Fifth stray dog of 2009

Although we've seen quite a few, our fifth stray dog of 2009 that we actually caught and turned in came only yesterday, almost ten months after the fourth. The frequency dropped way off after the first couple of months of the year--a sign of economic recovery, perhaps? (I wonder what the fact that we now regularly see coyotes in our neighborhood means...)

We found this beautiful brindle-coated female dog at Shawnee Park in Chandler, running around loose with a collar and no tags, while we were out with a dog from Arizona RESCUE (Scout, a Dane mix, another great dog). Nobody in the area knew who she belonged to, so we took her to the east side pound and put her picture up on Pets911.

Vocab Malone on abortion and personhood, part 1

Vocab Malone has put up his first post arguing for the position that "the unborn human embryo is a full person at the moment of conception and should be afforded the full rights due human beings by their very essence."

Criteria of Personhood or Humanity
He starts by looking at the question of what it is to be human or to be a person, citing a few historical references of individual characteristics--being rational, being "in relationship," and "the capacity for self-objectification." He expresses doubt that any single characteristic is appropriate, on the grounds that human beings undergo changes of state such as being asleep or being drugged, or not thinking. I agree with him that the characteristics he has listed won't do the trick, and I also agree with him that features that go away when we sleep are inadequate. But it doesn't follow that there is no single feature that can do the trick--if the feature is a capacity that we have, for example, that capacity doesn't cease to exist when it's not being used.

He goes on to note that lack of personhood doesn't entail that any treatment is morally permissible, pointing out animals as examples of nonpersons that deserve humane treatment. Again, I agree with him--and observe the converse, that possession of personhood doesn't mean that there are no cases where it can be moral to kill a person--cases of self-defense, euthanasia, capital punishment, or war come to mind as possibilities. But what makes animals deserve humane treatment is that they have certain capacities and interests, such as an inner mental life that includes at the very least the ability to feel sensations--and note that humane treatment doesn't necessarily entail a right to life on the part of an animal, or a duty on our part not to kill them.

Vocab appears to want to lay the groundwork for rejecting the use of a criterion of personhood in favor of a criterion of humanity as his standard for arguing against abortion, but here he only offers a promissory note and doesn't provide an argument to that effect. I think this is a mistake, however, because ethical distinctions should be based on morally relevant features, and I don't believe species membership is any more relevant in and of itself to being the holder of rights or of being the object of duties than is race or gender. If a member of an intelligent alien species capable of language were to make contact with us, my intuition is that we would attribute personhood to that entity and give it the same consideration as a human being. Likewise if we manage to build artificially intelligent, self-directed machines with beliefs, desires, and intentions, though the intuition is not as strong there unless I imagine them to have mental lives similar to our own.

Conception: Fertilization
Even though Vocab hasn't yet given a reason to reject a personhood criterion in favor of a human being criterion, the rest of his case is solely about human life rather than personhood, which I think is the wrong issue for the reasons I just gave. He argues that human life begins at conception, and clarifies that he means fertilization rather than implantation. This choice means that 30-50% of human lives are spontaneously aborted due to the failure of the fertilized ova to implant in the uterine wall. If Vocab thinks that this loss of human life is the loss of beings with rights and interests to whom we owe a duty to enable them to live out normal lives, then he has some explaining to do. First of all, why would a loving God create a human reproductive system that resulted in such a Holocaust of lives lost before they get a chance to start? Second, why has no one considered this to be a serious ethical problem that we need to urgently devote medical resources to address? We can call this the problem of natural abortion, which has both a natural evil and human evil component that requires justification.

Complete at Fertilization?
Vocab says that at conception (by which he means fertilization), "every human is complete and alive." I agree that a fertilized human ovum is alive--as life is a continuous process, arising from living components, at least until synthetic biology gets to the point of creating life from entirely nonliving components. Sperm and ova are also alive. But it is certainly not complete--zygotes have no brains, no central nervous systems, no organs, no body parts other than undifferentiated, identical cells.

An Individual at Fertilization?
Vocab also says that at fertilization and pre-implantation, "it is not merely a collection of cells lumped together but an actual individual." This also need not be the case. At fertilization, a zygote is an undifferentiated cell that undergoes a process of division without changing size for several days, to become a blastocyst by about the fifth day. During this period each of its cells is totipotent, meaning that each individual cell has the potential to become a full human being. Sometimes more than one of the cells does become a separate human being, as in the case of identical twins. In the case of identical twins, if they don't split completely, they may become conjoined twins or parasitic twins, or one twin may be completely absorbed into the other or otherwise fail to develop and become a vanishing twin. Where a vanishing twin occurs with fraternal twins, the resulting individual can be a chimera, with two sets of DNA. Should we also grieve for those twins who fail to develop, either due to failure to split off or failure to develop?

The science fiction scenarios of teleportation that create interesting philosophical puzzles for the notion of personal identity are real puzzles for a view that attributes personhood to zygotes, though without the additional problem of memories and experiences, since zygotes are undifferentiated cells.

Blastocysts
Once the zygote becomes a blastocyst, it forms into an outer layer of cells, which later becomes the placenta, and an inner cell mass of pluripotent embryonic stem cells, each of which is capable of differentiating into any kind of human cell. Only after this stage does the blastocyst implant in the wall of the uterus, about a week after fertilization, and begin taking nutrients directly from the blood of the mother--a dependency that can itself be of moral significance, as Judith Jarvis Thomson's violinist argument shows. As already mentioned above, a great many fertilized ova do not reach this stage. Further, the percentages of implant failure are higher for in vitro fertilization (IVF), a procedure which Vocab's criteria would have to declare unethical, even though it is the only way that many couples can have their own biological offspring.

It should also be noted that the process of therapeutic cloning involves taking a female ovum (which Vocab doesn't seem to indicate he considers to be a bearer of rights on its own), removing its haploid DNA, inserting the nucleus from a (diploid) human somatic cell (this is called somatic cell nuclear transfer), and giving it a shock to cause it to start dividing just like a fertilized egg. This occurs without fertilization by a human sperm. Once it reaches the blastocyst stage, its inner cell mass is harvested for embryonic stem cells, which destroys the blastocyst in the process. The natural process of fertilization never takes place, but there's little doubt that reproductive human cloning is possible via this process. Vocab's choice of fertilization as key suggests that there is no moral issue with this process, even though it also has some potential to become a human being. Further, if fertilization is a necessary, not just a sufficient, condition for rights, Vocab's view suggests that human clones would have no rights.

Fully Programmed?
Vocab goes on to say that "the embryo is already 'fully programmed' (to use computer language). This means the pre-implanted embryo needs no more information input at any further point in its development." While this was formerly believed to be the case about the individual embryo's biology, we now know that the environment of development can play a role in the characteristics that will come to be exhibited, such as from mRNA supplied from the mother to a developing embryo after fertilization and prior to zygote formation. But in any case, I would maintain that it's not our cellular biology that gives us moral value, as opposed to our capacities to have interests, desires, intentions, plans, sensations, and so forth--all capacities that zygotes lack.

Vocab ends this piece with some anthropomorphizing of zygotes, which appears to me to be a highly misleading form of argument--his analogies cannot be taken literally, since zygotes have no mental processes.

Human and Living = Human Being?
I agree with Vocab that a fertilized human ovum is living, that it's human, and that, if all goes well, it will become one (or more) individual human beings. I don't agree that it's yet a person or a "human being," since it lacks the requisite parts and capacities.

To sum up:

1. Vocab hasn't given a reason to favor a criterion of "being human" over personhood for determining when it's legitimate to attribute rights or incur duties on our part.
2. His choice of fertilization as the point at which rights begin is not when life begins (as it is continuous) and implies that a large percentage of rights-bearing entities die without any apparent concern from God or those who share Vocab's views, an inconsistency requiring justification and explanation.
3. A zygote has the potential to be not just one person, but multiple. The same lack of concern over non-actualized multiples that could have been born requires explanation.
4. Vocab's view suggests that IVF, which similarly loses even more zygotes or blastocysts (not even counting the embryos that are left frozen or discarded), is unethical.
5. Vocab's view so far gives no reason to classify human therapeutic or reproductive cloning as unethical--but might even entail that human clones have no rights, since there's no fertilization by a human sperm, if he thinks that fertilization is both a necessary and sufficient condition for rights.
6. In the stages of life described so far, we've gone from completely undifferentiated totipotent cells to a differentiation between two types of cell, the outer wall of the blastocyst (which we both agree is neither a person nor a human being, but what becomes a placenta) and an inner cell mass of embryonic stem cells. Vocab hasn't given a reason why we should give that rights or moral value.
7. At this state, the embryo is dependent upon the mother for its existence; Vocab will need to give an account of how the mother's rights are weighed against the embryo's in light of arguments like Judith Jarvis Thomson's violinist example.
8. Vocab calls a fertilized zygote a "complete" human being and implies that it has everything it needs to determine its future state, but this is neither the case biologically (given maternal effects on development, for example) nor regarding features that we consider quite important for human value, such as those that develop as a result of acquisition of language, ideas, experiences, and so forth.
9. Vocab has used some anthropomorphic language in describing the implantation process which is misleading since zygotes have no mental processes.

Continue to part two.

UPDATE (December 12, 2009): Added the sentence on chimeras.

UPDATE (December 13, 2009): Vocab has posted a brief rebuttal to this post.

Discussion on abortion and personhood w/Vocab Malone

Local Christian hip-hop artist and slam poet Vocab Malone, who I've interacted with online and met when Daniel Dennett spoke at ASU early this year, asked me in January for my thoughts on abortion and personhood. He's now written a paper on the subject which he's asked me to critique, and we thought it would be interesting to see how it would work out to do it in a public manner via our respective blogs. The plan is that he will post successive sections of his paper on his blog, and I'll respond here, with cross-links to share some traffic and discussion. Both of us allow blog comments; it probably makes the most sense to post your comments at the blog for the person you'd like to see a response from.

Vocab has posted an introduction and the comments that I originally sent to him on the subject at his blog, Backpack Apologetics. He's taking a position that I think is very difficult to justify, that full personhood and human rights are acquired at the moment of conception--we'll have to see which definition of conception he chooses, fertilization or implantation.

Just to throw out a little issue I raised this semester in one of my classes--some have argued that climate change raises the ethical issue of a duty to future generations. If we can have moral duties now to people who don't exist at all yet, what does that imply about duties to embryos?

Reed Esau on "Taking Ownership in Skepticism"

SkeptiCamp founder Reed Esau has finally taken the plunge and started blogging at "an illustrative account"--check out his interesting post on "Taking Ownership in Skepticism."

Bad news for agnostics?

While past studies have shown religious believers to be happier than nonbelievers, some new analysis shows that it's not quite so simple. Luke Galen has found that the convinced non-religious are also quite happy, but people who are uncertain are the ones who are dissatisfied. Adam Okulicz-Kozaryn has analyzed data from the World Values Survey and found some more interesting details:

• Religious people are both happier and unhappier. While a higher percentage of religious people report themselves as extremely happy than convinced nonbelievers, a higher percentage of religious people also report themselves as extremely unhappy.
• Those who attend religious services and belong to religious organizations tend to be happier. And that's whether or not they believe--in fact among that group, those with the stronger belief tend to be unhappier. So it's the social aspect, not the doctrine, that promotes happiness. And this is further supported by:
• The more religious a country is, the happier believers are, and vice versa. In religious countries, believers are happier; in nonreligious countries, nonbelievers are happier.

See more at the Epiphenom blog.

(Cross-posted to the Secular Outpost.)

Why not put Rom Houben's facilitated communication to the test?

I've posted comments about the reasons to be skeptical about Rom Houben's facilitated communication at a number of blogs, where the response of some seems to be that there is no point of such testing. The reasons for not testing have included (1) that the videos are a "straw man"; (2) that criticisms from a stage magician and a philosopher/bioethicist are not worthy of attention; and (3) the testimony from Dr. Laureys, the facilitator Mrs. Wouters, and Houben's family is much stronger evidence than what we can see in the videos, and that Dr. Laureys says he already conducted a single-blind test which showed that the communication came from Houben, not the facilitator, and to reject that is irrational hyper-skepticism that assumes they are lying.

The first argument makes no sense to me. The videos clearly show the facilitator rapidly typing away with Houben's finger even while he's looking away or has his eyes closed, which is by itself a very strong reason to be skeptical, especially in light of the past record of facilitated communication. The second argument is not only ad hominem, but further refuted by similar analysis by a neuroscientist. The last argument is a bit better, but wrongly assumes that the only alternative is that the doctor and family are lying. Facilitated communication isn't a matter of conscious fraud, it's a matter of self-deception of the facilitator (enhanced by the expectations and reactions of the family). Given the possibility of unconscious cuing of the facilitator by the doctor, as well as his own vested interest in a positive result, the test he described doing is still far from sufficient to overcome the evidence plainly displayed in the videos.

Unfortunately, there is a very strong incentive to believe on the part of the doctor, the facilitator, and the family. To find that the communications are coming from the facilitator would be emotionally devastating, and detrimental to the doctor's credibility. To test further is to risk a huge potential loss of what has apparently been gained, and I suspect it's unlikely that we'll see it happen.

But look at it from Houben's own perspective--further testing is absolutely in his own best interests. For if the facilitator is the one doing the communicating, not him, then he is being further exploited for the satisfaction of his doctor, facilitator, and family, not for his own benefit. He's not being treated respectfully or as an end, rather than as a means. If he is, in fact, minimally conscious as the brain scans suggest, then speaking on his behalf without his genuine input is doing him even greater harm.

If you reject the idea that an hour or so of Houben's time should be used to do a conclusive, double-blind test to see whether the communications are coming from him or from the facilitator, is it because you want to believe, rather than to know? There is clear possible harm to Hoeben from not doing such a test. There is no harm to Hoeben from such a test, though there's clearly the risk of painfully dissolving an illusion for the doctor, facilitator, and family. But Hoeben's interests should be placed above that risk.

(Previously on Houben, a post with many links and references.)

UPDATE (February 15, 2010): Houben has been put to the test, and it turns out the communications were, in fact, coming from the facilitator.

UPDATE (February 20, 2010): David Gorski at the Science-Based Medicine blog has a bit more from the Belgian Skeptics, who were involved in the test.

Dana Perino forgets about 9/11 and the Beltway snipers

Dana Perino says, "We did not have a terrorist attack on our country during President Bush's term."

Sean Hannity ignores it.



Terrorism is a strategy used by a militarily weak group against a militarily strong one, to create fear, dread, and uncertainty among the general population toward some political or ideological end, such as ending military actions by the strong group against the weak. It's not clear to me that Major Hasan's attack at Fort Hood meets the criteria of a terrorist attack, or even a religiously motivated one, though that's somewhat more plausible. His action did share the element of being an attack by the weak against the strong, but he also appears to have had mental issues and an ongoing battle with the military over his desire to get out and not be sent to Afghanistan. There were clear warning signs that were missed or ignored, but it doesn't appear that he was part of a broader plot.

The Fort Hood shootings were a tragedy, and possibly one that could have been avoided. But it certainly isn't an event that provides justification for torture, warrantless wiretapping, the revocation of habeas corpus, and the expansion of "homeland security" to the detriment of our civil liberties. Perino and Hannity want to argue that the Obama administration has made us less safe on the basis of this incident, which makes about as much sense as blaming the Bush administration for the Virginia Tech shootings.

UPDATE (November 27, 2009): As a couple people have correctly noted, I should also have mentioned the post-9/11 anthrax attacks as another terrorist act Perino forgot about. Richard Reid, the shoe bomber, was another.

UPDATE: Hume's Ghost notes that Perino has said via Twitter that she meant "since 9/11," and correctly points out how absurd it is to discount 9/11 for Bush (as well as these other subsequent events she's ignored), while blaming Obama for Hasan's shooting: "...while there were warning signs about Hasan's fitness for duty that could have been noticed by those around him, this is hardly something that would have been on the President's radar. No one was briefing President Obama that Major Hasan was determined to strike a military base; however, President Bush was briefed that Bin Laden was determined to strike in the United States prior to the 9/11 attacks."

Wikileaks to release over 500K text pager intercepts from 9/11

Wikileaks is releasing over 500,000 U.S. national text pager intercepts from September 11, 2001, over the next two days:

From 3AM on Wednesday November 25, 2009, until 3AM the following day (New York Time), WikiLeaks will release over half a million US national text pager intercepts. The intercepts cover a 24 hour period surrounding the September 11, 2001 terrorist attacks in New York and Washington.

The first message, corresponding to 3AM September 11, 2001, five hours before the first attack, will be released at 3AM November 25, 2009 and the last, corresponding to 3AM September 12, 2001 at 3AM November 26, 2009.

Text pagers are mostly carried by persons operating in an official capacity. Messages in the collection range from Pentagon and New York Police Department exchanges, to computers reporting faults to their operators as the World Trade Center collapsed.
This is a significant and completely objective record of the defining moment of our time. We hope that its entry into the historical record will lead to a deeper and more nuanced understanding of how this tragedy and its aftermath may have been prevented.

While we are obligated by to protect our sources, it is clear that the information comes from an organization which has been intercepting and archiving national US telecommunications since prior to 9/11.

The Transparent Society getting closer, it appears...

What would be more horrifying than "locked-in" syndrome?

Numerous mass media outlets and blogs are reporting on the misdiagnosis of Rom Houben of being comatose for 23 years when he was really conscious, according to Belgian neurologist Steven Laureys, who has claimed for years to be able to treat patients allegedly in a persistent vegetative state with electric shocks and find that they were really in a minimally conscious state. Videos of Houben show him allegedly communicating via a keyboard which is pressed by a single finger on one hand--but his hand is being held by a facilitator, and he's not even looking at the keyboard. Some still photos show the facilitator looking intently at the keyboard, while Houben's eyes are closed.

James Randi observes that this looks just like the self-deception of Facilitated Communication that was promoted as a way to communicate with severely autistic people, and Marshall Brain at How Stuff Works seconds that conclusion.

I think it's a bit too fast to conclude that Houben's not conscious--brain scans could indeed have provided good evidence that he is. But what would be worse than having "locked-in syndrome"? Having somebody else purporting to speak for you with ideomotor-driven Facilitated Communication, while you were helpless to do anything about it.

I'd like to see some double-blind tests of Houben, where he's asked questions about events that occur when the facilitator isn't present, as well as fMRI results during the process of facilitation (since there are brain activation differences between active and passive activities, which have been used to study such things as the perception of involuntariness during hypnosis--it shows features of both active and passive movement). I'd also like to see further opinion on Laureys methodology and diagnosis--it seems he has significant self-interest in promoting this case.

UPDATE: Brandon Keim at Wired Science has finally asked the questions that those who have reported this in the mainstream media should have been asking.

Here's a 2001 review of the scientific literature on facilitated communication.

UPDATE: The video on this story shows the facilitator typing for him while his eyes are closed and he appears to be asleep.

UPDATE: A Times Online story claims that Houben's facilitator, Linda Wouters, spent the last three years working with Houben to learn to feel tiny muscle movements in his finger, and that Dr. Laureys did tests to validate the technique:

The spectacle is so incredible that even Steven Laureys, the neurologist who discovered Mr Houben’s potential, had doubts about its authenticity. He decided to put it to the test.

“I showed him objects when I was alone with him in the room and then, later, with his aide, he was able to give the right answers,” Professor Laureys said. “It is true.”

and

Mr Houben’s “rebirth” took many painstaking months. “We asked him to try and blink but he couldn’t; we asked him to move his cheek but he couldn’t; we asked him to move his hand and he couldn’t,” Mrs Wouters said.

“Eventually, someone noticed that when we talked to him he moved his toe so we started to try and communicate using his toe to press a button.”

It was a breakthrough but much more was to come when a fellow speech therapist discovered that it was possible to discern minuscule movements in his right forefinger.

Mrs Wouters, 42, was assigned to Mr Houben and they began to learn the communication technique that he is now using to write a book about his life and thoughts. “I thought it was a miracle — it actually worked,” she said.

The method involves taking Mr Houben by the elbow and the right hand while he is seated at a specially adapted computer and feeling for minute twitches in his forefinger as his hand is guided over the letters of the alphabet. Mrs Wouters said that she could feel him recoil slightly if the letter was wrong. After three years of practice the words now come tumbling out, she said.

This still seems hard to rationalize with the video footage of the typing occurring while he's apparently asleep. Mrs. Wouters admits the possibility of "tak[ing] over" for him:

“The tension increases and I feel he wants to go so I move his hand along the screen and if it is a mistake he pulls back. As a facilitator, you have to be very careful that you do not take over. You have to follow him.”

UPDATE (November 25, 2009): Neurologist Steven Novella has weighed in. He suggests that Houben may have recovered some brain function and be conscious, but that the facilitated communication in the videos is positively bogus.

I've noted on the discussion page of Dr. Steven Laureys' Wikipedia entry that the paper in BMC Neurology that purportedly included Houben as a subject claims that all patients in the study were in a minimally conscious state (MCS) but had been misdiagnosed as being in a persistent vegetative state (PVS). The criteria of the study say that those that recovered and emerged from MCS were excluded, which seems at odds with claims that Houben's brain function is "almost normal." A story in Nature 443, 132-133 (14 September 2006) by Mike Hopkin, "'Vegetative' patient shows signs of conscious thought," which quotes Laureys, is about a different patient, in a persistent vegetative state, who showed some signs minimal consciousness. When asked to visualize herself playing tennis, for example, she showed corresponding brain activity. But, as that article noted, that kind of neural response isn't necessarily a sign of consciousness:

But what that 'awareness' means is still up for debate. For example, Paul Matthews, a clinical neuroscientist at Imperial College London, argues that the brain imaging technique used cannot evaluate conscious thought; fMRI lights up regions of brain activity by identifying hotspots of oxygen consumption by neurons. "It helps us identify regions associated with a task, but not which regions are necessary or sufficient for performing that task," he says.

Matthews argues that the patient's brain could have been responding automatically to the word 'tennis', rather than consciously imagining a game. He also points out that in many vegetative cases, the patient's motor system seems to be undamaged, so he questions why, if they are conscious, they do not respond physically. "They are simply not behaving as if they are conscious," he says.

Owens counters that an automatic response would be transient, lasting for perhaps a few seconds before fading. He says his patient's responses lasted for up to 30 seconds, until he asked her to stop. He believes this demonstrates strong motivation.

He does admit, however, that it is impossible to say whether the patient is fully conscious. Although in theory it might be possible to ask simple 'yes/no' questions using the technique, he says: "We just don't know what she's capable of. We can't get inside her head and see what the quality of her experience is like."

But then again, as someone who's been reading a lot of literature on automaticity and voluntary action lately, it appears to me likely that a lot of our normal actions are automatic, the product of unconsciously driven motor programs of routine behavior.

Laureys is quoted in the article with a note of skepticism:

"Family members should not think that any patient in a vegetative state is necessarily conscious and can play tennis," says co-author Steven Laureys of the University of Liège, Belgium."It's an illustration of how the evaluation of consciousness, which is a subjective and personal thing, is very tricky, especially with someone who cannot communicate."

The article goes on to note that this woman, who is possibly somewhere between PVS and MCS, "seems to have been much less severely injured than the permanently vegetative Terri Schiavo" (as the report from her Guardian Ad Litem (PDF) made clear).

If Houben is in a minimally conscious state, which he apparently was in order to be included in Laureys' paper that his Wikipedia page says published the Hoeben case in 2009, that appears to contradict news claims that Houben's brain function is "nearly normal," unless he has recovered further function since that paper was written.

UPDATE (November 26, 2009): This footage of Houben and Mrs. Wouters from Belgian (Dutch) state television seems to be the most extensive footage of the facilitation process, and while it starts out looking slightly more plausible, it also clearly shows fairly rapid typing while his eyes are closed (and the camera zooms in on his face).

UPDATE (November 28, 2009): Dr. Laureys and Dr. Novella have had some interaction, which demonstrates that Laureys doesn't get it.

UPDATE (February 15, 2010): Dr. Laureys almost gets it now, and has done additional tests, which have shown that the communications are coming from the facilitator, not Houben.

UPDATE (February 20, 2010): David Gorski at the Science-Based Medicine blog has a bit more from the Belgian Skeptics, who were involved in the test.

Climate Research Unit email scandal

Hackers got access to a trove of private emails from the University of East Anglia's Climate Research Unit that is being trumpeted by those who disbelieve in anthropogenic global warming as proof of scandal. I've looked through the data a bit myself--you can find a searchable archive of the emails here. I suspect this collection of emails may end up being put to good research use as the Enron email corpus was. While I found a few embarrassing things, I found no evidence of outright data fabrication or fakery.

The main email that has been cited as such evidence is an email from Phil Jones that says:

I’ve just completed Mike’s Nature trick of adding in the real temps to each series for the last 20 years (ie from 1981 onwards) and from 1961 for Keith’s to hide the decline.

Gavin Schmidt at RealClimate explains:

The paper in question is the Mann, Bradley and Hughes (1998) Nature paper on the original multiproxy temperature reconstruction, and the ‘trick’ is just to plot the instrumental records along with reconstruction so that the context of the recent warming is clear. Scientists often use the term “trick” to refer to a “a good way to deal with a problem”, rather than something that is “secret”, and so there is nothing problematic in this at all. As for the ‘decline’, it is well known that Keith Briffa’s maximum latewood tree ring density proxy diverges from the temperature records after 1960 (this is more commonly known as the “divergence problem”–see e.g. the recent discussion in this paper) and has been discussed in the literature since Briffa et al in Nature in 1998 (Nature, 391, 678-682). Those authors have always recommend not using the post 1960 part of their reconstruction, and so while ‘hiding’ is probably a poor choice of words (since it is ‘hidden’ in plain sight), not using the data in the plot is completely appropriate, as is further research to understand why this happens.

In other words, "hiding" in this case is using temperature measurement records instead of tree rings as a proxy for temperature records for a period of time where the tree rings are known not to be an accurate proxy, for whatever reason.

It's also claimed that these emails show a concerted effort to subvert the peer review process and stop publications by climate change skeptics, but most of those emails seem to center around an issue where the scandal was actually from the skeptics--the publication of a 2003 paper by Willie Soon and Sallie Baliunas in the journal Climate Research that was considered by 13 authors of papers cited to have misrepresented their work. Subsequently, half of the editorial staff of the journal resigned in protest at what they saw as a failure of peer review, and the managing director of the journal's parent company issued an apology (see Wikipedia's summary). The emails show that these scientists were upset by Climate Research's publication of bad science and encouraged protest and those resignations.

A few blog posts that seem to have good overviews of the issues:

• Skeptical Science, "What do the hacked CRU emails tell us?"
• Real Climate, "The CRU Hack" (followed by over 1,000 comments)
• Real Climate, "The CRU Hack: Context" (gives background on some of the issues, including the above Climate Research issue).
  
• Greenfyre's, "Climate change Deniers hoax themselves... again."
• Millard Fillmore's Bathtub, "Smoking guns in the CRU stolen emails: A real tale of real ethics in science" (what the CRU emails show about treatment of an erroneous climate science paper)
  

An interesting comparison to past scientific controversy is:

• Carbon Fixated, "Newtongate: the final nail in the coffin of Renaissance and Enlightenment 'thinking'"

And, to compare to the climate change skeptics:

• Bishop Hill, "Climate cuttings 33" (summary of the apparent worst issues)
• Essex County Conservative Examiner, "Hadley [sic] CRU hacked with release of hundreds of docs and emails"
• Climate Audit, "CRU Correspondence"
• Watt's Up With That, "Mike's Nature Trick"
• Watt's Up With That, "CRU Emails 'may' be open to interpretation, but commented code by the programmer tells the real story"
• Watt's Up With That, "Spencer on elitism in the IPCC climate machine"

The last of these posts, from Univ. of Alabama climate scientist and skeptic Roy W. Spencer, notes that:

If all of this sounds incompatible with the process of scientific investigation, it shouldn’t. One of the biggest misconceptions the public has about science is that research is a straightforward process of making measurements, and then seeing whether the data support hypothesis A or B. The truth is that the interpretation of data is seldom that simple.

There are all kinds of subjective decisions that must be made along the way, and the scientist must remain vigilant that he or she is not making those decisions based upon preconceived notions. Data are almost always dirty, with errors of various kinds. Which data will be ignored? Which data will be emphasized? How will the data be processed to tease out the signal we think we see?

Hopefully, the scientist is more interested in discovering how nature really works, rather than twisting the data to support some other agenda. It took me years to develop the discipline to question every research result I got. It is really easy to be wrong in this business, and very difficult to be right.

Skepticism really is at the core of scientific progress. I’m willing to admit that I could be wrong about all my views on manmade global warming. Can the IPCC scientists admit the same thing?

Another noteworthy comment, from Real Climate, is this one from caerbannog and Gavin Schmidt's reply:

Just a reminder: CRU is just one of many organizations focusing on climate research. The fact that its director has reacted badly (i.e. appearing to go for the “bunker” mentality) to repeated scurrilous attacks has no bearing on the validity of the science.

Hansen’s approach has been quite different — he’s basically said to his detractors, “here are all of the source code and data — go knock yourselves out”.

Under Hansen, the NASA/GISS data and source code have been freely available on-line for years. And all of the sceptics’ scrutiny of said data has uncovered only one or two minor “glitches” that have had minimal impact.

Just a quick question (or two) to Gavin, if you feel the need to spend even more of your weekend downtime answering questions here.

Given that all of your climate-modeling source-code has been available for public scrutiny for quite a long time, and given that anyone can download and test it out, how many times have climate-model critics have actually submitted patches to improve your modeling code, fix bugs, etc? Have you gotten *any* constructive suggestions from the skeptic camp?

[Response: Not a single one. - gavin]

I think this illustrates that it's far better to be completely open with your data and methods.

UPDATE (November 26, 2009): There's now an official response from the Univ. of East Anglia, the Climate Research Unit, and Phil Jones. Jones notes, regarding the Freedom of Information requests:

We have been bombarded by Freedom of Information requests to release the temperature data that are provided to us by meteorological services around the world via a large network of weather stations. This information is not ours to give without the permission of the meteorological services involved. We have responded to these Freedom of Information requests appropriately and with the knowledge and guidance of the Information Commissioner.

We have stated that we hope to gain permission from each of these services to publish their data in the future and we are in the process of doing so.

UPDATE (December 4, 2009): The journal Nature has weighed in on the controversy.

Climate scientist Judith Curry makes good points of criticism about climate scientists' behavior.

UPDATE (December 6, 2009): Univ. of East Anglia climate scientist Mike Hulme (author of Why We Disagree About Climate Change, a book that I read several chapters from in a class on human dimensions of climate change this semester) on the issue:

The key lesson to be learned is that not only must scientific knowledge about climate change be publicly owned — the I.P.C.C. does a fairly good job of this according to its own terms — but the very practices of scientific enquiry must also be publicly owned, in the sense of being open and trusted. From outside, and even to the neutral, the attitudes revealed in the emails do not look good. To those with bigger axes to grind it is just what they wanted to find.

This will blow its course soon in the conventional media without making too much difference to Copenhagen — after all, COP15 is about raw politics, not about the politics of science. But in the Internet worlds of deliberation and in the ‘mood’ of public debate about the trustworthiness of climate science, the reverberations of this episode will live on long beyond COP15. Climate scientists will have to work harder to earn the warranted trust of the public - and maybe that is no bad thing.

But this episode might signify something more in the unfolding story of climate change. This event might signal a crack that allows for processes of re-structuring scientific knowledge about climate change. It is possible that some areas of climate science has become sclerotic. It is possible that climate science has become too partisan, too centralized. The tribalism that some of the leaked emails display is something more usually associated with social organization within primitive cultures; it is not attractive when we find it at work inside science.

It is also possible that the institutional innovation that has been the I.P.C.C. has run its course. Yes, there will be an AR5 but for what purpose? The I.P.C.C. itself, through its structural tendency to politicize climate change science, has perhaps helped to foster a more authoritarian and exclusive form of knowledge production - just at a time when a globalizing and wired cosmopolitan culture is demanding of science something much more open and inclusive.

UPDATE (December 11, 2009): PolitiFact gives its analysis of the CRU emails, which is fairly balanced.

UPDATE (December 12, 2009): Deep Climate catches Stephen McIntyre engaging in quote mining of the CRU emails in order to mislead.

UPDATE (December 24, 2009): David Douglass and John Christy, in "A Climatology Conspiracy?", argue that the CRU emails show a concerted effort to delay the publication of their paper, publish another paper criticizing it along side of it, and deny them the right of final reply. Their case is somewhat weakened by the fact that the second paper points out a significant error in their paper and they have apparently not tried to publish a reply or correct the error.