Answering Barry Arrington's challenge: Darwinism predicted junk DNA

In my first post [Answering Barry Arrington's challenge: Darwinism] I established that Barry Arrington's version of "Darwinism" is actually "Neo-Darwinism" or the "Modern Synthesis." We all know why Intelligent Design Creationists would rather use "Darwinism"—this explains why they deliberately change the meaning to make it look like they understand evolution

Arrington's version of "Darwinism can be seen in the Uncommon Descent glossary. It focuses on natural selection as the mechanism of evolution and doesn't mention Neutral Theory of random genetic drift.

Barry Arrington's challenge to me is ...

Answering Barry Arrington's challenge: Darwinism

I posted something yesterday about Barry Arrington and irony [You should know the basics of a theory before you attack it]. This got Barry Arringon's attention so he put up his own blog post [Larry Moran’s Irony Meter] where he issues a challenge ....

OK, Larry. I assume you mean to say that I do not understand the basics of Darwinism. I challenge you, therefore, to demonstrate your claim.

Today I'm feeling optimistic—life is good and this evening we're going to a nice restaurant for dinner with our favorite nephew.¹ Let's try, once again, to convert this into a teaching moment. Hopefully, at least one or two ID proponents will learn something.²

What do they mean by "Darwinism"?

You should know the basics of a theory before you attack it

Turn off your irony meters. Really ... I'm not kidding. They will never survive if you leave them on and follow the link to this post by Barry Arrington on Uncommon Descent.

Don't say I didn't warn you!

You Should Know the Basics of a Theory Before You Attack It

The answer, of course, is “nothing.” Having studied Darwinism for over 20 years, I can tell you what it posits. Therefore, when I attack it, I am attacking the actual thing, not some distortion of the thing that exists nowhere but my own mind.

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God's Not Dead the sequel is coming soon - save the date

Oh how I miss Saturday morning cartoons. This will have to do.

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What does Stephen Meyer really think?

One of the most frustrating things about the current crop of Intelligent Design Creationists is that it's impossible to pin them down on what they really think happened in the history of life. We know that some of them are closet Young Earth Creationists so we can guess what they think. They may be arguing that bacterial flagella reveal the actions of a designer but they actually don't believe any of the data used to make that argument. They think that all species (or kinds) were created at once just a few thousand years ago.

Other Intelligent Design Creationists seem to believe in a different form of creation but who knows what it is? Take Stephen Mayer, for example, you can read his books from cover to cover and still not know what he thinks about the history of life. It's clear that the Cambrian Explosion is a big deal for him and it's clear that he thinks god is behind it all but he's remarkably noncommittal about what actually happened according to his interpretation of the evidence.

The cost of a new gene

Let's think about the biochemical cost associated with adding some new piece of DNA to an existing genome. Michael Lynch has been thinking about this for a long time. He notes that there certainly IS a cost (burden) because the new bit of DNA has to be replicated. That means extra nucleotides have to be synthesized and polymerized every time a cell replicates.

This burden might seem prohibitive for strict adaptationists¹ since everything that's detrimental should be lost by negative selection. Lynch, and others, ague that the cost is usually quite small and if it's small enough the detrimental effect might be below the threshold that selection can detect. When this happens, new stretches of DNA become effectively neutral (nearly neutral) and they can be fixed in the genome by random genetic drift.

The key parameter is the size of the population since the power of selection increases as the population size increases. Populations with large numbers of individuals (e.g. more than one million) can respond to the small costs/burdens and eliminate excess DNA whereas populations with smaller numbers of individuals cannot.

Canada's new Minister of Science, Kirsty Duncan, is NOT a Nobel Prize winner

Canada has a new government under the Liberal Party and a new Prime Minister, Justin Trudeau. I'm very excited about this change. I'm a member of the Liberal Party of Canada and I voted for the Liberal Candidate in my riding.

One of the big changes is supposed to be increased transparency of government, more openness with the press, and a promise to base decisions on evidence and science. In other words, truth is supposed to be the new buzzword on Parliament Hill. Trudeau's new cabinet even has a Minister of Science, unlike previous cabinets.

Justin Trudeau and his new cabinet

This is our new Canadian Prime Minister walking to Rideau Hall with his new cabinet ministers for the swearing in ceremony where he officially takes over the government. It's very exciting. No Prime Minister has ever done this before today.

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Was Jesus a real person? - see what denialism looks like

Jerry Coyne wrote up something about the historical Jesus where he suggested that there wasn't much evidence for his existence: BBC poll: 40% of Brits don’t believe that “Jesus was a real person,” but BBC assumes he was!].

Here's what Jerry said,

Now I may be wrong, but the more I read this, the more I think that reader Ant was right in his interpretation. What’s more galling is that the BBC is taking what “many scholars believe” as the gospel truth—pardon the pun—despite the fact that close scrutiny gives virtually no extra-Biblical evidence for a historical Jesus. I’m still convinced that the judgement of scholars that “Jesus was a real man” comes not from evidence, but from their conviction that the Bible simply couldn’t be untruthful about that issue. But of course we know of cases where myths grew up that weren’t at bottom derived from a historical individual.

There's nothing particularly wrong with what Jerry says. As far as I know the evidence that Jesus actually existed is not strong and, even more importantly, there's no independent evidence that he rose from the dead or performed miracles.

We are all Irish according to Ancestry.com

One of my wife's relatives just had her DNA tested by Ancestry.com and the results show that she is 61% Irish.¹ She was (pleasantly) surprised so she shared the information with her relatives, including Ms. Sandwalk.

I was also surprised because I have a pretty extensive genealogy of my wife's side of the family and there's no ancestor from Ireland. Her grandparents—the aunt's parents—have typically Scottish surnames and they are the product of several generations of Scottish ancestors from a small community in Eastern Ontario.

I know of all the ancestors of the aunt (and my wife's mother) for five generations. That's 32 ancestors—their great-great-great-grandparents (Ms. Sandwalk's great⁴-grandparents). There were four ancestors born in England and 28 born in Scotland, mostly around Glasgow. The original settlers of this district all came from Scotland. That means that to a first approximation about 87% of the aunt's DNA comes from Scotland.

Methodological naturalism at Dover

I'm one of those scientists who don't think that science as a way of knowing is restricted to investigating natural causes [John Wilkins Revisits Methodological Naturalism ]. I think that science can easily investigate supernatural claims and show that they are wrong. In theory, science might even show that the supernatural exists. Some (most?) philosophers agree. Maarten Boudry is the best known [Is Science Restricted to Methodologial Naturalism?].

This year is the tenth anniversary of Kitzmiller v. Dover Area School District. At that trial, the plaintiffs successfully convinced Judge Jones that intelligent design isn't a science because it invokes supernatural causes. The expert witnesses testified that, by definition, science is limited by methodological naturalism. I disagree with the expert witnesses at the trial and I agree with many leading philosophers that science is not restricted to methodological naturalism [Can Science Test Supernatural Worldviews? ].

Molecular evidence supports the evolution of the major animal phyla

For those of you who are interested in the evolution of the major animal phyla, let me introduce you to the topic.

See the little red circle on the phylogenetic tree on the right? That's what we're talking about.

Most of the major animal phyla are first observed as primitive fossils in the Cambrian about 540 million years ago. The fossils cluster around dates that only span a few million years (about 10 million years). This is the Cambrian Explosion (see little red circle).

There's considerable debate among evolutionary biologists about what caused this relatively rapid appearance of diverse and disparate large fossils. Intelligent Design Creationist, Stephen Meyer decided that such a debate casts serious doubt on evolution as an explanation for the history of life so he wrote a book called Darwin's Doubt.

Why does Evolution News & Views not allow comments?

The Discovery Institute blog, Evolution News & View (sic) doesn't allow comments. They're beginning to feel a bit guilty about that so there have recently been two posts on the topic.

David Klinghoffer says: Why No Comments at Evolution News?

Michael Egnor writes: Comments by Darwinists: Another Perspective

The problem from their perspective is that their opponents are rude, crude, and abusive so they have to ban all comments. Here's how David Klinghoffer puts it.

So what are we supposed to do when, under a free-for-all commenting policy, Darwinists like Moran -- who is far from scraping the bottom of the barrel as far as online evolutionists go -- post abusive, defamatory, and false comments on our own news site? Should we delete their comments? Edit them? But then we would be accused of "censorship."

Should we perhaps allow them to say whatever they like, fouling the carpet in our own living room? When they have every opportunity to write what they like where they like and receive an answer from us, if the challenge rises to the level of being worthy of a reply? Why in the world would we do that?

If we can't accept providing a free forum for a great deal of nasty, false, and vacuous chatter, the only alternative is to devote significant time to moderating the forum, policing the sandbox, and then defending that moderation at every step as it is challenged. That would require staffing that we can't afford.

The problem with that line of reasoning is that there already is an ID blog that allows comments. Check out Uncommon Descent to see who's fouling the carpet.

What they're really worried about isn't the "Darwinists." It's Mung, bornagain, Vy, Andre, Virgil Cain, Upright BiPed, Mapou and others like them who will dominate the comments section and give the Discovery Institute a bad reputation.

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Evolution as a foundational concept in biochemistry and molecular biology

The American Society for Biochemistry and Molecular Biology (ASBMB) has been promoting a new way of teaching undergraduate courses. The idea is to concentrate on fundamental principles and concepts rather than on trivial details. The various working groups came up with a list of these fundamental concepts under five main headings: Evolution; Matter and Energy Transformation; Homeostasis; Macromolecular Structure & Function; and Biological Information.

I've discussed the concepts before [ASBMB Core Concepts]. There are problems.

Various committees continue to meet in order to build a "concept inventory" to guide the new curriculum. There have been a series of workshops organized around the main themes. The participants in the workshops are, for the most part, teachers at small universities and colleges. They have lots of experience teaching undergraduate courses but they aren't necessarily experts in the subject material.

I saw this clearly when I attended a session at the last Experimental Biology meeting in Boston last April. The purpose of the meeting was to review the major concepts in Evolution and Homeostasis. I met a great deal of resistance from the workshop leaders when I tried to explain the concepts of neutral alleles and random genetic drift and show them why they were so important when comparing sequences and constructing phylogenetic trees.

INTEGRATING EVOLUTION AND HOMEOSTASIS WITH THE CORE CONCEPTS OF BIOCHEMISTRY AND MOLECULAR BIOLOGY
Symposium Tues. 9:45 am Boston Convention & Exhibition Center, room 256

Chaired: E. Bell

9:45 RCN-UBE: Integrating Evolution and Homeostasis with the Core Concepts of Biochemistry and Molecular Biology J.E. Bell, A. Aguanno, P. Mertz, M. Johnson and K.M. Fox. Univ. of Richmond, Union Col., NY, Univ. of Alabama, St Mary’s Col. of Maryland and Marymount Manhattan. (559.2)

Presenters:
Small Group Work: Integrating Evolution and Homeostasis into the Core Concepts E. Bell, Univ. of Richmond A. Aguanno, Marymount Manhattan Col.

Group Discussion on Core Concept integration with Homeostasis A. Aguanno, Marymount Manhattan Col.

Small Group Work: Question Development Involving Evolution and Homeostasis M. Johnson, Univ. of Alabama

Group Presentations and Discussion on Question Implementation K. Fox. Union Col.

This same group has published some of their findings in the July/August issue of the education journal, Biochemistry and Molecular Biology Education (BAMBED)¹ (Aguanno et al. 2015).

Here are the learning objectives they have developed under the "Evolution" concept.

• central importance of the theory of evolution
• Darwin's theory of evolution
• process of natural selection
• evidence for the theory of evolution
• molecular basis of natural selection

I really think this misses the boat in a biochemistry context where molecular evolution plays such an important role. It will be hard to discuss genome organization and junk DNA, for example, if students don't know about population genetics and random genetic drift. It will be hard to explain (correctly) why different proteins in different species have different amino acid sequences if students don't know about neutral alleles.

I pointed this out to the authors at the meeting and stimulated a discussion about these concepts. The authors, and the other teachers in the room, were pretty certain that the differences in amino acid sequences were all due to natural selection. Most of them had never heard of random genetic drift.

The problem here is that the learning objectives and the "capstone experiences" are being developed by teachers who don't really understand evolution. It is assumed that the best people to work on the new curriculum are experienced teachers but that's demonstrably false. (It applies to the other concepts as well.)

It turns out that biochemistry professors are not as knowledgeable about core concepts as you might imagine.

The authors surveyed 161 teachers in 143 institutions across the USA to find out what are the most important concepts in a biochemistry and//or molecular biology course.

The results, right, indicate that less than 8% of the respondents thought that evolution was an important concept.

This could be due, in part, to the fact that biochemistry courses are often taught by professors who are members of a chemistry department but no matter what the explanation it looks like we have a lot of work ahead of us if we are going to convince our colleagues to make evolution a core concept.

I'm pretty sure that many of the people who teach our introductory biochemistry courses at the University of Toronto don't see evolution as a core concept and don't understand modern evolutionary theory.

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1. Disclaimer: I am on the editorial board of that journal.

Aguanno, A., Mertz, P., Martin, D., and Bell, E. (2015) A National Comparison of Biochemistry and Molecular Biology Capstone Experiences. BAMBED 43:223-232. [doi: 10.1002/bmb.20869]

The birth and death of salmon genes

Modern Salmonidae (salmon and its relatives) have genomes that show clear evidence of an ancient duplication event. Berthelot et al. (2014) sequenced the rainbow trout genome and constructed a phylogenetic tree of all teleost fish. The genome duplication event in the Salmonidae lineage can be dated to approximately 96 million years ago (96 ± 5.5 Mya).

This event provides an opportunity to track the fate of the duplicated protein-coding genes. How many of the original duplicates are left and what happened to them?

There were able to get reliable data on 9,040 of the original genes in the ancestral genome. (That's about one third of the estimated 31,000 genes in the genome of the original species.) Of those 9,040 genes, 4,728 (52%) are now single copy genes because one of the duplicated genes has been lost. Many of these original genes are still detectable as pseudogenes at the right position in the genome.

By combining these results with studies of more ancient genome duplications in the vertebrate lineage, it looks like the average rate of gene loss is about 170 genes per million years (Berthelot et al., 2004). It's likely that in the majority of cases one of the duplicates will eventually become inactivated by mutation and that allele will become fixed in the genome by random genetic drift. (Some early inactivation events may be selected.)

4,312 (42%) of the original duplications have been retained in the trout genome as a small family consisting of two paralogues. In some cases the two paralogues have diverged and in some cases they are expressed in different tissues or at different stages of development. This suggests that the two copies have evolved different functions.

However, most of the duplicated genes seem to be performing similar functions and it's likely that there is no selective pressure to retain two copies. There just hasn't been enough time to inactivate one copy.

The trout genome contains 241 ancient microRNA genes and 233 of them still have two copies, one from each of the duplicated genomes. The authors suggest that this is significant and it indicates that multiple copies on these microRNA genes are needed. I'm not sure if this is true since these genes are quite a bit smaller than the average protein-coding gene so they will take longer to inactivate by mutation.

In any case, the big picture provides us with lots of data on the birth of new genes by duplication and death of genes by pseudogene formation.

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Berthelot, C., Brunet, F., Chalopin, D., Juanchich, A., Bernard, M., Noël, B., Bento, P., Da Silva, C., Labadie, K., and Alberti, A. (2014) The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nature communications, 5:3657 April 22, 2014 [doi:10.1038/ncomms4657]