Field of Science

Six digit cat

Today a very affectionate cat walked up to my son and me as we were walking back from basketball practice. He wanted a lot of attention, and I noticed he had very peculiar front paws.

He really wanted some company, so my son and I obliged.

As I took a closer look, I realized he had six claws on each front paw. Looked like double thumbs. Nice!

I ran inside and got my camera, and tried to take some pictures for documentation, but they weren't good enough to show the six digits. I then held up his paws pretty firmly. He was good enough not to put his claws in my flesh, even though he clearly didn't much care to be constrained like that. I think he understood that this was a very important scientific investigation. No anthropomorphism here, I swear.

Click images to enlarge in order to see both claws on the thumb.

So why does he have six digits? Well, it could be a developmental "defect", even though I hesitate to even call it a defect - he was clearly doing very well, and my fitness assay was inconclusive (I didn't see any offspring). In that case, his kittens wouldn't have six. More interesting, if was a genetic "defect", then it could be heritable. Wouldn't that be cool? With some human artificial selection, the trait might even become established (i.e., appear in non-vanishing numbers, without going to fixation, i.e., the whole population sharing the trait). I hope he already had offspring, because he looked neutered, the poor thing. If true, that would be a real waste.

Michael Egnor's answers for New Atheists

Michael Egnor has answered the questions he put to the Atheists the other day. My answers are here.

His answers are kind of longish, so allow me to summarize:

1) Why is there anything?

God made it. (The Roman Catholic one, because Egnor is a Roman Catholic, so he knows that it was that one that did it. Somehow.)

2) What caused the Universe?

God caused it.

3) Why is there regularity (Law) in nature?

Originates in God.

4) Of the Four Causes in nature proposed by Aristotle (material, formal, efficient, and final), which of them are real? Do final causes exist?

All four causes are real. Final causes exist.

[Final cause is the end, goal or purpose of a thing (the final cause of a rubber ball is to provide a bouncy toy). Egnor thus espouses the view so heavily criticized (though not universally so) by evolutionary biologists that every organ/trait has one purpose, and that purpose is why the organ/trait is there. No wonder true vestigial traits (those of no function at this time) is such a big problem for Egnor and his fellow Id proponents.]

5) Why do we have subjective experience, and not merely objective existence?

Because God gave us a soul.

6) Why is the human mind intentional, in the technical philosophical sense of aboutness, which is the referral to something besides itself? How can mental states be about something?

Apparently, that was an easy one: Intentionality is easily explained; my thought that is instantiated in my brain state refers to an apple because the form of the apple is grasped by- is actually taken into- my mind.

But seriously, I cannot possibly summarize his answer.

7) Does Moral Law exist in itself, or is it an artifact of nature (natural selection, etc.)

Moral law is objective, and made by God.

8) Why is there evil?

Because Adam and Eve sinned by eating a fruit that made them blush about their genitals and God became (and continues to be) really, really angry. In other words, God allows/created evil.

★ ★ ★

Egnor also refers to current evolutionary theory (and the rest of science) as incapable of explaining any of these things. For example:

7) The assertion that Moral Law is subjective or is a byproduct of evolution is incoherent at best, and has horrendous implications for mankind.

Sigh! Moral sentiments are rather easily explained by evolutionary theory. And the second statement is clearly false, because there are many atheists worldwide, and they are not the problem. (And despots were religious and irreligious, both.)

8) If mankind evolved by natural selection, we wouldn't even perceive the death of unrelated others as evil. It would be a real win- more offspring for me!

Yes we would. We do. Again, empathy can be explained by evolution, too. Plenty of good books on that, such as Evolutionary Origins of Morality or The Evolution of Morality.

Time Tree rocks

ResearchBlogging.orgI've just learned of a new online application, Time Tree, with which you can search on two species/taxa and get the time since they diverged from each other.

Cats and dogs share a common ancestor about 53 million years ago. Apes and monkeys (did you think they were the same?) about 30 mya. Fish and mammals go all the way back to the (pre-)Cambrian (455 mya). Birds and mammals: 325 mya.

I could go on. And I will.

Human and hedgehog: 97 mya. Crocodile and lizard: 275. Protostomes and deuterostomes: 910 mya.

Wait, there's more.

Everything: 4,200 mya. Archaea and eukaryotes: 3,806 mya. Cat and Hedgehog (carnivores and insectivores): 87 mya. Lion and tiger: 3.7 mya.

I'm so animal-centric.

Tomato and oak: 125 mya. Plants and animals: 1,628 mya. Fungi and animals: 1,368 mya. Plants and protists: 1,379 mya.

Try it!

Hedges SB, Dudley J, & Kumar S (2006). TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (Oxford, England), 22 (23), 2971-2 PMID: 17021158

Defining away the evidence

"There can be no evidence for X, because X must per definition have the property Y, and Y does per definition not exist."

Find X and Y.

Michael Egnor's questions for New Atheists

Michael Egnor has some questions for atheists, because he thinks there must be more to what we believe than just these:
1) There are no gods
2) Theists are IDiots
3) Catholic priests molest children.
Well, actually, being an atheist (in one common definition) only means number 1. An atheist believes there not to be a god. You can qualify this as much as you want (I do not believe in the existence of the god of the Northern Conservative Baptist Great Lakes Region Council of 1912, for example). The other things we believe are not contingent upon the unbelief of this or that god.

But still, I don't mind at all sharing what I believe. And I emphasize that these are beliefs, though not on faith. They are both informed by and amenable to evidence.

Oh, and there are rules:
The rules:

1) Answers can't be limited to the shortcomings of theism (e.g. 'So who caused God?'). I'm looking for an exposition of New Atheist belief, not a criticism of theist belief. Mutual criticism will come once all beliefs are on the table. If New Atheist belief can only be expressed by negation of the beliefs of others, just say so.
2) Myers' "Courtier's Reply" gambit is fine. If you think that a question is nonsense, say so.
3) No changing the subject. New questions are welcome, once the old questions are addressed.
4) The Law of Snark Conservation applies; thoughtful courteous answers get thoughtful courteous replies.
1) Why is there anything?

Because 'nothing' is unstable. There are many more ways for there to be something than nothing, so it's the more likely outcome.

2) What caused the Universe?

Nothing did. It was not caused at all. Perhaps a spontaneous reaction.

3) Why is there regularity (Law) in nature?

Good one. I can't come up with an answer that doesn't lead to a new question ad infinitum. Let me rephrase that question: When two particles interact (say, two electrons) in one way in our galaxy, then why do they interact the same way in the Andromeda galaxy? I don't know.

4) Of the Four Causes in nature proposed by Aristotle (material, formal, efficient, and final), which of them are real? Do final causes exist?

I can understand 'material causes', but I have no clue what the other means. Must I now believe in God of Egnor?

5) Why do we have subjective experience, and not merely objective existence?

We experience things with our brain, and we have our own, rather than sharing with the rest. We call that subjective.

6) Why is the human mind intentional, in the technical philosophical sense of aboutness, which is the referral to something besides itself? How can mental states be about something?

Aboutness?! My spellchecker does not compute. The brain is made such that it can think about what we experience. What's the question again?

7) Does Moral Law exist in itself, or is it an artifact of nature (natural selection, etc.)

There is no Moral Law. That we are moral is an artifact of nature.

8) Why is there evil?

There are actions that are deemed evil, because they cause harm. When people harm others (including animals), we call that evil. People harm others for a number of reasons. Because it benefits themselves, because they don't know any better, because they see no other way out of a situation, for examples.


Hey, that was fun!

New developments in the case for evidence for god

If you're following the debate about the possible existence of adequate evidence for a god, you should read Jerry Coyne's newest post on the topic. I am, as noted earlier, on Coyne's side in this debate, while most others think that no kind of evidence in principle would be enough to tentatively establish that any god(s) exists.

The problem has a lot to do with definitions, and Myers, Pigliucci, and Sweet set the bar pretty high (intolerably high, in fact, imo).

Jerry's post links to a paper by Boudry et al. that seems a must to read if you're interested in this topic. Apparently Rob Pennock is another proponent of the view that “science is simply not equipped to deal with the supernatural and therefore has no authority on the issue.” Pennock is here at MSU downstairs from me, so I will try to catch him and ask about it. Stay tuned...

What a species is

From now on I'm going to be close to requiring anyone I discuss the concept(s) of species with to have read John Wilkins' post on the subject, How many species concepts are there? Very clear and lucid, really.
What to think? My solution is this:

There is one species concept (and it refers to real species).

There are two explanations of why real species are species (see my microbial paper, 2007): ecological adaptation and reproductive reach.

There are seven distinct definitions of “species”, and 27 variations and mixtures.

And there are n+1 definitions of “species” in a room of n biologists.
I don't mean to say that Wilkins get the final word, but just that his categorizations is most germane to the topic. I, for one, (also) think that Ernst Mayr committed several blunders when emphasizing the Biological Species Concept. And the name itself was one of them. I'm the lone evolutionary biologist in a microbial lab a the moment, and we don't like not talking about different species of bacteria, for example. Sex is great, but not always for everybody.

It' still my birthday for a little while longer, so...

I know your name is Rita, 'cause your perfume's smelling sweeter.

Here's a nice birthday present I got earlier today: Genomic patterns of pleiotropy and the evolution of complexity. I'm planning to blog about this beauty later...

Why Intelligent People Watch More TV

Satoshi Kanazawa is writing a bunch of blog posts using his pet hypothesis ("The Hypothesis") to explain human behavior:
I believe evolutionary psychology is key to uncovering the origin of individual preferences and values. The Savanna Principle states that the human brain has difficulty comprehending and dealing with entities and situations that did not exist in the ancestral environment. The theory of the evolution of general intelligence suggests that general intelligence evolved as a domain-specific psychological adaptation to solve evolutionarily novel problems. Their logical conjunction suggests a qualification of the Savanna Principle and leads to a new hypothesis about individual preferences and values.

If general intelligence evolved to deal with evolutionarily novel problems, then the human brain’s difficulty in comprehending and dealing with evolutionarily novel entities and situations (proposed in the Savanna Principle) should interact with general intelligence, such that the Savanna Principle holds stronger among less intelligent individuals than among more intelligent individuals. More intelligent individuals should be better able to comprehend and deal with evolutionarily novel (but not evolutionarily familiar) entities and situations than less intelligent individuals.
The more intelligent people are, the more likely they are to do evolutionary novel things. Like drinking alcohol, smoking cigarettes, and be vegetarian, have sexual affairs, commit less crime, go to bed later, be atheist, and, of course, be politically liberal.

Some of these observations I don't dispute, but (while I am persuaded that human behavior is influenced by our evolutionary past), I have some trouble believing that it is correct to invoke The Hypothesis so widely. If this principle is true, then why stop at the obvious stuff? (Though I do not think smoking is so obvious, and apparently the data doesn't reflect it, either.)

How about watching TV. Since spending large amounts of time passively watching other people go about their lives is evolutionarily novel, should we not hypothesize that more intelligent people watch more TV? Somehow I have trouble seeing the data coming out in favor of that prediction.

More intelligent people drive cars? There were no cars on the savannah 100,000 years ago. So, intelligent people do it more? Can't wait to see those data.

Shop in supermarkets? Conversely, are people who hunt less intelligent than people who people who don't?

I'll have to admit, though, that coming up with crazy examples - like I trust you'll agree the these are - is far harder than construing examples that are likely to fit with The Hypothesis. Like reading books, traveling, using computers, sitting in offices all day, and having fewer children, or practice BASE jumping. It also neatly fits with the observation that political leaders are so darn dumb.

But then, if you read Kanazawa's post on smoking cigarettes, it turns out not to conform to The Hypothesis. Particularly, in the UK the trend is opposite. The more intelligent people are before the age of 16, the less likely they are to be smokers later in life. Kanazawa plans to address this incongruence in a later post, but I worry that the answer might be some explaining away how smoking really isn't that novel in evolution. Determining what is evolutionarily novel is probably not as straightforward as I have suggested above. They could be lots of exceptions that would render The Hypothesis unusable, I would think, without at least taking lots of other factors into account.

Update 10/23: Kanazawa has a new post about why the correlation between intelligence and smoking is opposite in the US and the UK. Short answer is that he doesn't know. Longer answer is one that he doesn't believe in himself.

Leigh Van Valen dies

Evolutionary biologist Leigh Van Valen has just died (1935-2010).

I'm currently writing a paper in which I use the Ecological Species Concept originated by Van Valen in a paper from 1976 with my favorite title of all time: Ecological species, multispecies, and oaks. It's a great paper with a fabulous title.

Van Valen also invented the famous Red Queen hypothesis to explain co-evolving systems.

What's adequate evidence for God in principle?

As an atheist, is there any evidence that I would persuade me to provisionally accept that God exists?

This questions has recently been dealt with by both PZ Myers and Jerry Coyne - who are both atheists and biologists, and usually agree on most things, as far as I can discern. This time they don't, however. PZ argues that nothing would persuade him, and Coyne explains how he could be persuaded (two other bloggers I follow, Massimo Pigliucci and John Wilkins - both philosophers with a heavy interest in biology, and both atheists, even though Wilkins doesn't know it, have indicated that they side with PZ on this one).

First off, the question as stated doesn't completely make sense. In order to refute a concept/hypothesis, it must be adequately defined. And quite frankly, those people who say they will not be persuaded by any evidence whatsoever, are exactly the ones who seem to me not to own up to this problem. If I just say 'God', then one can always refute positive evidence for the concept by saying that something else could explain it, by pushing further back what 'God' means. For example, if we define 'God' as that which caused a particular person with leprosy to be healed, then evidence that this particular person with leprosy was healed would be evidence of 'God'. Stupid definition, of course, but the problem is that all the definitions are stupid, in this sense. Events purported to be explained by some God-concept can all be explained in other ways, too. And this is exactly the problem, and the reason that tree quarters of people surveyed (see above) will say that no evidence is sufficient to persuade them.

Since we are people of science - people who believe that belief should be based solely on evidence - it seems a pretty big problem that there is something we just would not ever accept as true NO MATTER WHAT THE EVIDENCE. It is, quite frankly, a totally untenable position that we cannot afford to take, especially given that we are asking everyone else to accept the evidence we have for evolution.

Coyne gives an example that I think is pretty good. Take it away, Jerry:
Suppose that you, P.Z., were present at the following events, and they were also witnessed by lots of other skeptical eyewitnesses and, importantly, documented on film: A bright light appears in the heavens and, supported by wingéd angels, a being clad in white robe and sandals descends onto the UMM quad from the sky, accompanied by a pack of apostles with the same names given in the Bible. Loud heavenly music is heard everywhere, with the blaring of trumps. The being, who describes himself as Jesus, puts his hand atop your head, P.Z., and suddenly your arms are turned into tentacles. As you flail about with your new appendages, Jesus asks, “Now do you believe in me?” Another touch on the head and the tentacles disappear and your arms return. Jesus and his pack then repair to the Mayo clinic and, also on film, heal a bunch of amputees (who remain permanently arméd and leggéd after Jesus’s departure). After a while Jesus and his minions, supported by angels, ascend back into the sky with another chorus of music. The heavens swiftly darken, there is thunder, and a single lightning bolt strikes P.Z.’s front yard. Then, just as suddenly, the heavens clear.
PZ responded in a post consisting of ten eight points, and frankly I have trouble seeing how any of them aren't just skirting the matter at hand profusely. Quite a puerile 'no, no, no' objection, if you ask me. For example:

2. There's a certain unfairness in the evidence postulated for god. I used the example of a 900 foot tall Jesus appearing on earth; there is no religion (other than the addled hallucinations of Oral Roberts) that ever proposes such a thing, so such a being would not prove the existence of any prior concept of god, and will even contradict many religions. It's rather like proposing a crocoduck as a test of evolution.
Swoosh, swoosh. God should be able to make a 900 foot Jesus (and all sorts of other amazing things that aren't described in the Bible).
6. One other odd feature of the proposed evidence for god is that it is all so petty and superficial. Remember, this omnipotent god we're talking about has been called "the ground state of all being" and is supposed to be omnipresent and essential to the maintenance of the universe, so I expect the evidence for god to be rather more fundamental. No one seems to think to invent a property of nature that is supernatural; even the terms are self-contradictory. But shouldn't a god be as ubiquitous and consequential as bosons? Despite calling some particles "god particles", though, the fact of existence makes them natural and immediately disqualifies them from godhood.

We could then counter that those events could be explained by something else, of course. As people would. However, if we do that, then I would have to ask why? Why not at this point simply admit that, okay, there is indeed a god, and this god did this. We simply defined 'God' as the one who would cause these events to happen. Why not? Because God is more than that, you say? Well, then let's hear what that 'more', and I can come up with another (crazy) example of an event to add to Coyne's, and we could ask the same question. Suppose this 'God' said that he would now create a copy of Earth orbiting Earth One, and on it start creating life again, just like he tells us that he did some 6000 years ago. And he somehow let us all see it, and let all the scientists and atheists have front row seats of it all. Suppose this 'God' could tell each one of us what we were thinking, predict the future, explain away the fossil record, and make a stick that is longer than itself, etc. etc. At one point 'God' would have done everything we think that God is supposed to be capable of, and at that point we would have no other tactic than the claim that everything that is happening is some malfunction of our brains (all 6+ billion), and that it's all just an illusion. However, our daily (normal) lives might all be like that (The Matrix, yada-yada), and the way we think we are not living under a constant elaborate illusion is by verifying what we experience with other humans. "Did you see those planes fly into that building?" "Yes, dude, it was all over the news." "Did you see that ball of lightning?" "What?! You're crazy, balls of lightning don't exist!".

In the process of accepting that 'God' did the things that he says that he did (including creating us, say), we may learn something new about 'God', and this may be off-putting to a lot of people, who may not recognize their own idea of God (there are, after all, over 33,000 Christian denominations that disagree on some aspect of theology, amazingly). This may prompt some people to say that this 'God' is not God after all, but that is exactly the problem of definition that I referred to above. I personally don't think the concept of the 'supernatural' make any sense in the first place; if some 'supernatural' event occurred for us to see, then it happened in the natural world that we inhabit, and we would immediately set out to explain it in terms of natural laws (physics, biology, geology, chemistry, etc.). If we could not do this, then we would simply update our natural laws as we always do when some new phenomenon is observed. As Michael Shermer* puts it, "the job of science is to make the paranormal normal." Same goes for the supernatural.

If such a God really appeared and did all of the above, what would you say? How about, "Okay, God, you exist. You are truly a being of wonder, and all evidence points to you being the creator of ourselves, which we must thank you for. However, screw you for keeping us in the dark for so long. Why on Earth didn't you show yourself earlier? Can you really blame us for not believing in you? I mean, with all the fucked-up things going on here every day, couldn't you have come a little earlier to feed the starving children, and to punish all the sinners? Why the hell did you have to plant all that evidence to make it look like we evolved without any help from you? Do you really despise us so much that you had to deceive us? Did we really mean anything to you after all, or were those just lies in that super-self-contradictory book containing the only information hitherto about your doings in the past? Given the really, really apparent evidence for your existence and your powers, are you going to be much offended if I'm gonna have to pass on loving you "back", and devoting my life to your glory?"

Or something like that.

* Shermer sides with those who would not accept any evidence for a deity, even though I am unsure how he would feel about Coyne's example and my extension.

PhD PhD event

If you're in CA (still), here's an event at Biola "University" that might be great fun to go to.
God And Evolution:
Protestants, Catholics, and Jews Explore Darwin's Challenge to Faith

with Marvin Olasky, Ph.D., Jonathan Wells, Ph.D., Ph.D., Jay Richards, Ph.D., Denyse O'Leary, John West, Ph.D., David Klinghoffer, Casey Luskin, J.D., Craig J. Hazen, Ph.D., John Bloom, Ph.D., Ph.D.

(Free for students and pastors - the very people they want to "educate".)

I can't get over Jonathan Wells and his two PhDs. They're in religious studies and molecular and cell biology. He got his second one in science after being told by Reverend Sun Myung Moon to go fight Darwinism.

It's got no one on that list of speakers who are not Intelligent Design advocates, so it's basically a pad-ourselves-on-the-back event, where there will be no opposition to the delusions of these usual suspects, so I don't know how interesting it really would be to go.

Carnival of Evolution featuring Sandwalk

A new edition of Carnival of Evolution went up last night on its home turf.
It features Larry Moran's blog, Sandwalk, and a survey of readers.

We are too at war

It's his own damn fault for not enabling comments on his blog.

Satoshi Kanazawa blogs on The Scientific Fundamentalist, and in his newest post, We Are NOT at War, he argues that the word war always means interstate war, and therefore the Geneva Convention does not apply to the war in Iraq.
If we were suddenly attacked by space aliens from Alpha Centauri and got involved in interstellar war, the Geneva Convention would not be applicable then either, because its drafters did not imagine situations of interstellar war. The Geneva Convention is no more applicable to our current situation of global civil war than to interstellar war against Alpha Centaurians.

Another confusion occurs when others complain about “civilian casualties” in Iraq or Afghanistan. Contrary to popular belief, there has not been a single civilian casualty in Iraq or Afghanistan. The word civilians means individuals who are not officially designated as combatants, members of an organized army under the direction of the leadership of sovereign states. There are no combatants on our enemy’s side in our current situation, and without combatants there are no civilians. No civilians, no civilian casualties. By the same token, no civilians were killed by the atomic bombs in Hiroshima and Nagasaki.
Okay great. No civilians killed in Hiroshima. What the fuck were they, then? Child soldiers with Kalashnikovs? I just don't remember seeing them on the pictures.

I also think war always means white war, such that the Geneva Convention does not apply to war down in Africa or over in Asia. Which is damned convenient. Also, where do I go to sign up to be a civilian? When Europe colonized Africa, where should the children have gone to sign up to be a civilian, again?

I'm sorry, Sathoshi-kun, but methinks you have gone and lost it. Again.