Monthly Archives: May 2004

Life Moving On, #2

It’s been a bit since I’ve written something here. I am still working on the recovery. I can get up and move around easier now, but I still get tired very easily. Come next Tuseday, I will have my last dose of prednisone. It is good to be coming off that drug.

I have a picture of my parents, Diane, and I in front of our house…

Diane, Robin, and I visited the Marine Mammal Center at Marin County last week. This is the stranding network for northern California, and they had elephant seal pups, sea lions affected by domoic acid (an instance of bioconcentration of toxins produced by dinoflagellates), and harbor seal pups.

Before Robin left for Florida, she got to feed Beater, one of our male Harris’s hawks.

Diane’s parents, Sam and Marguerite, are visiting with us currently. We went up to Fairfield and had dinner with Diane’s brother Joe and his wife Angela:

I’ve been in to the office a couple of times this week for two or three hours each time.

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Darwinism In Crisis Again?

Let me start this off with a quote from Charles Darwin:


I have been struck with the likeness of many of the half-favourable criticisms on sexual selection, with those which appeared at first on natural selection; such as, that it would explain some few details, but certainly was not applicable to the extent to which I have employed it. My conviction of the power of sexual selection remains unshaken; but it is probable, or almost certain, that several of my conclusions will hereafter be found erroneous; this can hardly fail to be the case in the first treatment of a subject. When naturalists have become familiar with the idea of sexual selection, it will, as I believe, be much more largely accepted; and it has already been fully and favourably received by several capable judges.

(Descent of Man, preface)

And now let’s look at this news story that has as its focus a “challenge” to sexual selection.

Lunch with the FT: Rainbow warrior

“If you have a theory that says something is wrong with so many people, then the theory is suspect,” says Joan Roughgarden, looking up from her Caribbean chicken salad. “It is counter-intuitive that nature should have done such a bad job – or, if you prefer, that God should have made so many mistakes.”

The theory in question is Charles Darwin’s theory of sexual selection; the “mistakes” are homosexuals, bisexuals, transsexuals – anyone who does not fit into the neat categories of heterosexual male and female.

By challenging the great 19th-century naturalist, Roughgarden, a professor of biological sciences and geophysics at Stanford University, is making waves in academia and beyond. The implications, not only for science but also for society, could be profound. After all, you don’t need to be versed in the Origin of Species to share Darwin’s twin assumptions that, broadly, the purpose of sex is reproduction and that females select mates on the basis of genetic characteristics or traits.

Being versed in Darwin studies would mean that one would know that instead of Origin of Species one should be looking at Descent of Man for Darwin’s full explication of his theory of sexual selection. And when one looks there, does one find that sexual selection is founded strictly upon the two “assumptions” identified above? No, one does not.

The first assumption, that the sole purpose of sex is reproduction, is simply absent from Darwin’s work, so far as I can determine. Someone may have advanced that notion, but until I am presented with the particular passage from Darwin that confirms it I will remain unconvinced of the veracity of the claim that it is Darwin who advanced it. To this end, I have examined etexts of both Origin of Species and Descent of Man and have satisfied myself that such a passage is not to be found within these works.

Let’s look at how Darwin framed sexual selection.


We are, however, here concerned only with sexual selection. This depends on the advantage which certain individuals have over others of the same sex and species solely in respect of reproduction. When, as in the cases above mentioned, the two sexes differ in structure in relation to different habits of life, they have no doubt been modified through natural selection, and by inheritance limited to one and the same sex.

(Descent of Man)

There is no dependence given here by Darwin on sex itself having the purpose of reproduction, as represented by Roughgarden. Instead, Darwin presents sexual selection as a function of differential reproductive success — which says nothing about what the “purpose” of sex itself is.

What of the second assumption identified by Roughgarden, that of female choice? That certainly is part of Darwin’s theory of sexual selection. The problem lies not in what Roughgarden provides here, but in what she omits. Sexual selection as explicated by Darwin also concerned how the traits found in the males affected male-male interactions.


When the two sexes follow exactly the same habits of life, and the male has the sensory or locomotive organs more highly developed than those of the female, it may be that the perfection of these is indispensable to the male for finding the female; but in the vast majority of cases, they serve only to give one male an advantage over another, for with sufficient time, the less well-endowed males would succeed in pairing with the females; and judging from the structure of the female, they would be in all other respects equally well adapted for their ordinary habits of life. Since in such cases the males have acquired their present structure, not from being better fitted to survive in the struggle for existence, but from having gained an advantage over other males, and from having transmitted this advantage to their male offspring alone, sexual selection must here have come into action. It was the importance of this distinction which led me to designate this form of selection as Sexual Selection.

(Descent of Man)

Not only does Darwin recognize male-male interactions here, but he emphasizes the importance of these in his development of the theory of sexual selection. That seems a rather glaring oversight on Roughgarden’s part.

Consider this from the same interview with Roughgarden:

Her alternative paradigm, presented in Evolution’s Rainbow, starts with evidence that the natural world is more sexually diverse than usually appreciated. For example, about a third of the species of tropical fish swimming over coral reefs change sex at some point during their lifetime. The conclusion, she says, is that our tendency to divide creatures into neat piles labelled “male” and “female” is mistaken.

It’s funny how Roughgarden positions herself as breaking new ground in discussing diversity of sexual habits. It becomes especially funny when one peruses both Origin of Species and Descent of Man and finds the many discussions of hermaphroditism, gender change, and parthenogenesis contained therein.

Further on in the article on Roughgarden, we find this:

Roughgarden isn’t suggesting an overhaul of Darwin’s theory of sexual selection – she is proposing demolition and redevelopment. Her explanation is that Darwin was wrong to regard sex as solely a matter of reproduction. It also has a social role. Thus homosexual behaviour, she says, is a way of building same-sex relationships and strengthening the position of an individual within a group. Far from being an anomaly, she says it is widespread and useful.

It would appear that strawman construction and demolition is not only useful for career-building, but also seems to be lucrative, if book royalties amount to anything. Compare the grandstanding that comes through this text to Darwin’s own assessment of sexual selection quoted up at the top of this post. The comparison is not favorable to Roughgarden.

Roughgarden’s thesis of the social utility of homosexuality should properly be considered as complementary to Darwin’s theory of sexual selection rather than as a supplanting alternative theory. For while Darwin did not treat characters like homosexuality directly, there is nothing within what Darwin actually wrote on the topic that would exclude social behaviors of this sort from the general framework of sexual selection. But that, of course, would not give Roughgarden the iconoclast status that she apparently seeks.

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Life Moving On

May 9th – May 14th

Things have seemed hectic for someone as out of it as me. I’m sorry I’ve slipped on the updates lately. Anyway, this one covers a few days that have been pretty good for me. This means I haven’t spent quite as much time stuck on the sofa next to one computer or in a chair next to another, and thus have not been reminded as often to make a post.

As a reward for your patience, though, I have prepped some images to go with the text here.

I already mentioned the outing for a meal on May 9th. Above is a picture from that outing, with (from left to right) Mark Todd, me, Willard, and Margaret.

On the 10th, I had a longer walk with my parents. We went to the schoolyard that is just behind the back yard of the place we’re renting. Here is a view of the scenery:

And a view of my parents next to a nicely landscaped house in the neighborhood:

On the 11th, my parents and I had an outing up to Mount Diablo State Park.

This trip took a couple of hours. Fortunately, there were facilities up at the ranger’s station seven miles into the park.

The 12th was pretty uneventful. In coming off the prednisone, I’m doing a good deal more sleeping, almost like I’m catching up from all the sleep deprivation I had while on it.

On the 13th, my parents and I made a trip into Oakland to the National Center for Science Education, where they got to meet almost all the staff. We had a good visit there, then met with Diane for dinner at Fellini’s restaurant in Berkeley on University Avenue. Diane and I split a mushroom fettucine with grilled chicken dinner, and Willard and I split a pint of Newcastle Brown Ale.

The 14th was a good day. Willard and I had a long chat about things happening back in Lakeland, Florida. I had spaghetti leftovers for lunch, and a fresh batch of spaghetti and meat sauce for dinner, by request. My parents leave early on the 15th, so there was some packing and preparations that they made. They also did another run to the grocery store and stocked up on various staples. My niece, JoAnn Robin, will be arriving on the 15th to help out.

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Rest and Recuperation, #9

Friday, May 7th – Sunday, May 9th

Friday was the first full day my parents, Willard and Margaret, were here. I was a bit tired still from the activities of Thursday. Diane was off to Berkeley for more seminars. Glenn Branch and Nick Matzke dropped by in the afternoon to say hello and we chatted for a couple of hours. Dinner was spaghetti and meat sauce. We gave Margaret a bouquet of specialty cookies for Mother’s Day a little early (while the cookies were fresh) and a dozen chocolate chip cookies for Willard.

On Saturday, Diane had the dogs entered in a field trial in Rio Vista, so she was gone most of the day. With Willard’s help, I made a bit of progress in sorting through some of the old materials I had on artificial neural networks, setting aside proceedings and journals to go to the library, and other stuff for recycling. We had two walks, one after breakfast, and one in the afternoon, going down the street and a bit further.

On Sunday, breakfast was scrambled eggs with ham and cheese, grits, and sourdough toast. I think my appetite is almost back to normal. Had a bit of a nap around noon. Mark Todd dropped in for a visit, and we all went out to the “Fresh Choice” restaurant at the Sun Valley Mall for a late lunch or early dinner. I had a couple of the pasta choices from the salad bar and some other pasta. We did a bit of shopping in the mall afterward, and Mark headed off. This was the longest outing I’ve had so far since the surgery, and it worked out OK.

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Rest and Recuperation, #8

Wednesday, May 5th, and Thursday, May 6th:

Wednesday went well. I was able to spend some time catching up with some minor issues of configuration at work via the Internet connection. I do continue to have some pain in the abdomen which gets better with rest. Went for a walk with Diane to the end of our little street and a small bit further.

Thursday was a medical day. I had appointments with the ostomy nurse in charge of ordering supplies and my surgeon. We got to the hospital a bit late (a small accident involving a milk shake that tipped over in the car), but were able to see both anyway.

My surgeon removed the staples from my incision, which hurt a bit at the time and left that area irritated. He answered many of our questions, and gave us a copy of the pathology report on my removed colon. It seems that I’m a candidate for a “J” pouch procedure, which takes part of the small intestine and creates a reservoir for stool out of it. This will be a two-stage procedure, with the first part removing what’s left of the rectum, forming the “J” pouch, and putting it in place. After that has had time to heal, the rest of the small intestine will be hooked up to it. It’s expected that this should give me a more normal bowel habit. The first part of this would not happen until at least August. There will probably be another three months after that before the final surgery would take place. Diet will be more restricted directly after each surgery.

The ostomy nurse changed out my pouch and examined the ostomy, declaring it “perfect”. She is setting us up with a “variety pack” order, so that I can try out the two piece pouch system. This has a patch that goes over the ostomy, and then pouches with a complementary flange can be sealed to this. I’m not sure whether this is much of an improvement, as the frequency of changing the ostomy patch is about the same as for the regular one-piece pouch system.

After the appointments, there was the usual additional stuff to take care of: prescriptions to be filled, paperwork to be filled out. Having arrived around 11:15 AM, we left the hospital around 3:00 PM. We hadn’t really had a chance for breakfast or lunch, so we went by IHOP to catch up on breakfast, at least. We split a swiss cheese, bacon, and mushroom omelette, and Diane had crepe pancakes with lingonberries. It’s amazing how food can improve one’s mood. Then we went back home, where Diane hurriedly made some housekeeping preparations for the arrival of my parents, Willard and Margaret. Then she went off to the Oakland airport to pick them up. They did some grocery shopping on the way back, so it was pretty late when they arrived back here.

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Rest and Recuperation, #7

Sunday, May 2nd – Tuesday, May 4

My appetite is improving and my ability to take in food seems to be catching up.

On the down side, I sneezed once on Sunday and again on Monday. This was not a good thing for my abdomen. On Tuesday, I spent a good deal of the day asleep, which seems to have helped considerably with the level of discomfort I’m feeling in the abdomen.

Nick Matzke and Alan Gishlick visited on Monday afternoon. Alan brought over some “anime” on DVD to introduce me to the genre.

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Rest and Recuperation, #6

Friday, April 30th, and Saturday, May 1st, proceeded pretty uneventfully. I do seem to have uncomfortable tension in the abdomen on standing and whenever I remain standing. That’s annoying.

On Friday, Joe and Angela returned for another visit and brought chicken and sourdough bread for supper. On Saturday, I got a call from Jeff Shallit. We talked about medications and information theory.

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Anti-Spam: Better Late Than Never

There is one moment when a spammer must be truthful. No matter how many lies are in his materials, when he makes a connection to an intended recipient’s mail transport agent (MTA), he must reveal the IP address of his machine or one which translates his address. In other words, he has to tell where he is calling from, or he will never get the chance to transfer the data that makes up his spam email.

It’s taken me a long time to get interested in actively doing something about the burgeoning amount of spam that I’ve been receiving. I handle sysadmin duties for a Unix server that does email for a couple of dozen friends. Once I started looking into anti-spam techniques, the course that seemed best to me was to utilize some of the “blackhole” lists that are publicly available. These are lists of IP addresses of known spammers, or of misconfigured MTAs that could serve as “open relays” for spammers, or dialup IP addresses, or other suspicious sources. A query to a “blackhole” service with an IP address will get a response saying whether the IP address is one of the suspicious ones. At that point, the MTA can terminate the email exchange with an error message pointing to the service that marked it as suspicious. The data of the spam email does not have to be transferred and examined, saving lots of bandwidth.

Like I said, I’m late on this. I put in rules for my MTA to utilize several “blackhole” lists around 10 PM on April 29th. By 10 PM on April 30th, the MTA terminated session on almost 2,900 email sessions with suspicious sources. I noticed a precipitous drop in the number of spam emails that actually made it into my inbox.

It is important to note that “blackhole” lists will interfere with some legitimate email. If someone uses an ISP that is friendly to spammers, they may find it difficult to send email to hosts that utilize “blackhole” lists to exclude spam. The tradeoff here is whether one is willing to accept the amount of spam that will come in in order to receive every last legitimate email, or whether it is best to lose some legitimate email and a lot of the spam. I’m comfortable with the tradeoff of stemming the bulk of spam while losing a few possible legitimate emails. I was already overlooking legitimate email because of the sheer numbers of spam messages I was receiving. Now, I may also be missing a few emails, but I don’t have to look at the spam, either.

Some resources I found useful:

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