Sean Carroll: "What Is Science?"

I've been meaning to comment on Sean Carroll's post from last July (July 3, 2013) but there always seems to be something else that commands my attention. The issue is important, in fact I've just finished an entire book on the question (Philosophy of Pseudoscience: Reconsidering the Demarcation Problem edited by M. Pigliucci and M. Boudry).

Sean Carroll (the physicist)¹ has a view that's quite similar to my own. Read his post at: What Is Science?. Here are some key points.

Better Biochemistry: Teaching ATP Hydrolysis for the MCAT

I'm digesting the idea that many American biochemistry courses teach to the MCAT exam [see Better Biochemistry: Teaching to the MCAT?]. What this means is that the scientists who teach biochemistry are willing to let the curriculum be established by a group of American medical schools (AAMC). That organization has put up a website to guide faculty members and students in preparation for the 2015 MCAT exam [MCAT2015: Biological and Biochemical Foundations of Living Systems].

One of the links takes you to a chemwiki at the University of California, Davis: Biological Chemistry. From there you can click on several topics. I picked ATP/ADP to see what kind of information the MCAT thinks is appropriate. The information on the ATP website is provided by Tiffany Lui of the University of California, Davis so it's not something that AAMC created. Nevertheless, it is presumably indicative of the sort of thing that might appear on the MCAT exam.

Humans Are Still Evolving

Sir David Attenborough said something stupid the other day [Sir David Attenborough: Humans have stopped evolving]. (Not for the first time.) He said ...

Because if natural selection, as proposed by Darwin, is the main mechanism of evolution – there may be other things, but it does look as though that’s the case – then we’ve stopped natural selection.

We stopped natural selection as soon as we started being able to rear 95–99 per cent of our babies that are born.

We are the only species to have put a halt to natural selection, of its own free will, as it were.

The headline says that humans have stopped evolving. If that's what he really said then it's easy to prove him wrong by showing that there's a lot more to evolution than natural selection [Have Humans Stopped Evolving?].

But what about his specific claim that natural selection doesn't work on humans any more? I covered that in earlier posts but John Hawks has corrected him today [Humans are still evolving, and soon we'll know a lot more about it]. I love it when I agree with John Hawks! (That's me, visiting him in his lab in Madison, Wisconsin.)

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Better Biochemistry: Teaching to the MCAT?

Theme

Better BiochemistryI view science education as a way of teaching students how to think critically. In that sense, it's not any different than education in the arts and humanities. In my opinion, biochemistry should be taught as a bunch of fundamental concepts and principles that will help students understand the basics of life at the molecular level. The course will demonstrate how to think critically and how we come to know what we know—if we teach it correctly. I believe that biochemistry should be taught from an evolutionary perspective since that's the best way to achieve fundamental understanding.

The last thing we should be doing in an undergraduate biochemistry course is to ask students to memorize enzymes, structures, and pathways and regurgitate them on an exam. We should not just be teaching the biochemistry of humans since that does not provide students with a broad view of life and where humans came from. Such an approach also makes biochemistry seem like it's only important because it can contribute to health. We have plenty of evidence that this is the wrong way to teach.

The Happiest Countries

Why do the people of these countries think they are happy? Why isn't the USA in the top ten? [World’s Happiest Countries In 2013, According To The UN]

I recently visited #1, #2, #5, #7 and #9 and I can confirm that the citizens of those countries do, indeed, think they are happy. I also visited #17 a few months ago and the citizens of that country do not seem happy. It's probably worse today than it was a few months ago.

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Science and Mystery

One of the criticisms of science (narrow definition) is that its reductionist approach is simplistic and materialistic. Here's how Jesus and Mo dealt with that issue last month.

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What Is "Science" According to George Orwell?

I'm about to start teaching my course on "Scientific Misconceptions" and one of the most important issues is defining science and dealing with the demarcation problem. Vincent Joseph Torley is also interested in this question—for a different reason—and he discovered an 1945 essay by George Orwell (Eric Arthur Blair (1903-1950)).

It's worth quoting the relevant passages.
Doublethink means the power of holding two contradictory beliefs in one's mind simultaneously and accepting both of them.

George Orwell

In last week’s Tribune, there was an interesting letter from Mr. J. Stewart Cook, in which he suggested that the best way of avoiding the danger of a “scientific hierarchy” would be to see to it that every member of the general public was, as far as possible, scientifically educated. At the same time, scientists should be brought out of their isolation and encouraged to take a greater part in politics and administration.

As a general statement, I think most of us would agree with this, but I notice that, as usual, Mr. Cook does not define Science, and merely implies in passing that it means certain exact sciences whose experiments can be made under laboratory conditions. Thus, adult education tends “to neglect scientific studies in favour of literary, economic and social subjects”, economics and sociology not being regarded as branches of Science, apparently. This point is of great importance. For the word Science is at present used in at least two meanings, and the whole question of scientific education is obscured by the current tendency to dodge from one meaning to the other.

Science is generally taken as meaning either (a) the exact sciences, such as chemistry, physics, etc., or (b) a method of thought which obtains verifiable results by reasoning logically from observed fact.

If you ask any scientist, or indeed almost any educated person, “What is Science?” you are likely to get an answer approximating to (b). In everyday life, however, both in speaking and in writing, when people say “Science” they mean (a). Science means something that happens in a laboratory: the very word calls up a picture of graphs, test-tubes, balances, Bunsen burners, microscopes. A biologist, and astronomer, perhaps a psychologist or a mathematician is described as a “man of Science”: no one would think of applying this term to a statesman, a poet, a journalist or even a philosopher. And those who tell us that the young must be scientifically educated mean, almost invariably, that they should be taught more about radioactivity, or the stars, or the physiology or their own bodies, rather than that they should be taught to think more exactly.

Every war when it comes, or before it comes, is represented not as a war but as an act of self-defense against a homicidal maniac.

George OrwellI agree with Orwell when he prefers the broad definition of science. I see it as a way of knowing that can be applied to any discipline. I think that everyone should become more scientifically literate but by that I don't mean they should lean more about metabolic pathways or quantum chromodynamics. I mean that they should become more familiar with the scientific approach to acquiring knowledge. That's the fundamental skill that we need to learn.

Clearly, scientific education ought to mean the implanting of a rational, sceptical, experimental habit of mind. It ought to mean acquiring a method – a method that can be used on any problem that one meets – and not simply piling up a lot of facts. Put it in those words, and the apologist of scientific education will usually agree. Press him further, ask him to particularise, and somehow it always turns out that scientific education means more attention to the sciences, in other words – more facts. The idea that Science means a way of looking at the world, and not simply a body of knowledge, is in practice strongly resisted. I think sheer professional jealousy is part of the reason for this. For if Science is simply a method or an attitude, so that anyone whose thought-processes are sufficiently rational can in some sense be described as a scientist – what then becomes of the enormous prestige now enjoyed by the chemist, the physicist, etc. and his claim to be somehow wiser than the rest of us?

A hundred years ago, Charles Kingsley described Science as “making nasty smells in a laboratory”. A year or two ago a young industrial chemist informed me, smugly, that he “could not see what was the use of poetry”. So the pendulum swings to and fro, but it does not seem to me that one attitude is any better than the other. At the moment, Science is on the upgrade, and so we hear, quite rightly, the claim that the masses should be scientifically educated: we do not hear, as we ought, the counter-claim that the scientists themselves would benefit by a little education. Just before writing this, I saw in an American magazine the statement that a number of British and American physicists refused from the start to do research on the atomic bomb, well knowing what use would be made of it. Here you have a group of sane men in the middle of a world of lunatics. And though no names were published, I think it would be a safe guess that all of them were people with some kind of general cultural background, some acquaintance with history or literature or the arts – in short, people whose interests were not, in the current sense of the word, purely scientific.

Where did the George Orwells of this world go? Why don't we have more people like him today? Have they just been drowned out by idiots with access to a microphone?

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Irony Upon Irony

For those (few) of you who are interested in the pathology of IDiots, you have to read Irony of the Day. It's posted on Uncommon Descent and the author is Barry Arrington.

This is a satirical summary of his point.

Many skeptics say that the Flying Spaghetti Monster is imaginary. However, it's impossible to prove that the Flying Spaghetti Monster doesn't exist. Even Richard Dawkins says that you can't prove a negative.

Therefore, when you say that the Flying Spaghetti Monster is imaginary, you aren't being a true skeptic. Instead, you are expressing "uncritical arrogant dogmatism that would make the most committed fundamentalist blush. And that, my friends, is the irony of the day."

You can't make this stuff up.

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Reviews of Darwin's Doubt: Keeping Score

Several scientists have reviewed Stephen Meyer's latest attack on science [see Slaying Meyer’s Hopeless Monster]. Don't think the IDiots haven't noticed ... they've responded to several specific criticisms (and ignored others).

I know it's hard to keep score so David Klinghoffer has done it for us in: More Evidence of Darwinian Short-Term Memory Loss.

As far as I'm aware, no reviewer has yet genuinely laid a hand on "Darwin's Doubt," not for lack of trying. Well, there's always tomorrow.

The IDiots are learning to master the basic skills of propaganda and they're doing a pretty good job. For example, here's a video promotion of Darwin's Doubt. See if you can recognize the lies, the tricks and the deceptions.

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Monday's Molecule #214

Last week's molecule was 6-phosphogluconate, the second intermediate in the pentose phosphate pathway. Nobody got the right answer! [Monday's Molecule #213].

Classes have now started at most universities in North America so let's celebrate by picking a very simple molecule—one that most undergraduates should recognize if they've taken a biochemistry course. Derivatives of this molecule are essential components of several fundamental pathways; which ones? Give me the common name and the official IUPAC name.

Email your answers to me at: Monday's Molecule #214. I'll hold off posting your answers for 24 hours. The first one with the correct answer wins. I will only post the names of people with mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.

There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your email message.)

Darwin's Doubt: The Genes Tell the Story?

The main goal of Intelligent Design Creationism is to cast doubt on modern science, especially evolutionary biology. Most of the IDiot books are devoted to attacks on evolution. The underlying assumption is that if modern science is discredited then "god-did-it" becomes a viable alternative.

The latest book by Stephen Myer is no exception. The theme is that evolutionary biologists cannot explain the Cambrian Explosion; therefore, God must have created all the animals in the space of a few million years back in the Cambrian Era (about 530 million years ago).

Most of the book is about the lack of transitional fossils that document the slow transition from primitive worm-like creatures to modern phyla such as arthropods and chordates. Others have dealt with this and I'm not going to comment because it's outside of my area of expertise.¹

There is strong evidence from molecular evolution that the major animal phyla share common ancestors and that these common ancestors predate the Cambrian by millions of years. In other words, there's a "long fuse" of evolution leading up to the Cambrian Explosion. Meyer refers to this as the "deep-divergence" assumption.

There are many versions of these trees. The one shown here is from Erwin et al. (2011). It's the one shown in the book The Cambrain Explosion by Douglas Erwin and James Valentine. It isn't necessarily correct in all details but that's not the point.

The point is that molecular phylogenies demonstrate conclusively that the major groups of animals share common ancestors AND that the overall pattern does not conform to a massive radiation around 530 million years ago. Also, it's very clear that the pattern is consistent with evolution and not with God creating all the animals at once.

Stephen Meyer has to address this evidence because it casts doubt on his main theme (God did it). I suppose I don't need to tell you what he says ... it's typical creationist denial. He claims that the evidence doesn't exist. Here are his reasons ...

1. There are no fossils to support the earliest branches in the molecular phylogenies.
2. There are many different molecular trees and they don't all agree with each other in terms of branching order and timing.
3. Evolutionary biologists cherry-pick the data by only picking molecules that give reasonable trees.
4. The trees rely on questionable assumptions; namely, that the molecular clock ticks at a constant rate and that there is a universal tree.
5. The molecules being compared must be homologous but this is what is being tested so the argument is circular.

The conclusion is ....

Comparative genetic analyses do not establish a single deep-divergence point, and thus do not compensate for the lack of fossil evidence for key Cambrian ancestors—such as the ur-bilateran or the ur-metazoan ancestor. The results of different studies diverge too dramatically to be conclusive, or even meaningful; the methods of inferring divergence points are fraught with subjectivity; and the whole enterprise depends on a question-begging logic. Many leading Cambrian paleontologists, and even some leading evolutionary biologists, now express skepticism about both the results and the significance of deep-divergence studies.

I'm hoping to find time to go over each of Meyer's objections since they reveal a lot about IDiot misconceptions of evolution (and science) and a lot about how they employ strawmen, lies, quote-mining, and distortions in order to discredit an entire field (molecular evolution).²

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1. Most IDiots are experts in everything. I'm not as smart as they are.

2. It always amazes me to discover that IDiots like Stephen Meyer think they know more than thousands of expert biologists who do this sort of stuff for a living.

Erwin, D.H., Laflamme, M., Tweedt, S.M., Sperling, E.A., Pisani, D. and Peterson, K.J. (2011) The Cambrian conundrum: early divergence and later ecological success in the early history of animals. Science 334:1091-1097. [doi: 10.1126/science.1206375]

Goodbye Women's College Hospital

My son was born in this building 35 years ago. It will look very different when the destruction/construction is complete (Women's College Hospital).

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Majority Of Americans Approve Of Sending Congress To Syria

From the Onion: Poll: Majority Of Americans Approve Of Sending Congress To Syria

WASHINGTON—As President Obama continues to push for a plan of limited military intervention in Syria, a new poll of Americans has found that though the nation remains wary over the prospect of becoming involved in another Middle Eastern war, the vast majority of U.S. citizens strongly approve of sending Congress to Syria.

The New York Times/CBS News poll showed that though just 1 in 4 Americans believe that the United States has a responsibility to intervene in the Syrian conflict, more than 90 percent of the public is convinced that putting all 535 representatives of the United States Congress on the ground in Syria—including Senate pro tempore Patrick Leahy, House Speaker John Boehner, House Majority Leader Eric Cantor, and House Minority Leader Nancy Pelosi, and, in fact, all current members of the House and Senate—is the best course of action at this time.

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Citing overwhelming support from the international community—including that of the Arab League, Turkey, and France, as well as Great Britain, Iraq, Iran, Russia, Japan, Mexico, China, and Canada, all of whom are reported to be unilaterally in favor of sending the U.S. Congress to Syria—the majority of survey respondents said they believe the United States should refocus its entire approach to Syria’s civil war on the ground deployment of U.S. senators and representatives, regardless of whether the Assad regime used chemical weapons or not.

Sounds like a good idea but shouldn't Barack Obama and John Kerry go with them?

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The Importance of Sequence Alignments

There are several required steps in constructing phylogenetic trees from sequence data. The first step is to align the sequences so you can make direct comparisons. It used to be the case that multiple sequence alignments had to be checked manually because none of the available computer programs were as good as an experienced scientist. That hasn't changed. What's changed is that the data sets have become so large and complicated that nobody wants to even look at the sequence alignments to see if they can be improved.

Drew et al. (2013) suggest that sequence alignments should be made available.

Until recently, uploading sequences to GenBank (or EMBL) was generally considered sufficient to ensure reproducibility of phylogenetic studies using DNA sequence data. Increasingly, however, the systematics community is realizing that archiving raw DNA sequences is not adequate, and that the underlying alignments of DNA sequences as well as the resulting phylogenetic trees are pivotal for reproducibility, comparative purposes, meta-analyses, and ultimately synthesis. Indeed, there has been a growing clamor for journals to adopt and enforce more rigorous data archiving practices across diverse disciplines [4]–[8]. As a result, about 35 evolutionary journals [5],[9] have adopted policies to encourage or require authors to upload alignments, phylogenetic trees, and other files requisite for study reproducibility [5] to TreeBASE (http://treebase.org/) and/or other public repositories such as Dryad (http://datadryad.org). Unfortunately, enforcement of such data deposition policies is generally lax, and most journals in systematics and evolution still do not require DNA sequence alignment or tree deposition. As a result, the alignments and trees underlying most published papers in systematics/phylogenetics and evolutionary biology remain inaccessible to the scientific community at large [8],[10].

I sympathize with the goal but I doubt that it can be achieved. I strongly suspect that many scientists don't even bother to produce sequence alignments. They just feed the electronic data directly into their tree-making algorithm.

I wonder how many anomalies could be resolved if they just looked at the alignments? Would they even know if bad sequence data was being used for one or two species in their alignment?

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Drew, B.T., Gazis, R., Cabezas, P., Swithers, K.S., Deng, J., Rodriguez, R., Katz, L.A., Crandall, K.A., Hibbett, D.S., and Soltis, D.E. (2013) Lost Branches on the Tree of Life. PLoS Biol 11(9): e1001636. [doi: 10.1371/journal.pbio.1001636]

Darwin's Doubt: A Synopsis

David Klinghoffer wonders why I'm not criticizing Stephen Myer's new book Darwin's Doubt [see On Darwin's Doubt, Still Waiting to Hear from Big Shots in the Darwin Brigade].

Where is Jerry Coyne in this debate? Where is Dawkins? Even PZ Myers? Or Lawrence Moran, who promised "I'm planning to read [Darwin's Doubt] as soon as I can get a hold of a copy -- probably sometime in August in Canada." (I'm still puzzled by that one. The book was published in June in Canada as well.) It would seem noble for the generals to go into battle alongside the ordinary foot soldiers, putting themselves at risk as well, instead of hanging back at a safe distance.

I preordered the book three months ago and received my copy from Amazon.ca on August 1st. I've been busy with other things for most of the month so I've only turned my attention to the book in the past few days.

David Klinghoffer probably thinks that reviewing another creationist book is my highest priority. That's not the case. In fact, I never promised to review it and after reading it, I never will. There are plenty of others who know more about the subject and some of them are taking the book apart, chapter by chapter [Slaying Meyer’s Hopeless Monster]. If you want details, you can do no better than Darwin’s Doubt – A Review on Skeptic Ink.

For those of you who want a brief summary, I can do no better that point you to the tree of eukaryotes on the left (Keeling et al., 2005). It summarizes tons of molecular data showing the relationships of various eukaryotes. The tree is based on solid molecular evidence that Darwin never knew existed and that evidence is direct conformation of evolution, properly defined. It represents the fixation of nearly neutral alleles by random genetic drift. Of course, you have to read very carefully to find any mention of modern evolutionary theory in Meyer's book—he prefers to focus his attack on mutation + natural selection.

I've drawn a little red circle around the part of this tree that Stephen Meyer discusses in Darwin's Doubt. It's the evolution of animals and, in particular the early fossil evidence of multicellular animals. Most of these appear rather suddenly in the fossil record during the Cambrian (about 530 million years ago). Scientists have long been puzzled about this rapid evolution of complex animals and there are many hypotheses that attempt to account for it. In fact, there's a recent book by Douglas Erwin and James Valentine that summarizes the science behind The Cambrian Explosion. It all seems quite reasonable to me.¹ I don't know exactly why complex animals evolved so rapidly but I don't see any reason to doubt the facts of evolution and I don't see any reason to propose that God must have been responsible for this little bit of the tree of life.

Myer does and that's what his book is all about.

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1. I don't agree with everything in that book.

Keeling, P.J., Burger, G., Durnford, D.G., Lang, B.F., Lee, R.W., Pearlman, R.E., Roger, A.J. & Gray, M.W. (2005) The tree of eukaryotes. Trends in ecology & evolution 20:670-676. [doi: 10.1016/j.tree.2005.09.005]