Behe on Behe, and Behe on evolution

I hadn't seen before that Leo Behe gave an interview last year.

He says as well as anyone what is wrong with the argument from design:

As for the arguments from design, such as irreducible complexity or the so-called fine-tuning of the six cosmological constants, I have many reasons for dismissing them each in particular, but one overarching reason would be the common refutation of William Paley’s classic watchmaker argument—the only reason that complex objects appear to be designed is because we as humans create complex objects, and we then assume that complexity is indisputably indicative of a designer. This is an association we make only as a result of what our “common sense” tells us.

A much too much unappreciated fact.

And Behe Jr. on Behe Sr.:

I would like everyone to realize that he doesn’t have any sort of religious agenda and he’s not trying to denigrate science in any way. Long-held beliefs, especially beliefs developed during childhood, operate on a very deep and basic level of thought—almost subconsciously. These beliefs can exist independently in a perfectly honest and intelligent scientist who is simply doing his part to further theories or ideas that he believes are supported by the scientific data. The best way to progress is through respectful and thoughtful discussion and debate, as it has always been.

I wish this to be true. I've met Michael Behe briefly at a conference, and I would like to believe that his mind is merely clouded by his religious thinking (and I hasten to say, in much the same way that most of us are clouded in our thinking in some ways or other - to me, one of the greatest joys* in life is to discover my own delusions).

That being said, take a look at Michael Behe's take on the newest research out of Lenski's lab: More from Lenski's Lab, Still Spinning Furiously (not a site I spend a lot of time on nor link to much, but making this one exception). He goes:

So at the end of the day there was left the mutated bacteriophage lambda, still incompetent to invade most E. coli cells, plus mutated E. coli, now with broken genes which remove its ability to metabolize maltose and mannose. It seems Darwinian evolution took a little step sideways and two big steps backwards.

Seems to me that what he's doing here is confuse the evolution of the whole system consisting of bacteria and virus (which from the outside does end up with the same dynamics of infection), but ignores the really interesting thing that goes on in the virus in response to the changes in its host (the bacterium). First, what a shame that he can't appreciate the evolutionary processes that took place in these experiments. If this is not a blatant example of inability to break free of dogma, then something else is.

Second, I have always had a problem understanding proponents of Intelligent Design, because they seem to at some level agree that evolution does occur, and yet they have problems with research that shows how new things are made. This is the domain of the "designer", apparently. But then, why not just say that that's what he did? ID proponents still - as far as I am aware - haven't described how evolutionary events such as viruses evolving new ways to attack the bacteria look different from when they happen naturally. In other words, there's no way of distinguishing the two ways (which would be a great step forward for the "debate" if someone would take this question seriously), so why don't the ID proponents just say that this is the way the designer does it in the first place? I mean, instead of this yapping about whether some research is profound or not.

* Along singing, dancing, playing, drinking, thinking, eating, winning, losing, procreating, baking, kissing, camping, biking, skiing, and writing in dew.

Link between political views and physiology

It is becoming more and more clear that political views are in fact not completely decided by rational considerations, as common sense would have us believe. Rather, previous studies have shown a link between emotional (i.e., largely uncontrollable) responses and position on the left/right spectrum: "those on the right are ‘distrustful of differences … fear change, dread disorder, are intolerant of nonconformity, and derogate reason’."*

A new study takes this even further, showing that there are physiological differences between people to the political left and right: "compared with individuals on the political left, individuals on the right direct more of their attention to the aversive despite displaying greater physiological responsiveness to those stimuli."

The researchers measured skin conductivity of people as they were looking at aversive images (spider on a face, maggots in a wound, crowd fighting with a man) and appetitive images (happy child, bowl of fruit, cute rabbit).

In the physiological session, participants were shown a series of 33 still images. Each image was shown once and was preceded by a fixation point that was displayed during an inter-stimulus interval. The order of slides was initially randomized and then presented in the same order to all participants. During the slide show, electrodermal activity (in the form of skin conductance readings) was collected using a pair of Ag|AgCl electrodes and standard psychophysiological equipment. Since eccrine glands release moisture as part of sympathetic nervous system activation, and since the rate of movement of electricity across the surface of the skin is a good indicator of the presence of moisture, electrodermal activity has long been accepted as a fairly direct and pure representation of sympathetic activity, making it a good measure of the psychological concepts of emotion, arousal and attention.

The skin of test subjects on the political right conducted more electricity than those on the left when presented with "aversive" images. That is, conservatives react more strongly to disturbing images.


Triangles: political right. Squares: political left.

As good researchers always should, the authors here moderate their discussion of these findings to not condemn:

Rather than using colourful adjectives, perhaps, the proper approach is simply to state that the aversive in life appears to be more physiologically and cognitively tangible to some people and they tend to gravitate to the political right.

They conclude that we can best understand political inclinations as being partly determined by something other than rational discourse, and propose a way forward:

Rather than believing those with political views opposing ours are lazily uninformed or wilfully obtuse, political tolerance could be enhanced and cultural conflict diminished if it is widely recognized that at least part of our political differences spring from subconscious physiological and cognitive variations that lead people to experience the world in fundamentally different ways and therefore to believe that fundamentally different political policies are appropriate.

Even if we recognize that people on the political right experience the world in a different way than those on the left, and that these differences are strongly influenced by genetic and physiological predispositions - perhaps prompting us to view them as pathological - and thereby fostering greater acceptance, it is in my mind by no means given what "left" and "right" means. The far left and far right have quite different meaning in different societies. In Denmark, for example, being on the far right does not imply that one is against welfare or abortion, while in the USA those go hand in hand. In other words, the Overton window can be moved, and the result will be that people who are on the far right will shift their actual political views, while still associating with the political right. What people identify as may be determined by non-rational factors to a large degree (but most likely not entirely), but where it is even possible to locate yourself is evidently affected by public discourse. We should therefore not view public outreach as futile because people anyway (mostly) can't change their minds, but as imperative to shifting what it means to be liberal and conservative.

* The rest of the quote from the paper goes "while Block & Block [53, p. 395] find that those on the right are ‘easily victimized, easily offended, indecisive, fearful, rigid, inhibited, relatively over-controlled and vulnerable’." Hell yeah!

Reference:

Dodd MD, Balzer A, Jacobs CM, Gruszczynski MW, Smith KB, & Hibbing JR (2012). The political left rolls with the good and the political right confronts the bad: connecting physiology and cognition to preferences. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 367 (1589), 640-9 PMID: 22271780.

SOPA and PIPA

These US House and Senate bills will censor the internet. Sign the petition to vote no on both.

What determines rates of ecological speciation?

Speciation models are the most beautiful thing in evolutionary biology. This is widely known, and those who disagree are the crazies. Other models have their place, and empirical evidence for speciation, and insights from there into how speciation takes place are crucial for progress. But real understanding of this question of questions in evolutionary biology only comes once a model is constructed and validated. It is the ultimate goal of scientific work to condense knowledge in terms we can share and peruse, and this we do in models - which you may call theory, but I tend to regard this distinction with distrust.

Case in point is a model of ecological speciation in a population of sexually reproducing diploids adapting to different resources scattered heterogeneously in the environment: Patterns of Species Ranges, Speciation, and Extinction.

Specific questions asked and answered include: What is the effect is limited vs. wide dispersal, i.e., how is the rate of speciation affected by individuals occupying a small geographical area? How does the distribution of resources (food, a place in the sun, etc.) affect the rate of speciation?

And the answers are: The more widely the individuals roam, and the more mixed resources are in the environment, the lower the rate of speciation is. So when individuals only get their resources from a small geographical area, and when there are few types of resources within that area, the more speciation happens.


Examples of environments with many types of resources within a small area (A) and resources distributed such that individuals will mostly find only one type within the area they roam.

With four different types of resources, the simulations are started with only 20 identical individuals in the corner of an area like the ones above. By reproduction and mutation the population grows and diversifies. Whether resource specialists or generalists emerge depends primarily on the two factors already mentioned: range and resource distribution. Specialists, which are very good at utilizing a single resource, can coexist with other specialists when they use different resources. You eat the bananas, and I'll the the leaves, and then we can get along. However, different generalists, in this model defined as those who use more than one resource, may not get along so well, because they overlap in resource use, and so one will tend to outcompete the other. We thus have that the emergence of specialists equates to higher rates of speciation.

Here are some results:



A and B: highly mixed resource environments. C and D: fragmented resources. A and C: low dispersal range. B and D: large dispersal range.

In A there are three specialists using only one resource (red), five generalists using two resources (blue), and two three-resource generalists (green) coexisting.

In B there is only a single generalist (no speciation).

In C there are four specialists coexisting.

In D there is one specialist and two two-resource generalists.

And Birand et al. did lots of simulation runs to get a good handle on the importance of the different parameters governing speciation rates. In addition to the two already mentioned (dispersal and resource distribution), another important one is the strength of trade-offs. It can be set as more or less difficult for individuals to be good at utilizing more than one resource. As an example of trade-offs, think of lemurs: Some lemurs eat leaves, and in order to digest the hard-to-digest cellulose, they have really long intestines. Other lemurs eat fruit containing lots of sugar, which is easy to digest. They don't need to have long intestines for that, so they have short ones, and thus can't digest leaves very well. At the same time, lemurs with long intestines can't eat fruits, because they tend to rot while making it all the way to rectum, which makes the lemurs sick. Thus, there is a trade-off between which foods the lemurs can eat, which makes the two species able to coexist (at least in theory - I don't know if they have overlapping ranges). Competitive exclusion (wiki) prevents lemurs that use the same resources from coexisting in the same area, while two species that occupy different niches won't have a problem with each other.

But, while trade-off are important to have for speciation to occur, varying the strength of it had little effect compared to the effects of limited dispersal and resource distribution.

In fact, geography turns out to be the most important feature in this model:

Indeed, when resources were distributed randomly, which resulted in highly fragmented landscapes (figs. S1, S11), there was always only one species regardless of the dispersal range D and trade-off coefficient b (of the 90 simulations initiated with all the parameter combinations of b and D, only one simulation resulted in two species).

That is to say, if it wasn't because resources are distributed in a patchy way, then speciation just doesn't occur at all. When individuals can find all four types of resources within their dispersal range, then generalists are always of higher fitness, and specialization is not favored. This also means that this model cannot account for (strict) sympatric speciation, where there is no geographical structure, and where individuals are not limited to mate with those close by, or use resources in their neighborhood. Not surprisingly, parapatric and allopatric speciation (where geography is a factor) is much easier than sympatric speciation (where geography is not). For that something else is needed. Stay tuned.

Reference:
Birand A, Vose A, & Gavrilets S (2012). Patterns of species ranges, speciation, and extinction. The American Naturalist, 179 (1), 1-21 PMID: 22173457

My time with Hitchens

So Christopher Hitchens died. It is sad when someone dies, mostly, and it is a good time to remember the good thing about the deceased. When the dead is a person like Hitchens, troublemaker extraordinaire, people will do the usual an extoll his accomplishments, but will also point out the extent to which they disagree with him. I don't personally have a problem with either (and feel quite certain that Hitchens wouldn't either, for what that's worth), and he has been given a lot of praise and taken a lot of flak since his death. But I see it as I do with other great contributors to thought - scientists in particular - that we can take from them what we appreciate and leave the rest for historians. Newton was not a nice person, and likely died a virgin (pft!), but we admire him as the greatest thinker of all time because of his accomplishments. And as for Hitchens, what does it matter to me that he was a drunk and supported the Iraq War? None. What matters is the things he said that I can use.

In spring 2008 I took a course with Michael Shermer at Claremont Graduate University called Evolution and Society. Shermer assigned us to answer the same question that he asked a bunch of luminaries via the Templeton Foundation: Does science make belief in God obsolete? Hitchens' answer is in the newest edition of eSkeptic, titled "No, but it should." That sums it up pretty well, and the substance of his reason why religion ought to be obsolete is captured by his sentence "It [religion] is how we came up with answers before we had any evidence," and thus captures the essence of what is exactly wrong with religion and faith: a lack of evidence and dismissal of evidence.

My own essay is listed here (comments by Shermer in Brackets):

Does Science Make Belief in God Obsolete?

As an atheist scientist, I dismiss the supernatural, and am therefore tempted to rule belief in God obsolete. There are many obvious reasons why – from a scientific point of view - science and religion cannot both be true. To cite just one example, Genesis 1 - what we have learned through science directly contradicts this biblical story of creation. They cannot both be the correct model of our origins.

By itself, however, this fact doesn’t render belief in God obsolete Because belief in God serves multiple purposes. Although science is superior at predicting and describing the world around us, has brought us true insight and utility, and has been used for a broad range of purposes, both good and bad, it cannot do some things that religion does very well.

Judaism, Christianity, and Islam are nearly identical in the way they are utilized by some of their followers, most notably in ways that science cannot replace. This God of a bronze age desert people continues to serve many people very well today.

What this God does for people is to tell them how to behave by word and by example. This frees people from thinking about such moral matters, and justifies the behavior of those who live and act as commanded by God. Many people still believe that it is through God we have our morals, and they cannot imagine a world without a deity to guide them. Logically, there exists no way of inferring how we should behave from what we can learn through science (the so-called “is-ought” problem, or the naturalistic fallacy), and religion thus trumps science in this matter. Science can explain what we come from, but it cannot tell us how to behave.

Belief in God allows some people to make a living without producing anything of value to society. Interpreting scripture and telling people how to live as God commands, they are generously supported by the rest of society [in what way?]. They [who is “they”?] do not contribute anything tangible, but purport instead to be a link to God, and to know what God wants from us [do you mean priests and pastors? In America they are voluntarily supported by their customers, the members of the church, who by making donations signal that they do, in fact, believe there is something of value being presented]. While science requires scientists devoted to the pursuit of knowledge, scientists cost society far less than what it earns from the resulting discoveries.

Throughout history, belief in God has given rulers the justification for their positions of superiority [I think you mean here the divine right of kings concept]. Oppression and tyranny has been, and continues to be, done in the name of God. Kings and emperors would never have been able to control the masses without the belief that God had personally chosen them. World leaders today continue to justify their means by invoking God, and they are often supremely confident that they have the moral high ground over those people who do not share their particular belief, let alone over those who do not believe at all. Science does not do this. It cannot, because it deals only in knowledge, and thus doesn’t speak of superiority. [what about Marxism, and Marxism-Leninism, supposedly grounded in solid social science and applied throughout the Soviet Union and Mao’s China?]

But perhaps more than anything else, belief in God comforts. People are scared of life, and they are scared of death. It’s a frightening world, and we are but dust blowing in the wind, with minimal control over our own fate. Death is final, and that’s all there is [too colloquial, best suited for a bumper sticker] [these short toss-off lines are not sentences]. Belief in God means, perhaps more than anything else, that once you die, you get to go to a better place, where you will stay forever together with your loved ones. Your life on Earth is merely a test, and if you pass it, you will fear no more, forever. Those lewd unbelievers can go to Hell, where they will burn and suffer forever for their unbelief, by will of God, loving and omnipotent. All science does in this respect is tell you that this life is all you’ve got. That’s it.

So belief in God is by no means made obsolete by science. While my professed disbelief strongly suggest a heap of sarcasm [I’ll say!], I honestly mean it when I say that belief in God is extremely useful, just not in any way in which I would like to participate.

I believe that this world would be better place without belief in God. Science has been a way for me to gain comprehension, and thus a way to accept who we really are, and what life has in stall for us. I am also afraid, but I have come to accept that fear as part of who we are. I refuse to join those who extort and oppress others in the name of God. I am a scientist, and I shall not waiver. Faith is obsolete for me – there is nothing that I dare not question.

I met Hitchens when he came to Pitzer College in 2008 to give a talk before a student audience. He hadn't prepared a presentation particularly for this event, but asked a small group of us over dinner what we would prefer, and it was generally agreed that he should talk about atheism. However, at one point he noted that he also had a great memory for limericks, and asked if we wanted to hear some. Second question: Can we handle some dirty ones? General excitement, except from one woman behind me who gloomily went "No. No. No." Among the many he shared, I only recall this one:

There once was a hooker from Q
who filled her pussy with glue.
She said with a grin,
if they'll pay to get in
they can damn well pay to get out too.

And for that, we thank you.

Pun five