idea whether I’m right and may well be engaging in a Straussian lie. But, if Islam, as a faith, isn’t going away — and I don’t think it is — Muslims must be convinced that a more liberal, sober and rational understanding of their faith is the authentic one. This is exactly what Madison tried to do with Christians in his Memorial and Remonstrance.

Can we identify a scientifically convenient authentic religion?

As I read this, I immediately thought of the ways in which we atheists approach religion. It's a hot topic in the blogsphere -- is religion the enemy of science? Or is religion (the "right" religion, of course) compatible with science?

The hardline approach is that religion and science are implacably opposed. Individuals may find a personal reconciliation; but only at the cost of their own personal consistency. It's an uneasy truce between opposing forces, and it invariably means that theists descend into unscientific nonsense at some point in this alleged reconciliation.

The conciliatory approach -- mine -- is that religion itself is consistent with science; though of course there are individual believers (creationists, for example) who hold views that are unambiguously falsified by the findings of scientists. But we tend to say that science is a process for finding things out, and that it can't find out everything. We tend not to think of science as requiring a belief in metaphysical naturalism, even though most of us actually do seem to be metaphysical naturalists -- disbelievers in God and in the supernatural. No matter; we admit that some of our scientific colleagues may have radically different metaphysical perspectives; and as long as they don't try to bring in the supernatural as a way of distorting the actual methods of scientific investigation, we don't mind what they believe. If you really can form your beliefs in such a way as to avoid being directly falsified by a line of empirical evidence, then you can be consistent with science.

Now there's something to be said for the notion that we are promoting as "authentic" a form of religion that is highly unusual and quite distinct from traditional religion all down the ages. It's not quite a total humbug, because religion does change over time; and there are plenty of religious leaders trying to promote an expression of their religion that remains fully consistent with all the discoveries of modern science. We tolerant atheists approve and encourage them.

But what if we succeed?

What will be the result? In the short term, I think the tolerant approach is pragmatic, and it may even succeed in making it possible for many in the churches to drag themselves out of the nineteenth century and share in the marvelous insights that are gained into our world when you look at it directly. And it seems that it worked for the founding fathers as well; modern religion (Christianity, at least) now recognizes many of the ideals of the enlightenment; ideals of human freedom and liberty and individual rights. Indeed, most Christians insist that this is "authentic" Christianity, and that the modern secular state only manages to retain such "Christian" ideals because of the beneficient influence of believers.

That's humbug. Religion has matured; and modern secular humanism has had a substantial positive effect. The process is not complete; but it's there, in my opinion.

And yet, and yet. Look at what we have today. The influence of religion on the social and political life in the USA is immense -- far greater than in other first world nations -- and it is to your detriment. Perhaps your founding fathers would have been better to discard any religious rhetoric altogether, and not be shackled with the Sisyphean task of dragging religion along with them as they built a new society.

You see, even if individuals of wisdom and circumspection manage to live peacefully with science, or with unbelievers, in each new generation this needs to be rediscovered. In each new generation, there are bound to be new believers who are intolerant, irrational and unwise. It's right there in the holy book; it is not a natural thing to impose tolerance and scientific literacy in ancient texts going right back to the bronze age.

Perhaps the USA would had avoided the problems she now has with such a substantial influence of religion on political and social life, if there had been less of a deliberate attempt to promote an improved modernized version of religion.

Here I stand, for the time being.

I'm still a tolerant atheist. I still think that religion can be compatible with science, for those believers who deliberately let all the findings of modern science inform the content of their faith.

I can't manage it myself; but I don't charge that others who find a stable reconcilation are necessarily being inconsistent. I'm not particularly concerned to persuade them to change, unless they want to engage in mutually respectful debate and discussion, in which case I will argue that there's excellent reason to think no God exists. I do aim to be persuasive for that position, though relaxed if others are not persuaded.

I am much more concerned with promoting a good education in science and history, and to that end I am happy to hold up as examples of "reasonable" religion those who do manage the reconciliation. And in this I am actively trying to influence the shape of religion in the future, despite the fact that I am not religious.

My own guess is that this is the most effective approach for addressing the problems with science education posed by creationism and other forms of pseudoscience. My own guess is that shifts in religion of this form will also tend to erode religion. There is an inertia to our beliefs. It's not easy to move them, but once they start to shift they do tend to continue to slide. It's not my objective, but it is my expectation that in encouraging a more "reasonable" religion, in the sense of one that is reconciled with the findings of science, I am also contributing to the gradual erosion of religion.

But I think I do understand the concerns of my more hardline fellow unbelievers. What do you think?

(Thanks to Bob Englehart for the cartoon. See it in his blog.)
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Duas Quartunciae on the Blogging Blues

I have more ideas for blog material than I have time to put them together. The blog has been up now for nearly a month, and it's off to a good start. I have a little to-do list of blog posts, that grows faster than the post get completed. I also have thoughts about the design and layout of the blog itself; I want to learn more about the underlying systems and put them to best possible use. And I have a real life, to which I allocate a bit of time occasionally.

Feel free to drop a comment here if you have some suggestions for what works and what does not, or what should change.

Here's an idea others may like to consider. On my sidebar I have a list of some of the posts on other blogs where I have left a comment. I spend time reading what other people are saying and engaging on their blogs. This list gives a gong to those blogs for saying something interesting, whether I agree with it or not. It might be something to consider including on your blogs as well.

More ideas after the fold: I don't like the blogger comment system at blogger.com. A few more html tags would be nice, and especially something for quoting a previous commenter. I'd also prefer the text box to appear on the same page as the other comments, rather than a special pop-up.

Here's a suggestion for colleagues at blogspot... put the little orange feed icon next to your feed links.

I'm thinking of getting a few pages set up at googlepages or some other hosting service, and having them linked from my blog front page, for certain kinds of information -- like a large blogroll or whatever -- that I don't think should load up everytime someone looks at my front page.

I don't know what kinds of functionality is appreciated by visitors. Technorati button, stumbleupon, or anything else. A blog can easily get overloaded with functionality like that; so what gives real added value?

As for posts, I want to have a few more of useful content. I have ideas for posts on a few simple maths topics, on some more religion/unbelief issues, on some cosmology. I'm considering a bit of a childhood autobiography which shows up some influences that continue to impact on how I do things.

I want to redesign the template of the blog, to use tags better, like the heading tags, as recommended by some of the style guides.

And what about my feeds? The standard blogger feeds seem to be missing a description of some kind. At least, they don't show up properly for Pharyngula's blog harvest systems. And should I use a full feed, or a partial feed? I'm not sure.

Suggestions, on anything, will be very welcome!

(Thanks to icanhascheezbuger.com for the lolcat lion. Follow the link for lots more lolcats.)

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One hundred books meme

To keep the blog ticking over until I get around to my next topic blog, here is a quick meme contribution. I picked this up from Grrlscientist at Living the Scientific Life. The idea is to take this list of 100 books (how was it originally chosen?) and record it with all the ones you have read in bold, and the ones you want to read in italic. The ones in which you are not interested stay unemphasized. Please check my list and draw my attention to those I SHOULD want to read, but have failed to emphasize!

I've left unchanged any I did not recognize; and this is bound to include some serious omissions. I propose that commenters should please single out any one (or more) that I SHOULD want to read!

It is also amusing to click back through the history of the meme. Grrlscientist links to her source, and you can keep going back.

1. The DaVinci Code (Dan Brown)
2. Pride and Prejudice (Jane Austen)
3. To Kill A Mockingbird (Harper Lee)
4. Gone With The Wind (Margaret Mitchell)
5. The Lord of the Rings: Return of the King (Tolkien)
6. The Lord of the Rings: Fellowship of the Ring (Tolkien)
7. The Lord of the Rings: Two Towers (Tolkien)
8. Anne of Green Gables (L.M. Montgomery)
9. Outlander (Diana Gabaldon)
10. A Fine Balance (Rohinton Mistry)
11. Harry Potter and the Goblet of Fire (Rowling)
12. Angels and Demons (Dan Brown)
13. Harry Potter and the Order of the Phoenix (Rowling)
14. A Prayer for Owen Meany (John Irving)
15. Memoirs of a Geisha (Arthur Golden)
16. Harry Potter and the Philosopher’s Stone (Rowling)
17. Fall on Your Knees (Ann-Marie MacDonald)
18. The Stand (Stephen King)
19. Harry Potter and the Prisoner of Azkaban (Rowling)
20. Jane Eyre (Charlotte Bronte)
21. The Hobbit (Tolkien)
22. The Catcher in the Rye (J.D. Salinger)
23. Little Women (Louisa May Alcott)
24. The Lovely Bones (Alice Sebold)
25. Life of Pi (Yann Martel)
26. The Hitchhiker’s Guide to the Galaxy (Douglas Adams)
27. Wuthering Heights (Emily Bronte)
28. The Lion, the Witch and the Wardrobe (C. S. Lewis)
29. East of Eden (John Steinbeck)
30. Tuesdays with Morrie (Mitch Albom)
31. Dune (Frank Herbert)
32. The Notebook (Nicholas Sparks)
33. Atlas Shrugged (Ayn Rand)
34. 1984 (Orwell)
35. The Mists of Avalon (Marion Zimmer Bradley)
36. The Pillars of the Earth (Ken Follett)
37. The Power of One (Bryce Courtenay)
38. I Know This Much is True (Wally Lamb)
39. The Red Tent (Anita Diamant)
40. The Alchemist (Paulo Coelho)
41. The Clan of the Cave Bear (Jean M. Auel)
42. The Kite Runner (Khaled Hosseini)
43. Confessions of a Shopaholic (Sophie Kinsella)
44. The Five People You Meet In Heaven (Mitch Albom)
45. The Bible
46. Anna Karenina (Tolstoy)
47. The Count of Monte Cristo (Alexandre Dumas)
48. Angela’s Ashes (Frank McCourt)
49. The Grapes of Wrath (John Steinbeck)
50. She’s Come Undone (Wally Lamb)
51. The Poisonwood Bible (Barbara Kingsolver)
52. A Tale of Two Cities (Dickens)
53. Ender’s Game (Orson Scott Card)
54. Great Expectations (Dickens)
55. The Great Gatsby (Fitzgerald)
56. The Stone Angel (Margaret Laurence)
57. Harry Potter and the Chamber of Secrets (Rowling)
58. The Thorn Birds (Colleen McCullough)
59. The Handmaid’s Tale (Margaret Atwood)
60. The Time Traveller’s Wife (Audrew Niffenegger)
61. Crime and Punishment (Fyodor Dostoyevsky)
62. The Fountainhead (Ayn Rand)
63. War and Peace (Tolstoy)
64. Interview With The Vampire (Anne Rice)
65. Fifth Business (Robertson Davis)
66. One Hundred Years Of Solitude (Gabriel Garcia Marquez)
67. The Sisterhood of the Traveling Pants (Ann Brashares)
68. Catch-22 (Joseph Heller)
69. Les Miserables (Hugo) unabridged, thank you very much!
70. The Little Prince (Antoine de Saint-Exupery)
71. Bridget Jones’ Diary (Fielding)
72. Love in the Time of Cholera (Marquez)
73. Shogun (James Clavell)
74. The English Patient (Michael Ondaatje)
75. The Secret Garden (Frances Hodgson Burnett)
76. The Summer Tree (Guy Gavriel Kay)
77. A Tree Grows in Brooklyn (Betty Smith)
78. The World According to Garp (John Irving)
79. The Diviners (Margaret Laurence)
80. Charlotte's Web (E.B. White)
81. Not Wanted On The Voyage (Timothy Findley)
82. Of Mice And Men (Steinbeck)
83. Rebecca (Daphne DuMaurier)
84. Wizard’s First Rule (Terry Goodkind)
85. Emma (Jane Austen)
86. Watership Down (Richard Adams)
87. Brave New World (Aldous Huxley)
88. The Stone Diaries (Carol Shields)
89. Blindness (Jose Saramago)
90. Kane and Abel (Jeffrey Archer)
91. In The Skin Of A Lion (Ondaatje)
92. Lord of the Flies (Golding)
93. The Good Earth (Pearl S. Buck)
94. The Secret Life of Bees (Sue Monk Kidd)
95. The Bourne Identity (Robert Ludlum)
96. The Outsiders (S.E. Hinton)
97. White Oleander (Janet Fitch)
98. A Woman of Substance (Barbara Taylor Bradford)
99. The Celestine Prophecy (James Redfield)
100. Ulysses (James Joyce)
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Explaining theistic evolution to Martians

PZ Myers has requested an explanation of the difference between theistic evolution and intelligent design. Furthermore, he suggests that we imagine he's a Martian. This is a constructive suggestion, and I shall give it my best shot. I'm not sure what Martians are really like, so I'll presume that they are like PZ.

Background on Martians, for any human readers

Martians have good understanding of the natural world, and good appreciation of the areas where we don't have answers as yet. Technologically and scientifically, Martians are pretty much at the same position as humanity. Martians are social animals; who form stable family groups, and also like to engage constructively with others of their species. They are willing to put significant time and energy into their wider society, and put high importance on the well being of their fellows. They are curious about the world and seek to learn about it, and to share what they have learned, with passion and enthusiasm.

However, Martians have no concept of religion, or of a supernatural, or of Gods. They've heard about such things, since they regularly tap into the broadcasts we humans have been making; but this is one aspect of human society that Martians just don't get. They are inclined to think that humans who believe such things are, well, "a couple of tentacles short of a full cranium".

---

Welcome and Introduction

Honourable Ambassador, welcome to the third planet. You are aware, of course, that humans have a range of curious notions about the nature of the world. One common belief, in which you have expressed particular curiosity, is the notion of "God", an invisible intangible powerful conscious being. The reasons people believe such a thing are many and varied. None of them are particularly good. Humans are prone, from time to time, to have strange beliefs without any good evidence. A few other examples: We were meant to be together. I can still drive just fine. This shirt brings me luck.

The diversity of human beliefs about "God" is enormous, and many of them are in direct conflict with easily confirmed common knowledge about the world. Other beliefs about God are technically consistent, in the sense that they don't seem to make any empirical difference to anything we can effectively observe or sense.

Many people believe that such a being is responsible for making the world. The term "creator" is used, suggesting that in some way the putative intangible "God" causes other more tangible things to exist in the forms we can observe. This belief in a creator takes an enormous variety of forms.

Although none of these beliefs are well founded, it has still been convenient to classify some common themes. I shall attempt to describe three, and explain the utility for these broad classifications.

Creationism

This term is used for a belief that "God" used an act of special intervention to create things, in particular the universe, this particular planet, and the first living things. This belief has real substantive content (albeit ludicrous). It represents the creative act as a genuine alternative to the conventional discoveries we have made about how things were actually formed. It is common to hold that the interventions occurred comparatively recently, though there are exceptions. Creationists reject the notion that the form of living organisms, and humans in particular, can have evolved. They reject the discovery of biological evolution, the discovery that contemporary living forms developed from radically different ancestors by the agency of cumulative variation along a lineage modulated by natural selection.

Intelligent design

This is a form of creationism that has been shorn of any actual content. For political reasons they avoid explicit mention of God. In an effort to avoid refutations they avoid making any positive claims about, well, anything at all. They do reject the efficacy of natural processes and biological evolution in particular as the means by which living things take the forms we now observe, and their reasons and arguments are the same as those used by other creationists. They hold that living forms must have been "intelligently designed" instead – though they have no actual account of what that might mean. It's basically conventional creationism cut down to remove anything positive or any explicit mention of God.

Theistic evolution

The creationist position can be pared down even further, so that nothing is left except the statement that God is creator. To this, theistic evolution makes one new addition – explicit recognition of the validity of evolutionary biology. The theistic evolutionist considers that natural processes like evolution are the means by which the creator creates. How this works is unclear, and it is not something that is argued from an empirical basis.

Why distinguish intelligent design and theistic evolution?

Although intelligent design is a form of creationism, the same cannot be said for theistic evolution – at least given the ways of using terms I have described here. Creationism, including intelligent design, sees the action of God as something that is contrasted with the action of natural processes. Creationism is incompatible with evolutionary biology, because it is presented as an alterative to evolutionary biology.

Theistic evolution, on the other hand, recognizes evolution as a valid description of how living things came to have their currently observed physical forms. Theistic evolution sees God as in some sense responsible to the establishment of the evolutionary process itself; either by setting up initial conditions so as to enable evolution, or else by continuously maintaining the existence of a universe in which evolution can occur. There is no evidence for either proposition; but theistic evolution is not claimed to be a scientific model based on evidence; but rather a nebulous faith statement about some unevidenced responsibility of "God" for the ongoing operation of all aspects of the natural world.

The reason this distinction is of any interest to those who do not believe in God arises largely from a concern about science education.

Creationism, including intelligent design creationism, incorporates an explicit rejection of basic science. The cut down version of creationism called intelligent design is specifically tailored to avoid the social protections we have set up for education. Advocates for these notions are active in trying to degrade and distort science education, by inclusion of various trivially fallacious and pseudoscientific notions under the basically dishonest guise of alternative scientific models. They necessarily see the teaching of basic science as teaching a denial of their own beliefs.

Theistic evolution, on the other hand, is an unscientific add-on to conventional science. Most theistic evolutionists recognize that this add-on is not science, and do not seek to include it in the teaching of science. They do not regard the teaching of conventional science as a denial of their own beliefs.

Two design arguments

A convenient way to identify this subtle but significant distinction is to look at the perspective of the two groups on design. The arguments or apologetics given for beliefs about design and a creator come in two diametrically opposite forms.

Intelligent design and creationism claim that the natural processes studied by science are inadequate as an explanation for complex living things, and on that basis they claim that some other better explanation is required, which they label "design".

Theistic evolution considers that the natural processes studied by science are extraordinarily effective as an explanation for complex living things, and on that basis they claim that this fecundity was established by design.

One group sees design in the putative inadequacy of natural processes. The other sees design in the efficacy of natural processes.

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Update: May 16 12:45. On reflection, I think the term "theistic evolution" is potentially confusing. What I really mean by that is "theism and evolution". The actual scientific descriptions of evolution remain totally unchanged. It's not a different theory of evolution; but the position of accepting perfectly conventional evolutionary biology while also being a theist. How theism can be consistent with evolutionary biology is a problem for theology, or for general theism/atheism debates. Such debates are fine by me; I engage in them also.

I was prompted to make this remark by reading these comments left at another blog, by Tyler DiPietro. I've also acknowledged below in comment #9.
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Gervais explains Creationism from the source

Lots of people have picked up on this, and rightly so. Very funny. An excellent comic considers creationism. I sometimes think a good belly-laugh achieves more than any of our scholarlary demolitions. Part two below the fold.



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Landing an F15 with only one wing.

What do you do when a wing is torn off your F15?

If you are Captain Zivi Nedivi, of the Israeli airforce, you break off from your training exercise and return to base. You've only got one wing, but you make up for that by flying twice as fast.

This really happened, on May 1 1983, over the Negev desert. The F15 Eagle collided with an A4 Skyhawk. The Skyhawk was destroyed, though I understand that the pilot ejected automatically and survived. The Eagle had a wing torn off, but the pilot incredibly managed to regain control and return safely home.

There's a great video reenactment of this, and I've added a partial transcript of the pilot's own account. The video was made by the history channel. All the moving pictures are reconstructions of some kind, but there are authentic still photos of the F15 after landing, at the end of the clip.

I've made a rough transcript, with a few "um" and "er" omitted. Portions in italic are spoken by the pilot.

Captain Zivi Nedivi experiences a pilot's worst nightmare when a training exercise goes horribly wrong.

He is flying a simulated airfield defense mission and is tasked with intercepting hostile aircraft, when disaster strikes

I saw what in hindsight was the number three, which is the leader of the second, the rear air, and he was upside down and I was around thirteen, fourteen thousand feet and I shot a missile.

Even though he was upside down, he continued to go up, and I was like this so it was stomach to wing, we couldn't see each other, and, uh, we collided.

Big commotion, big bang. The A4 basically fireballed immediately and I found myself with maybe thirty degrees nose down attitude and the aircraft was spinning.

Right after the crash I told my navigator "Prepare to eject, we're going to eject".

I opened afterburner, which is a totally opposite instinct when you're spinning towards the ground. Then the roll slowly stopped and slowly I was able to bring the nose back up.

I told my wingman to come close and to inspect me. There was a huge spray of fuel that was being drawn out of the wing, and it basically camouflaged what was going on there.

Nedivi survives the midair collision. He is ten miles out from the nearest airfield and hopes to still land safely. The pilot cannot see what has happened behind the spray of leaking fuel. His F15 has been so badly damaged in the collision that he is flying on just one wing.

[…]

After a devastating midair collision, Captain Zivi Nedivi finds himself flying a seriously damaged F15. Somehow he is able to regain control over his aircraft, and attempt a landing.

I approached the airfield. I crossed the threshold. Where usually in an F15 you cross at 130 knots, I crossed at anywhere between 250 to 260 knots.

He was landing at approximately twice the normal landing speed.

I put the tailhook down. There was a cable at about a third of the runway, and we went into that cable. But because of the speed, the hook is not built for those speeds and the hook basically tore off the aircraft.

We stopped maybe twenty feet short of the barrier.

As I was running the last fifty knots, bleeding off, my wingman said: "You're not going to believe what you flew on."

And I opened the canopy and I reached back to shake the hand of the navigator. And as I was reaching back, that was the first time that I looked and I saw that I didn't have a wing on the right hand side.

It's highly likely that if I would have seen it clearly I would have ejected, 'cause it was obvious you couldn't really fly an aeroplane like that. I don't think any other aircraft could have taken that amount of damage or that portion of its flight surfaces removed and continue to bring us home safely.

The best testament was a good friend of mine who was an F16 pilot, and he crossed and he saw that there was no wing, and his first words was "Can I transfer to F15s?"

It should be aerodynamically impossible for an aircraft to fly with one wing missing. McDonnell Douglas sends a team to investigate the incident.

Their first inclination was it was a taxiing accident. It couldn't happen in air in the aeroplane, and only when they later went to analyse it and said: "OK. The F15 has a very wide body, and you fly fast enough and you're like a rocket. You don't need wings."

The story has been told in various other locations. Here is another widely cited article: Mission Impossible. Apparently, the aircraft was repaired, with a few new parts (like a wing, for example) and restored to active duty in two months.

I found this just mind blowing. Hope you enjoy it as well!

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Teach the controversy

Evolutionary biology is a vibrant field of science, and full of active dispute and uncertainty and new discovery. Science education ideally gives students the basic background so that can find their way around popular descriptions of what is going on at the bleeding edge of research.

Here are some of the controversies that could easily be part of a lesson even in high schools.

1. The Cambrian Explosion. About 530 million years ago, and over a period of some 10 million years or so, there was a dramatic diversification of animal life, the like of which has never been seen before or since. There are a host of unanswered questions and hypotheses about what is involved. When it occurred, how long it lasted, what are the antecedents, what changes took place, what mechanisms were involved. It is seen as an artefact of sampling, giving limited insight to a much more spread out period of change, or as a comparatively abrupt phase shift in the biosphere. It's seen as driven by evolution of exoskeletons, or of vision, or of predation, or of HOX genes. It is seen as driven by oxygenation, or warmer temperature, or changes in the sea floor. On going investigations continue to shed light on this fascinating period, but it's still wide open for new research and ideas.

2. Horizontal transfer verses variation through descent. For the most part, we carry within our bodies the genetic heritage of our ancestors; but there are also possibilities for genetic information to become incorporated into the genome from other organisms or a virus. This is particularly common in bacteria, but it can also occur for more complex organisms. The extent and importance of this is an open research question.

3. Particulars of lineage and relationships. There are many cases in which scientists are uncertain as to the relationships of different organisms. A classic example is the whole dinosaurs to birds issues, though this one is now all but resolved. There are plenty more that remain wide open. One example would be relationships between insectivores (insect eaters -- shrews, hedgehogs, moles, tenrecs, etc). There are many other examples.

4. Drift verses positive selection. It's a common misconception to think of evolution as a kind of continuous progress in improved fitness. Recent decades have given strong support for a notion of neutral drift, and the development of characteristics that are not adaptive, but simply a consequence of accumulated neutral change. What features of an organism actually are adaptive, or a result of positive selection? There are ways to measure this when we have access to a DNA sequence. With fossils and paleospecies it gets more difficult.

5. Target of selection. People often think they understand selection; but what is selected? Is it genes? Individuals? Populations? Species? All of these have been proposed as targets for selection, and the debate continues as to their relative importance.

6. Evolution and behaviour. We are more than our physical forms; we also have tendencies and predilections for different kinds of behaviour. To what extent is behaviour subject to evolution? This is a very difficult and contentious dispute!

7. Physical details of microevolution. There's still a lot we don't know about how development works, and how variation accumulates from generation to generation. What kinds of change can arise in the genome? Genes are far more than a coded protein sequence. They come with promoter regions and splicing points, and ways of encoding multiple proteins depending on how exons are combined. Evolution can duplicate whole genes, or combine them, or alter the regulatory promoters. Some parts of the genome are much more subject to variation than others. What kinds of variation are possible? What is their relativity frequency and importance? What proportion of variation is deleterious? How important is the piggyback effect where selection for one variation carries along other consequences? I'm only touching on the huge range of active research questions here.

I'm not a biologist. If you can educate me further in any of these or add some more, please leave me a comment!

(Disclaimer: this post is a repeat with minor revisions of something I wrote sometime ago in a discussion forum.)

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Update: I omitted to say why I wrote this. It was originally given in the context of creationist notions about teaching the controversy. I intended to contrast what genuine scientific controversy looks like, as opposed to the screwy notions of creationists.
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