arm about the degradation of the taliban and the ability of afghan political lead yooers to fashion a fair transition of power from karzai who-to-whoever comes after. all ofhese assumptions look quite shaky and you don't want to ask american men and women to make the ultimate sacrifice if you're not willing to confront the facts head on and think honestly about where they may lead you. >> rose: we conclude with kathy freston, a well-known vegan, her book is called "the lean, a revolutionary and simple plan for lasting weight loss." i want to enjoy my life, celebrate food and have things i grew up loving with my family, with my friends. so for me i think the best thing that has worked-- and i think it's translated to other people-- is that if we set our intention to move toward health sand we lean into it and take steps in the direction of eating better what happens is that we start a momentum by these tiny little things because we can do things that are not difficult and those gradual, practical, easy steps start the pathway toward healthy eating. >> rose: seth jones, steve coll and kathy freston when we continue. captioning sponsored by rose communications from our studios in new york city, this is charlie rose. >> rose: seth jones is here, he is a senior political scientists at the rand corporation. he specialized in counterterrorism and counterinsurgency and afghanistan. his latest book details a history of al qaeda and where it stands today. it comes in t one-year anniversary of the raid that killed osama bin laden. it's called-- the book-- "hunting in the shadows: the pursuit of al qaeda since 9/11." i am pleased to have seth jones back at this table. welcome. >> thank you, charlie. >> rose: good to see you. why do you call it "hunting in the shadows"? >> well, i think argument as we look historically at what's been effective is not a large american presence with large numbers of boots on the ground. it's been a war that's happened in the shadows by clandestine units, special operation forces, law enforcement. so the for... we've been more effective when we've had limited presence that's clandestine, covert in nature than a large boots on the ground presence like we had in iraq. >> rose: does that mean that you would have argued for counterterrorism versus counterinsurgency if there was an either or about it or would you have argued something different at the time the president was making decisions about an afghanistan policy and then a time the president rewas examining policy. >> no, i don't think smaller numbers of boots on the ground means counterterrorism as oppose to counterinsurgency. i think what we've seen starting with general stanley mcchrystal in 2009 and leading to petraeus in afghanistan was the use of special operations forced to train afghan national and local police forces, including tribal subtribe clan elements. it turns out you can do a lot of counterinsurgency with a smaller number of forces. >> i can't get my hands around the idea of how well the afghan troops are being trained and how much of the load they're prepared to take. certainly with the date of 2014 in mind. general allen here said it's coming along much better than we think. >> well, i think we've got to look at different kinds of units the afghan special units, the commandos, afghan national army special forces are very well trained, very competent units. the ones working with our joint special operations command doing night raids now that the afghans have the lead are very competent forces. the national army forces vary. they're better than they were five years ago. we're still having problems with national police forces on the ground which are sometimes corrupt which don't often get out of district centers and that's led to an increasing use of local community watch, what's called afghan local police in these areas. some of them good. so the answer depends on which kinds of forces we're talking about. >> what's the presence in afghanistan today? >> it appears to be relatively small. most al qaeda sits across the border in pakistan but the areas we've got to watch very closely where they've pushed in some presence in kunar provinces. an area that they have a historical relationship with the pashtun and other tribes. we've also seen an indication of al qaeda trying to push some foreign fighters in the east in places like khost co-lee lowe kated with the haqqani network. so i would say al qaeda is looking carefully at the u.s. downsizing withdrawal. >> rose: prepared to do what? >> well, is preparing to establish a sanctuary possibly like they had in the 1990s. >> rose: if mullah omar was back in power would he welcome al qaeda back or would he likely to say we've moved on beyond that? >> well, what the recently declassified bin laden documents those that have been released, are starting to indicate is a relationship between senior al qaeda leaders, including al-zawahiri who's al qaeda number one, and mullah omar, a relationship often through an individual in the senior taliban leadership so we know that they kept up a fairly regular communication. what it appears to be the case is that the taliban has some concerns about a public senior al qaeda presence in afghanistan. certainly okay within w an al qaeda presence. certainly case with other afghan insurgents groups like the haqqanis, al qaeda has a better presence. i would suspect that the taliban would be okay with an al qaeda presence in their territory. they would probably be careful about making too public of a deal about that. >> rose: what do you think the outlook is for afghanistan? >> a lot depends on what the united states does and a lot depends on what afghanistan's neighbor-- primarily pakistan, does. if the u.s. moves quickly in trying to get out of afghanistan while pakistan government continues to provide large numbers of support and amounts of support to the taliban and other groups i think we're in for a long ride in this country as the taliban gains control of territory. >> rose: you don't expect the pakistanis to change, do you? >> no, what we've seen is their support the afghan insurgents is likely increased. they see a departure of the u.s. as a way too maximize... >> rose: it's a hedge for the future? >> against what they believe is an indian afghan access in afghanistan. >> rose: so their fear is what happens... what india might do so therefore they want to have a better relationship, who they expect to be perhaps the winners? >> you have to look from pakistan's perspective it has india on one border with whom it's fault several wars and it has a country, afghanistan, whose president, hamid karzai, has a close strategic relationship with the indians. so that puts pakistan strategically in circles so ideally what pakistan is pushing for is what they had in the 1990s which is a regime in kabul that support pakistan, supports islamabad. so a friend. >> let's look at back to the book and towards where we are today. you talk about waves of al qaeda. give me the four waves that you see. >> well what's interesting is when you look at the last decade and a half or so in... against al qaeda, al qaeda's strength does not... is not linear. we see it rise and fall in part depending on u.s. effectiveness against it and in other organizations and their ability to gain a sanctuary. so we saw in president 1990s and through 2001 what you might call the first wave-- embassy bombings in africa, targeting the u.s.s. "cole" in yemen and then leading up to and peaking at the september 11 attacks. that was then followed by... al qaeda lost its sanctuary in afghanistan. several senior leaders were captured over the next two to three years so it was severely decreased in strength and one of the interesting things, i looked at the now declassified al qaeda documents. a senior al qaeda leader who is believed to be based in iran right now argues by 2003 al qaeda was severely weakened and desperate. >> rose: by 2003. could we have or anybody at that moment delivered what might be considered an effective end to al qaeda? >> well, it's possible at that point if both bin laden and possibly ayman al-zawahiri were targeted it would have lost its sanctuary in afghanistan but also al qaeda was facing something it's not facing right now and that's a tight u.s./pakistani relationship. that does not exist now but that existed at that time. the joint raid to capture khalid sheikh mohammed was an effective joint pakistan/u.s. operation long since gone. >> rose: and did it happen because of... what caused it to fall apart. >> well, there were a range of things. as the war in afghanistan became more serious and more severe the u.s. began to see growing signs of pakistan support to insurgent groups. afghan insurgent groups. that certainly contributed to it. the drone strikes that the u.s. started conducting in pakistani territory began to work against the pakistan government. >> rose: because there was civilian casualties or... >> well, actually, it appeared to be less civilian casualties and more that it was the u.s. doing them and not the pakistan... >> rose: on their territory. >> on their territory. >> rose: in terms of sovereignty issue as well. >> sovereignty issue i think was a major one. >> rose: and what did the mission to kill osama bin laden do to the relationship? >> the relationship... well, initially it severely undermined it because it showed several things. one is it showed the... from the pakistan standpoint it showed how it will it will u.s. actually trusted pakistan. from the pakistan... from the american standpoint it also showed in a sense how the u.s. could not trust pakistan that he was so deep in pakistan territory. >> rose: so back to 2004 to 2008. what happened to al qaeda during that period? >> that's a great question. this is what we call the second wave. and the second wave really begin around the time of the u.s. invasion of iraq. what al qaeda is able to do that did not have is establish a foothold after the invasion led by in december, about 2004 al qaeda really gets an affiliate. >> rose: right. >> abu musab al-zarqawi pledges allegiance to bin laden and we see a major increase in attacks by al qaeda in iraq and then we see in 2004 we see the madrid attacks done to get the spanish government to pull its forces out of not just anywhere but out of iraq. then we see in 2005 mohammed siddiqui kahn in a range of four individual pakistani british conduct the attacks on london. so we're getting a surge in activity and a lot of the radicalization happens because of the war in iraq. all the senior f.b.i. officials i talked to said they begin to see a massive increase in radicalization in the u.s. because of the iraq war. well, by 2005 and 2006 al qaeda in iraq overplays its hand and we see an interesting trend. was what it does is starts conducting a number of civilian casualties, not just embassies and that undermines its support so the u.s. marines, the army, the central intelligence agency and special operations support iraqis as they turn against al qaeda in iraq in anbar province and others. so that contributes to the... the end of the second wave, these kinds of clandestine efforts. and we saw them a range of other... >> rose: and that's when the surge came in... >> the surge is after that. so the anbar awakening happens in 2006. >> and it was afghan beginning to take place and the members were former sunnis, turning against al qaeda. >> sunnis were turning. not just shi'a but sunnis were turning against al qaeda well before the surge. >> rose: the awakening was mostly sunni, was it not? >> yes but there were shi'a elements over time that certainly supported the effort. >> rose: so what's the next wave? >> the next wave begins around 2008 and into 2009. so al qaeda had been weakened across iraq to some degree if pakistan after the capture of al-libi and the head of external operations for al qaeda was killed in a drone strike. then you get an interesting development. if the first wave is tied to afghanistan, the second one iraq, the third one is tied very closely to anwar al-awlaki and the seizing of territory in yemen. and it's interesting, because it's a wave that is not just tied directly to a spot in yemen but is also tied to an effective use of the internet and social media by al qaeda to recruit individuals elsewhere. >> rose: al-awlaki was very good at that. >> al-awlaki was an amazing terrorist in the sense that he was good at pushing out propaganda and information on youtube, on myspace, on facebook and on internet jihadi sites but as we know and as i document in the book he was also operationally involved and tactically involved as he was with the christmas bomber. telling him when he left yemen actually helping on the training end. when he left yemen telling him where he had to go, telling him to wait until he got over american soil to detonate the bomb. but he provided a range of tactical and operational advice to umar farouk abdulmutallab before his attempted detonation. and that made him extremely dangerous. he didn't just talk a game, he acted it. >> rose: so put... play as well though when president obama comes to power. he instruct it is c.i.a. director, then leon panetta, "my number one priority is to get osama bin laden and do grievous damage to al qaeda." did that have an impact on al qaeda? >> it had an impact in particular on core al qaeda in pakistan. and it wasn't just the targeting of osama bin laden. it was a targeting of a range of senior leaders. the key general managers. first almasry was killed, then his successor was killed. the head of external operations was killed with a drone strike. and they will ilyas kashmiri. so a range of senior individuals that were at very high levels of the organization in addition to the bin laden killing what they did is they made it very difficult for al qaeda and pakistan, at least for the time being to operate because they were so paranoid about surviving. >> and would you say beyond osama bin laden now dead al-zawahiri is still alive that they got 70% of the top al qaeda leadership? >> they've probably got over 50%. >> rose: over 50? that's a significant number when you take away 50% of the leaders of a terrorist organization. >> except if you can replace them effectively. >> rose: that's easy for them to do? >> it's not easy for them to do. it does take time. the other component of this is what we've seen al qaeda do and we've seen al-zawahiri do now, the number one in al qaeda, is adopt a mergers and acquisitions strategy. in a sense, making pakistan less important than it once was, encouraging franchises on multiple continents. >> rose: and where are these franchises located? certainly one is in yemen. >> there are four major ones. and these are... their leaders have sworn allegiance, loyalty to al-zawahiri. one is in yemen. the second is iraq. a third is in somalia, that's al-shabab and that was the most recent one. then the final one is in north africa, what we call al qaeda in the islamic maghreb. >> rose: so where are we today? >> well, it depends on what indicators we look at. the core in pakistan has been weakened temporarily. if you look at other indicators they present a big more of a concerns picture. if you look at the number of affiliated groups, we've now increased them. al-shabab joined in 2012. the number of attacks in some areas has increased and we've seen this in even iraq. the u.s. has pulled out its hill tear forces from iraq, the levels of violence have gone up by al qaeda in iraq and now we've seen them in some countries like yemen al qaeda in the arabian peninsula has expanded its territory around the gulf of aiden. so some al qaeda is bigger. it's involved in more violent activity and expanded its control in some countries. that's not good. >> rose: if you had to guess where al-zawahiri is today, where would you guess? >> pakistan. >> rose: certainly pakistan. but in an urban environment or in the north? >> i would say based on the drone strikes against senior al qaeda leaders today he's probably out of range of drones. so... which would force the u.s. to do something along the lines of what they did against bin laden is put american forces into helicopters and push them deeper into pakistani territory. that's a much more... >> rose: and going back and forth and getting access and confirmation. >> that's right. we've seen al qaeda interested in getting out of the tribal areas if at all possible. >> rose: how good have they been-- obviously not good enough in osama bin laden's case-- in terms of being able to shut down on cell phone usage, to be able to do things that will, in a sense, make them more immune to attack? >> rose: well in one of the last chapters i talked briefly about a note from al-zawahiri to bin laden not long before the... bin laden's fay almay attack where same al-zawahiri is saying "we have to have better security procedures, the drone strikes are killing us." so i would say what we've seen... it's almost a darwinist approach. those al qaeda operatives who have not been effective in getting rid of cell phones, minimizing communications and then actually going out into public areas like marketplaces, they're killed. those that are much more careful about how long they say in a location, going out in public and picking up a phone, like al-zawahiri, like his deputy now abu ya ya al-libi. and don't forget we have many who have survived. >> rose: what should we be doing that we're not doing? >> well, a couple things i would say. we're in a difficult period right now. the u.s. has said it's now going to focus on the asia-pacific so the department of defense guidance signed by the president pushed out in january 2012 says "we're going to move to asia-pacific. " i would say we have got to be very careful if what that means is it makes us more vulnerable in north africa, the middle east. >> rose: this is reflected both in terms of pentagon policy as well as state department policy? >> right. so afghanistan is a great case. marines have been pulled out of afghanistan-- or at least the numbers have decreased-- and where they v they shown up now? australia. it's a reflection of a rising... response to a rising china. i think we've got to be really careful here that we keep focused on where the threats to the homeland are coming from. >> rose: and they're still coming from... well, the reason for the shift to china had everything to do with relationships with people who are neighbors in china as much as sending a support to them as much as it did to fearing i assume some direct chinese military threat? >> that's true. still if that is where the... what is called in department of defense lingo "rebalancing" if it means shifting too many resources away from... take nigeria. we've now seen the rise in capabilities of boca haar ram with the osama bin laden documents we now know that bin laden was in touch with the boca haaram leaderships as early as 2009. so this is a concerning development. in somalia we have americans from communities like minneapolis and phoenix regularly coming to fight in somalia. >> rose: when you look at techniques and what we have learned, first osama bin laden. what did we learn? was there a treasure trove of information, actionable information, that came out of that taking... having access to those computer drives? >> as with any capture or killing of an individual, if you can get a ahold of their computer day e-mail exchanges, letters, cell phones-- and i've done this when i was in special operations-- you can getting access to actionable information. geographic locations, cell phone numbers can be tracked and monitored and e-mail addresses. >> rose: did you see jose rodriguez on "60 minutes" on sunday? >> i did. yes. >> rose: give me your assessment of what he is saying. the argument he makes. >> well, i mean, part of the issue hi