Discussing the conflict between science and religion with Denis Alexander

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Model organisms and translational research

Ewan Birney (Genomic's Big Talker of ENCODE notoriety) has a new post called In defence of model organisms.

He brings up two points that are worth discussing.

What is a model organism?

There are two common definitions. Birney leans toward defining a model organism as one that models human biochemistry and physiology. This is a common definition. It emphasizes the meaning of "model" as "model of something."

Rethinking medical education at the University of Toronto

Watch two medical educators from my Faculty of Medicine at the University of Toronto. They are being interviewed by Steve Paiken of The Agenda. They rightly deplore the traditional lecture style of learning that's common in my university but their solution is more online learning.

The real problem with medical education is that much of the first two years is based on the "memorize and regurgitate" model that we know is ineffective. The best way to change the system is to use evidence-based methods that emphasize student-based learning. The idea is to teach medical students how to access information and how to interpret it rather than have them memorize facts. When teaching biochemistry, for example, it's pointless to ask medical students to take an exam based on structures and pathways that they will forget the day after the exam.

These two physicians are in charge of reforming medical education. They want to please the students by creating a new way of teaching that emphasizes the way "millennials" want to learn. (Short online courses, no lectures.) You'll watch the entire show without hearing any references to the pedagogical literature and what's known to work. Is there any evidence that undergraduate medical students are experts on medical education? (Hint: ... no.)

If this is the wave of the future, I fear that future doctors are not going to be any more informed that the current crop. They will still not be capable of critical thinking.

The way we teach needs to change, but not this way.

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Targets, arrows, and the lottery fallacy

Sandwalk readers have been discussing the way Intelligent Design Creationists have been calculating probabilities [see Intelligent Design Creationists are very confused about epigenetics and Waiting for multiple mutations: Michael Lynch v. Michael Behe].

We've known for a long time that the most common mistake is assuming that there's only one solution to a problem. They see an end result, like a bacterial flagellum, or resistance to malaria, or the binding of two proteins, and assume that a few very specific mutations had to occur in a specific sequence in order to produce that result.

judmarc calls this the "lottery fallacy" and I think it's a good term [see lottery fallacy],

This is of course what I like to call the "lottery fallacy." It's used by virtually every ID proponent to produce erroneously inflated probabilities against evolution.

Lottery fallacy: The odds against any *particular individual* winning the PowerBall lottery are ~175 million to 1. But there were three winners just last night. That's because *someone* winning the PowerBall is not an especially rare occurrence. It happens every few weeks throughout the year.

In exactly the same way, Axe, Gauger, Behe, and the rest of the ID folks always base their math on the chances that a *particular* neutral or beneficial mutation will occur, and just as with the lottery, the chances of a *particular* outcome are utterly minuscule. The occurrence of *some* neutral or beneficial mutation, however, is, as with the lottery, so relatively common as to be completely unremarkable.

To summarize: ID proponents misuse probability math to make the common appear impossible.

As it turns out, someone on Evolution News & Views (sic) just posted an excellent example of this fallacy [Intelligent Design on Target]. Here's what he/she/it says,

In his second major treatise on design theory, No Free Lunch: Why Specified Complexity Cannot Be Purchased without Intelligence, William Dembski discusses searches and targets. One of his main points is that the ability to reach a target in a vast space of possibilities is an indicator of design. A sufficiently complex target that satisfies an independent specification, he argues, creates a pattern that, when observed, satisfies the Design Filter. There are rigorous mathematical and logical proofs of this concept in the book, but at one point, he uses an illustration even a child can understand.

Consider the case of an archer. Suppose an archer stands fifty meters from a large wall with a bow and arrow in hand. The wall, let us say, is sufficiently large that the archer cannot help but hit it. Now suppose each time the archer shoots an arrow at the wall, the archer paints a target around the arrow so that the arrow sits squarely in the bull's-eye. What can be concluded from this scenario? Absolutely nothing about the archer's ability as an archer. Yes, a pattern is being matched; but it is a pattern fixed only after the arrow has been shot. The pattern is thus purely ad hoc. [No Free Lunch, pp. 9-10, emphasis added.]

Most people have experience with target shooting of some kind, whether with bows and arrows, guns (including squirt guns), snowballs, darts, or most sports like baseball, soccer, basketball, hockey, and football. Children laugh when they picture an archer who "couldn't even hit the broadside of a barn" and rushes up to the arrow and paints a bull's-eye around it. Grown-ups might compare that to a biologist looking at an irreducibly complex biological system and simply stating, "It evolved." In each of these cases, Dembski would say that since the pattern was not independently specified, therefore it is ad hoc.

The unknown author included the image shown above in order to illustrate the point (Image: © Kagenmi / Dollar Photo Club).

Do you see the fallacy? Just because we observe a complex adaptation or structure does NOT mean that it was specified or pre-ordained. There are certainly many different structures that could have evolved—most of them we never see because they didn't happen. And when a particular result is observed it doesn't mean that there was only one pathway (target) to producing that structure.

To continue the analogy—at the risk of abusing it—there may be hundreds of targets in the woods and most of them have very large bullseyes. Imagine you're out for a walk in the woods and you see that almost every tree has a big target with a large bullseye. You find an arrow stuck at the edge of one of the bullseyes and lots of arrows stuck in the trees, the ground, and parts of most of the targets outside of the central bullseyes. Would you write a book about how good the archer must have been?

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Intelligent Design Creationists are very confused about epigenetics

I've been trying to figure out why Intelligent Design Creationists are so excited about epigenetics. They seem to think it's going to overthrow everything we know about evolution (= "Darwinism"). That means, in their minds, that "naturalism" and "materialism" aren't sufficient to explain biology.

The logic escapes me.

Denyse O'Leary has added a new wrinkle in her latest post (as "News") on Uncomon Descent. She reveals a profound misunderstanding of epigenetics [Could epigenetics change perspectives on adoption?].

I'll just quote the relevant part and let you try and figure out whether Denyse represents mainstream Intelligent Design Creationism. 'Cause if she does, the movement is in far worse shape than even I imagined.

I remember one adoptive mother, taunted by a rebellious teenager who wanted to find her “real” mother, taking the girl by the shoulders and saying, “Look, I raised you from when you were seven days old; I supported you, sat with you in emergency rooms and juvenile court, laughed and cried with you, … and got you into a good school in the end. I don’t know who or where your birth mother is. But I do know this: I am the only ‘real mother’ you have ever had or ever will have. Look at me. Get used to it. It doesn’t GET better than this.”

I hope the kid smartened up. Meanwhile what if she discovers, when she has children, that their genome reflects in part traits she acquired growing up in the adoptive home? Maybe that would allay some of the sense of alienation.

Might epigenetics could provide some basis for understanding? Time will tell.

See also: Epigenetic change: Lamarck, wake up, you’re wanted in the conference room!

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Answering two questions from Vincent Torley

Vincent Torley read a post by Jerry Coyne where Jerry wondered if Intelligent Design Creationism was in trouble because the Discovery Institute has lost Bill Dembski and Casey Luskin [Is the Discovery Institute falling apart?].

Torley disagrees, obviously, but he focuses on a couple of the scientific statements in Jerry Coyne's post and comes up with Two quick questions for Professor Coyne.

I hope Professor Coyne won't mind if I answer.

Before answering, let's take note of the fact that Vincent Torley has been convinced by the evidence that most of our genome is junk. I wonder how that will go over in the ID community?

Here's question #1 ...

Waiting for multiple mutations: Michael Lynch v. Michael Behe

Casey Luskin is trying to help out a university student by describing some important ID contributions to science [No ID Research? Let's Help Out This Iowa State Student].

One of those contributions is a paper by Michael Behe and David Snoke published eleven years ago in Protein Science (Behe and Snoke, 2004). I described the result in a previous post: Waiting for multiple mutations: Intelligent Design Creationism v. population genetics.

If Behe & Snoke are correct then modern evolutionary theory cannot explain the formation of new functions that require multiple mutations.

Cassey Luskin is aware of the fact that this result has not been widely accepted. He mentions one specific criticism:

In 2008, Behe and Snoke's would-be critics tried to refute them in the journal Genetics, but found that to obtain only two specific mutations via Darwinian evolution "for humans with a much smaller effective population size, this type of change would take > 100 million years." The critics admitted this was "very unlikely to occur on a reasonable timescale."

He's referring to a paper by Durrett and Schmidt (2008). Those authors examined the situation where one transcription factor binding site was disrupted by mutation and another one nearby is created by mutation. The event requires two prespecified coordinated mutations.

Waiting for multiple mutations: Intelligent Design Creationism v. population genetics

Casey Luskin is worried about university students. Apparently, they aren't getting enough correct information about intelligent design. Luskin uses the example of a student named Michael Heckle at Iowa State University. Mr. Heckel said; "So far, there has been no research done by intelligent design advocates that has led to any sort of scientific discovery."

This happens to be a true statement but Casey Luskin takes exception in a blog post that appeared the other day on Evolution News & Views (sic) [No ID Research? Let's Help Out This Iowa State Student].

Here's why Alain Beaudet, President of the Canadian Institutes of Health Research, should resign

The Canadian Institutes of Health Research (CIHR) is the main source of research funding for Canadian health researchers, including those doing basic research like most of the researchers in my biochemistry department.

A few years ago, CIHR decided to revamp the process of applying for and obtaining research grants. They did this without taking into consideration the wishes of most applicants. (They did "consult," but consulting isn't the same as listening.)

The result has been a disaster. Most researchers are confused and discouraged by the new process and there's great fear that the results of the next competitions will be harmful to basic research and harmful to new investigators.

But even before the new rules came into play the funding of basic, curiosity-motivated, science was taking a major hit. Many mid-career basic researchers at the University of Toronto have lost their grants or are struggling to make do with a lot less money. This is partly due to a lack of money in the system but it's been exacerbated by a deliberate shift in priorities under the previous Conservative government of former Prime Minister Stephen Harper.

These are some of the reasons why Canadian researchers have been calling for Alain Beuadet to resign [Support basic research with new leaders at the Canadian Institutes of Health Research (CIHR)].

Joe Hanson tells us about evolution

Joe Hanson Ph.D. (Biology) of It's Okay To Be Smart is posting a series of videos on evolution. They're called The 12 Days of Evolution.

The first one is "What Is Evolution Anyway?" You won't surprised to learn that Joe Hanson conflates "evolution" with "natural selection" and fails to mention the most important features of evolution [see What Is Evolution]. You WILL be surprised to learn that Jerry Coyne has the same objections I do! [Twelve Days of Evolution: #1: What’s evolution?]

We need to do a much better job of educating the general public about the meaning of evolution but first we need to educate the teachers. It's okay to be smart but it's not okay to just pretend to be smart.

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Strolling around slopes and valleys in the adaptive landscape

Another article about evolution and the attainment of perfection has appeared. This one was published by Nathaniel Scharping on the Discover website [Could Evolution Ever Yield a ‘Perfect’ Organism?].

The article focuses on a recent paper from Richard Lenski's group at Michigan State University (Lenski et al., 2015). Lenski's group asked a different question. They wanted to know whether there was a limit to the increase in fitness in their evolving E. coli populations in the Long-Term Evolution Experiment (LTEE). It's a different question than whether evolution can select for a "perfect" organism because Lenski and his collaborators understand modern evolutionary theory. They know that mutations causing small fitness increases are beyond the reach of natural selection in their evolving populations and they know that deleterious mutations can be fixed by random genetic drift.

They know that real evolving populations can never reach the summit of an adaptive peak or, if they do, they can never stay there.

Intelligent design explanations and speculations have all been refuted, discredited, or shown to be unnecessary

Intelligent Design Creationism is a movement based on bad science. Every single one of their positive, science-like, claims about ID have been refuted, or discredited, or shown to be completely unnecessary in the face of robust evolutionary explanations. Some of them have the distinction of being unnecessary AND refuted AND discredited (e.g irreducible complexity).

In addition to a small number of claims in support of ID, the proponents of Intelligent Design Creationism also advance dozens and dozens of arguments against evolution. In fact, this is by far the main activity of most adherents to the movement. Some of their arguments focus on legitimate scientific controversies. They are legitimate criticisms of some aspects of evolution but, even then, ID proponents often misrepresent and/or misunderstand the science behind the controversy (e.g. junk DNA).

However, the vast majority of their attacks on evolution are just as bad as their attempts to build a positive case for intelligent design. A disturbingly large number of such attacks exhibit a profound ignorance of science and how it works. In particular—surprisingly—they are ignorant of evolution. The movement is full of kooks. It will never become a credible source of information unless it purges itself by getting rid of the kooks.

Speaking of kooks,¹ Casey Luskin has been publishing a series of articles on the Kitzmiller v. Dover trial that was decided ten years ago. Some of the articles make valid points but the latest one is a joke: Ten Myths About Dover: #4, "The Dover Ruling Refuted Intelligent Design".

You should read the article. It's a remarkable example of apologetics and why lawyers shouldn't try and explain science. While it's true that Judge Jones said lots of things we could quibble about, the big-picture take-home lesson from the trial is correct. No ID explanation stood up to the scrutiny of science. They were all shown to be either irrelevant or wrong.

That's why none of them should be presented in science class except as examples of bad science and faulty scientific reasoning.²

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1. Luskin won't even admit that Young Earth Creationism is absurd.

2. In my opinion, they SHOULD be discussed in class since it's important to teach critical thinking and that requires that you directly confront common misconceptions.

How many different proteins are made in a typical human cell?

There are about 20,000 protein-coding genes in the human genome. Protein products for about 18,000 of these genes have been detected in at least one human tissue (Kim et al, 2015; Wilhelm et al., 2015) [see How many proteins do humans make?].

About 10,000 of these proteins are present in all cells (Wilhelm et al., 2015) and somewhere between 1500 and 2000 are derived from genes that are essential in the average human cell (Blomen et al., 2015; Wang et al, 2015; Hart et al., 2015) [see How many human protein-coding genes are essential for cell survival?].

Let's assume there are about 10,000 protein-coding genes that are expressed in a typical human cell. Does this mean that there are only 10,000 different proteins in those cells? The answer is "no" but the differences are often subtle. The activities of some proteins, for example, are regulated by covalent modification so a typical cell will contain different versions of the protein: some are modified and some are not (e.g. phosphorylated and non-phosphorylated). These would be genuine versions of different proteins although you probably wouldn't want to make a fuss about it.

In some cases, there are various intermediates produced during protein synthesis. For example, some proteins destined for the mitochondria have an N-terminal tag that's cleaved when the proteins reach their destination. There are two different versions of the protein but, again, this isn't really a big deal. We should really only count the steady-state, terminal, stage of processing and modification.

Similarly, there are proteins that are glycosylated in various ways and cells will always contain intermediates including non-glycosylated versions that have just entered the ER. These don't count as different versions of the protein.

Some genes are alternatively spliced to give proteins that have different internal amino acid sequences. These are genuinely different proteins produced from the same gene.

If you add up all the genuinely different versions of proteins produced from 10,000 protein-coding genes, how many proteins are present in a typical human cell?

Here's a standard answer given in a recent news article in Nature (Savage, 2015)

The human body contains roughly 20,000 genes that are capable of producing proteins. Each gene can produce multiple forms of a protein, and these in turn can be decorated with several post-translational modifications: they can have phosphate or methyl groups attached, or be joined to lipids or carbohydrates, all of which affect their function. “The number of potential molecules you can make from one gene is huge,” says Bernhard Küster, who studies proteomics at the Technical University of Munich in Germany. “It's very hard to estimate, but I wouldn't be surprised to have in one cell type 100,000 or more different proteins.”

I suspect that Küster is one of those scientists who think that almost all human protein-coding genes are alternatively spliced to yield several different proteins in each cell. He has to imagine that there are, on average, ten different versions of a protein produced from each gene that's expressed in a typical cell.

That means ten different versions of each of the subunits of pyruvate dehydrogenase and RNA polymerase. It means ten different versions of triose phosphate isomerase and each of the ribosomal proteins. There should be ten different versions of actin and ten different versions of cytochrome c.

This seems very unlikely to me.

Discuss.

(There may be a few genes that have thousands of different variants, although I'm skeptical. In that case there may be 100,000 different proteins in a human cell but surely this is misleading even if it's accurate?)

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Blomen, V.A., Májek, P., Jae, L.T., Bigenzahn, J.W., Nieuwenhuis, J., Staring, J., Sacco, R., van Diemen, F.R., Olk, N., and Stukalov, A. (2015) Gene essentiality and synthetic lethality in haploid human cells. Science, 350:1092-1096. [doi: 10.1126/science.aac7557 ]

Hart, T., Chandrashekhar, M., Aregger, M., Steinhart, Z., Brown, K.R., MacLeod, G., Mis, M., Zimmermann, M., Fradet-Turcotte, A., and Sun, S. (2015) High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities. Cell 163:1515-1526. [doi: 10.1016/j.cell.2015.11.015]

Kim, M.-S., Pinto, S.M., Getnet, D., Nirujogi, R.S., Manda, S.S., Chaerkady, R., Madugundu, A.K., Kelkar, D.S., Isserlin, R., Jain, S., Thomas, J.K., Muthusamy, B., Leal-Rojas, P., Kumar, P., Sahasrabuddhe, N.A., Balakrishnan, L., Advani, J., George, B., Renuse, S., Selvan, L.D.N., Patil, A.H., Nanjappa, V., Radhakrishnan, A., Prasad, S., Subbannayya, T., Raju, R., Kumar, M., Sreenivasamurthy, S.K., Marimuthu, A., Sathe, G.J., Chavan, S., Datta, K.K., Subbannayya, Y., Sahu, A., Yelamanchi, S.D., Jayaram, S., Rajagopalan, P., Sharma, J., Murthy, K.R., Syed, N., Goel, R., Khan, A.A., Ahmad, S., Dey, G., Mudgal, K., Chatterjee, A., Huang, T.-C., Zhong, J., Wu, X., Shaw, P.G., Freed, D., Zahari, M.S., Mukherjee, K.K., Shankar, S., Mahadevan, A., Lam, H., Mitchell, C.J., Shankar, S.K., Satishchandra, P., Schroeder, J.T., Sirdeshmukh, R., Maitra, A., Leach, S.D., Drake, C.G., Halushka, M.K., Prasad, T.S.K., Hruban, R.H., Kerr, C.L., Bader, G.D., Iacobuzio-Donahue, C.A., Gowda, H., and Pandey, A. (2014) A draft map of the human proteome. Nature, 509:575-581. [doi: 10.1038/nature13302]

Savage, N. (2015) High-protein research. Nature 527:S6-S7. [doi: 10.1038/527S6a]

Wang, T., Birsoy, K., Hughes, N.W., Krupczak, K.M., Post, Y., Wei, J.J., Lander, E. S., and Sabatini, D.M. (2015) Identification and characterization of essential genes in the human genome. Science, 350:1096-1101. [doi: 10.1126/science.aac7041]

Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A.M., Lieberenz, M., Savitski, M.M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., Mathieson, T., Lemeer, S., Schnatbaum, K., Reimer, U., Wenschuh, H., Mollenhauer, M., Slotta-Huspenina, J., Boese, J.-H., Bantscheff, M., Gerstmair, A., Faerber, F., and Kuster, B. (2014) Mass-spectrometry-based draft of the human proteome. Nature, 509:582-587. [doi: 10.1038/nature13319]

Did Michael Behe say that astrology was scientific in Kitzmiller v. Dover?

Yes he did. But it doesn't mean what you think it means according to Casey Luskin [Ten Myths About Dover: #8, "Michael Behe Admitted that ID Is No More Scientific than Astrology"

I agree with Casey Luskin. During the trial, Behe was asked to define scientific theory and of course he adopted the broad view of science. He said, "Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences."

Here's the exchange that took place during the trial [Dover: Day 11].

Q In any event, in your expert report, and in your testimony over the last two days, you used a looser definition of "theory," correct?
A I think I used a broader definition, which is more reflective of how the word is actually used in the scientific community.
Q But the way you define scientific theory, you said it's just based on your own experience; it's not a dictionary definition, it's not one issued by a scientific organization.
A It is based on my experience of how the word is used in the scientific community.
Q And as you said, your definition is a lot broader than the NAS definition?
A That's right, intentionally broader to encompass the way that the word is used in the scientific community.
Q Sweeps in a lot more propositions.
A It recognizes that the word is used a lot more broadly than the National Academy of Sciences defined it.
Q In fact, your definition of scientific theory is synonymous with hypothesis, correct?
A Partly -- it can be synonymous with hypothesis, it can also include the National Academy's definition. But in fact, the scientific community uses the word "theory" in many times as synonymous with the word "hypothesis," other times it uses the word as a synonym for the definition reached by the National Academy, and at other times it uses it in other ways.
Q But the way you are using it is synonymous with the definition of hypothesis?
A No, I would disagree. It can be used to cover hypotheses, but it can also include ideas that are in fact well substantiated and so on. So while it does include ideas that are synonymous or in fact are hypotheses, it also includes stronger senses of that term.
Q And using your definition, intelligent design is a scientific theory, correct?
A Yes.
Q Under that same definition astrology is a scientific theory under your definition, correct?
A Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.
Q The ether theory of light has been discarded, correct?
A That is correct.
Q But you are clear, under your definition, the definition that sweeps in intelligent design, astrology is also a scientific theory, correct?
A Yes, that's correct. And let me explain under my definition of the word "theory," it is -- a sense of the word "theory" does not include the theory being true, it means a proposition based on physical evidence to explain some facts by logical inferences. There have been many theories throughout the history of science which looked good at the time which further progress has shown to be incorrect. Nonetheless, we can't go back and say that because they were incorrect they were not theories. So many many things that we now realized to be incorrect, incorrect theories, are nonetheless theories.
Q Has there ever been a time when astrology has been accepted as a correct or valid scientific theory, Professor Behe?
A Well, I am not a historian of science. And certainly nobody -- well, not nobody, but certainly the educated community has not accepted astrology as a science for a long long time. But if you go back, you know, Middle Ages and before that, when people were struggling to describe the natural world, some people might indeed think that it is not a priori -- a priori ruled out that what we -- that motions in the earth could affect things on the earth, or motions in the sky could affect things on the earth.

I mostly agree with Behe.¹ Astrology was an attempt to explain human behaviors by relating them to the position of the Earth on the day you were born. There is no connection. So today we think of astrology as bad science. It's not true that the stars determine your behavior and whenever we make this claim to an astologist we make sure to point out that the evidence is against it.

What we don't do is tell astrologers that they are entitled to believe whatever they want because astrology is not science and therefore we can't make a scientific statement about whether it's correct or not.

Intelligent Design Creationism is bad science. So is most of evolutionary psychology and some of genomics. So is the attempt to find god in a football helmet [The God Helmet: Your Brain on Religion].

It's disingenuous to make fun of Behe's testimony without understanding that the real issue is epistemology and the demarcation problem. Behe's view of science is perfectly legitimate but it didn't jibe with what the plaintiffs were trying to establish during the trial. They wanted to prove that ID isn't science and the best way to do that was to show that something can't be science unless it's true. In other words, science isn't a "way of knowing," it's the end result.

What does this mean? It means that every discredited attempt to explain something using science as a way of knowing becomes "not science" with hindsight. All those people who tried to show that genes were proteins were wrong so it means that what they were doing is not science. It means that of the two sides arguing about junk DNA, one of them will be wrong so, at some time in the future, their current activities will be seen as "not science."

Isn't that bizarre?

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1. He should have been defining "science" not "scientific theory." That's the fault of his lawyers who failed to make this point during his direct testimony.

Did Kitzmiller v. Dover kill Intelligent Design Creationism?

The 10th anniversary of Judge Jone's decision in Kitzmiller v. Dover is coming up on Dec. 20, 2015. See the post at Panda's Thumb: Kitzmas is Coming!.

ID proponents are also marking the event in various ways. If you are interested in the discussion, you should read the posts on Evolution News & Views covering the Ten Myths about Dover. The first one (#10) is Ten Myths About Dover: #10, "The Intelligent Design Movement Died After the Dover Decision".

Of course the ID movement didn't die after Kitzmiller v. Dover. From the outside (i.e. not in the USA) it seems to be as strong as ever. State legislatures all over America are still trying to suppress the teaching of evolution and promote creationist perspectives. The movement has captured the attention of many (most?) prominent politicians and much of the American public still believes that scientists are wrong about evolution.