Update: My full response to Holden is now here.

As Holden said, I generally think that Holden's objections for SI "are either correct (especially re: past organizational competence) or incorrect but not addressed by SI in clear argumentative writing (this includes the part on 'tool' AI)," and we are working hard to fix both categories of issues.

In this comment I would merely like to argue for one small point: that the Singularity Institute is undergoing comprehensive changes — changes which I believe to be improvements that will help us to achieve our mission more efficiently and effectively.

Holden wrote:

I'm aware that SI has relatively new leadership that is attempting to address the issues behind some of my complaints. I have a generally positive impression of the new leadership; I believe the Executive Director and Development Director, in particular, to represent a step forward in terms of being interested in transparency and in testing their own general rationality. So I will not be surprised if there is some improvement in the coming years...

Louie Helm was hired as Director of Development in September 2011. I was hired as a Research Fellow that same month, and made Executive Director in November 2011. Below are some changes made since September. (Pardon the messy presentation: LW cannot correctly render tables in comments.)

SI before Sep. 2011: Very few peer-reviewed research publications.
SI today: More peer-reviewed publications coming in 2012 than in all past years combined. Additionally, I alone have a dozen papers in development, for which I am directing every step of research and writing, and will write the final draft, but am collaborating with remote researchers so as to put in only 5%-20% of the total hours required myself.

SI before Sep. 2011: No donor database / a very broken one.
SI today: A comprehensive donor database.

SI before Sep. 2011: Nearly all work performed directly by SI staff.
SI today: Most work outsourced to remote collaborators so that SI staff can focus on the things that only they can do.

SI before Sep. 2011: No strategic plan.
SI today: A strategic plan developed with input from all SI staff, and approved by the Board.

SI before Sep. 2011: Very little communication about what SI is doing.
SI today: Monthly progress reports, plus three Q&As with Luke about SI research and organizational development.

SI before Sep. 2011: No list of the research problems SI is working on.
SI today: A long, fully-referenced list of research problems SI is working on.

SI before Sep. 2011: Very little direct management of staff and projects.
SI today: Luke monitors all projects and staff work, and meets regularly with each staff member.

SI before Sep. 2011: Almost no detailed tracking of the expense of major SI projects (e.g. Summit, papers, etc.). The sole exception seems to be that Amy was tracking the costs of the 2011 Summit in NYC.
SI today: Detailed tracking of the expense of major SI projects for which this is possible (Luke has a folder in Google docs for these spreadsheets, and the summary spreadsheet is shared with the Board).

SI before Sep. 2011: No staff worklogs.
SI today: All staff members share their worklogs with Luke, Luke shares his worklog with all staff plus the Board.

SI before Sep. 2011: Best practices not followed for bookkeeping/accounting; accountant's recommendations ignored.
SI today: Meetings with consultants about bookkeeping/accounting; currently working with our accountant to implement best practices and find a good bookkeeper.

SI before Sep. 2011: Staff largely separated, many of them not well-connected to the others.
SI today: After a dozen or so staff dinners, staff much better connected, more of a team.

SI before Sep. 2011: Want to see the basics of AI Risk explained in plain language? Read The Sequences (more than a million words) or this academic book chapter by Yudkowsky.
SI today: Want to see the basics of AI Risk explained in plain language? Read Facing the Singularity (now in several languages, with more being added) or listen to the podcast version.

SI before Sep. 2011: Very few resources created to support others' research in AI risk.
SI today: IntelligenceExplosion.com, Friendly-AI.com, list of open problems in the field, with references, AI Risk Bibliography 2012, annotated list of journals that may publish papers on AI risk, a partial history of AI risk research, and a list of forthcoming and desired articles on AI risk.

SI before Sep. 2011: A hard-to-navigate website with much outdated content.
SI today: An entirely new website that is easier to navigate and has much new content (nearly complete; should launch in May or June).

SI before Sep. 2011: So little monitoring of funds that $118k was stolen in 2010 before SI noticed. (Note that we have won stipulated judgments to get much of this back, and have upcoming court dates to argue for stipulated judgments to get the rest back.)
SI today: Our bank accounts have been consolidated, with 3-4 people regularly checking over them.

SI before Sep. 2011: SI publications exported straight to PDF from Word or Google Docs, sometimes without even author names appearing.
SI today: All publications being converted into slick, useable LaTeX template (example), with all references checked and put into a central BibTeX file.

SI before Sep. 2011: No write-up of our major public technical breakthrough (TDT) using the mainstream format and vocabulary comprehensible to most researchers in the field (this is what we have at the moment).
SI today: Philosopher Rachael Briggs, whose papers on decision theory have been twice selected for the Philosopher's Annual, has been contracted to write an explanation of TDT and publish it in one of a select few leading philosophy journals.

SI before Sep. 2011: No explicit effort made toward efficient use of SEO or our (free) Google Adwords.
SI today: Highly optimized use of Google Adwords to direct traffic to our sites; currently working with SEO consultants to improve our SEO (of course, the new website will help).

(Just to be clear, I think this list shows not that "SI is looking really great!" but instead that "SI is rapidly improving and finally reaching a 'basic' level of organizational function.")