Editor's Note: William Gilly, a professor of biology at Stanford University's Hopkins Marine Station, embarked on new expedition this month to study jumbo squid in the Gulf of California on the National Science Foundation–funded research vessel New Horizon. This is his seventh blog post about the trip.

After traveling all night we approach Isla San Pedro Martir in mid-morning. We've had unbelievably good weather with little wind for this entire trip, but now that has changed. Last year it was too windy to do much useful work here, and a similar situation now presents itself.

A few sperm whales are sighted in the area of deep water to the west of the island, which probably means squid are here as well. But it is windy, and we are running out of time. We decide to once again pass this remote island by and proceed south to the Guaymas Basin, where we know there will be plenty of small squid for our ongoing experiments. It's time to focus on these aims of the trip.

We have no live squid right now, because of the Salsipuedes red tide problem, and we have all day ahead of us before reaching our marked spot in the Guaymas Basin sometime after sunset. So we spend time catching up on other necessities, including email, analysis of experiments already carried out, laundry or just relaxing. But for the restless, the transit time provides a perfect opportunity to photo-document the squid cleaning process. Many people are afraid of squid in the kitchen, because they think it is difficult to clean. In reality, squid are much easier than fish to clean and don't require the skill and sharp knife that are essential to a nice filet.

The instructions below (and photos) pertain to the Humboldt squid, but the general procedures apply to all squid. Like any other consumable, it's important to use fresh squid that has not been frozen for a year and then steeped in its own juices as it thaws. One of my general rules is that if something smells bad, don't eat it, be it squid, mushrooms or just about anything else.

Cleaning Humboldt (and any other) Squid

Both the mantle (body) and the eight arms are edible. There are also two tentacles that differ from the arms in that they are extensible, and in life are used for catching prey. Arms can bend and writhe, but they cannot stretch or retract. The difference in muscular structure between arms and tentacles that underlies this functional difference also makes the tentacles extremely tender. If you have a lot of large, Humboldt squid, it is not difficult to collect a good quantity of tentacles, and you can use them in any preparation as you would use scallops. The fins are the least desirable portion and can be discarded without regret.

In most dishes, only the mantle of the squid is used, but even here transforming the whole squid to table fare requires more than a sharp filet or meat knife—you need a plan. Depending on the final product, you will need to decide at the outset as to the final topology of the cleaned piece—sheet, tube or cone. Arms and tentacles are another matter.

Mantle sheets

1.  Place the squid on a flat surface with the ventral (bottom) side up—this is the side with the siphon between the head and the mantle. Slice the mantle open down the ventral midline from the anterior (head) end to posterior (fins). Be careful not to let the knife go deep enough to puncture the large, brown liver-like digestive-gland or the black ink-sac, as this will make a huge mess and probably cause you to put a premature halt to your project.

2. Open up the mantle at the anterior end and pop open the two cartilaginous structures that connect the head to the mantle. Notice how they act as locking mechanism. These rather elaborate structures keep the head firmly attached to the mantle, which allows the squid to make a powerful, high-pressure jet by squeezing water out of the mantle and through the siphon without blowing its head off the body. This would defeat the whole purpose of trying to escape from a predator.

3. Use the knife to scrape out all internal body parts ('guts') with the head attached, starting from the posterior end and pushing everything out the anterior end. You should now have a triangular shaped mat of squid with the fins still attached. Again, do not puncture the digestive gland or ink sac during this process.

4. Remove the pen by freeing the anterior end with the knife and pulling the whole thing out.

5. Make a cut across and through the mantle at the mid-fin level. Remove the fins and discard.

6. Remove the red skin and the white membrane underneath. The membrane can be removed by using the knife to separate it from the mantle at the posterior end and then working your fingers underneath to separate further. Eventually you will be able to grab the membrane and pull it off. This operation may take some practice—a gentle but firm prodding and pulling will eventually work. Think Rolfing and fascia manipulation.

7. Rinse the cleaned mantle off in fresh seawater if you have it, fresh if not, and it's ready for use.

Generally the mantle is cut into smaller portions—rectangular or square 'steaks' or short strips. If the squid is large, these smaller pieces should be cut into thinner slices in a direction parallel to the original mantle surface. Slices should be as thin as possible, about 1/3 to 1/4 inch. This will tenderize the largest squid.

Mantle Cones or Tubes—For small squid only!

Cones (open at one end) and tubes (open at both ends) are used to prepare stuffed squid dishes or for those dishes that call for rings—cross-sections of the entire mantle. These preparations should only be attempted with small Humboldt squid—a plate-sized squid ring of 12 inches might be a bit daunting for most diners. On the other hand, a stuffed squid with a 24-inch mantle might one day replace the 20-pound Thanksgiving turkey.

To make tubes, do not slit open the squid as described above. Instead, cut the squid completely through at the mid-fin level and use a knife to remove the internal organs from the posterior end while pulling the whole mess out by the head. Pull out the pen, wash and you have a tube. Remove the skin and outer membrane the best you can. In small squid, the membrane is not such an issue.

I don't recommend using cones from Humboldt squid, but you can easily prepare cones from many other smaller species of squid like California market squid (Loligo opalescens, a lovely name changed to Doryteuthis). For a cone, the technique is a combination of pulling the guts out of the intact mantle by the siphon-neck-head assembly and squeezing the mantle from the posterior end with the back-side of a knife blade. After you remove what you can, pull out the pen and clean out any material remaining inside from the inside with a knife or by squeezing from the outside. Generally the skin and fins are removed before use.

Arms and tentacles

Cut off the arms and tentacles at their base and remove the beak and attached muscles (the buccal mass). What you have left looks rather like an octopus without a body. Poach briefly, a few minutes for tentacles and 20 min or so for arms. Add onion, bay leaf, and other seasonings to the water as you wish. Remove the appendages and let them cool so they can be comfortably handled. Working from the base, pull off the skin and sucker cups—everything should easily slide off, leaving the meat ready for use. Arms can be cut into small pieces and used in stews or tacos; tentacles can sliced into disks and marinated with lime and other ingredients to make traditional Mexican ceviche. I am eager to try tentacles in the Calamares Kilawin preparation described in a previous post.


Isla San Pedro Martir: W. Gilly (June 2010)

Tentacles vs Arms and Cleaning Calamar: Patrick Daniel, Stanford Univesity

Map: Google Earth, adapted by W. Gilly