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.
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.
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.
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.
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? ].
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.
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.
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.
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.
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]
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.
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]
I've been trying to argue a few points on the creationist blogs but I have to admit that I'm not making any progress at all. Even the simplest, most obvious, points are vigorously contested by the ID crowd over there.
My latest attempt was on the post, Suzan Mazur’s Paradigm Shifters is now available from Amazon, where I tried to explain that Denyse O'Leary's version of Darwinism is not the best description of evolutionary theory and that many of Suzan Mazur's "Paradigm Shifters" have missed the revolution that occurred in the late 1960s.
Didn't work.
Now someone named "Florabama" has posted a comment that illustrates the problem we're up against. I thought I'd share it with Sandwalk readers. It may not be possible to teach such a person anything about science.
They did no such thing. What they discovered was about 3,000 previously unidentified transcripts expressed at very low levels in human B cells and T cells. They declared that these low-level transcripts are lncRNAs and they assumed that the complementary DNA sequences were genes. Their actual result identifies 3,000 bits of the genome that may or may not turn out to be genes. They are PUTATIVE genes.
Let's look a a recent paper published by a large group of medical researchers at the University of California, Los Angeles (USA). The paper was published online a few days ago (Oct. 26, 2015) in Nature Immunology.
The authors clam to have discoverd 3,000 previously unknown genes in the human genome.
I think there's some serious attempts to do science among ID proponents but I also think it's bad science. It's fun, informative, and challenging to debate real science with knowledgeable, informed members of the ID community.
However, that same community embraces many, many advocates who are not knowledgeable about evolution and not informed about how science works. They are not scientists by any stretch of the imagination but they pretend to be scientific. Many of them are Young Earth Creationists who seriously think that the universe was created pretty much as it is only 6000 years ago. While it's true that every ID proponent is a creationist (i.e believes in the existence of a supernatural creator) there are some versions of creationism that are more irrational than others.
The theistic evolution version of creationism rejects the views of their anti-science YEC friends but Intelligent Design Creationism embraces all comers as long as they are vehemently opposed to materialism and evolution. That's fine, but then ID can't claim to be scientific. You can't have your cake and eat it too. Either you try to act like scientists, in which case you have to oppose the kooks and YECs in your movement, or you admit that you are a religious and social movement, in which case you stop pretending to be a science.
I hope that the knowledgeable, informed, members of the ID community will abandon the ridiculous path they've taken where they try to make a scientific case for ID knowing full well that the majority of their supporters disagree strongly with their premises (e.g. common descent). That's an untenable position.
We've seen recently that some ID proponents are attempting to do this. I'm thinking of Jonathan McLatchie and Vincent Torley right now but there are others. How is it working out? Look at the Torley post on Uncommon Descent where he's trying to explain evolution to IDiots: Human and chimp DNA: They really are about 98% similar. It's an uphill battle. The kooks are accusing him of becoming a Darwinist.
But that's exactly what the ID community needs to do in order to gain credibility. They need to shed the kooks and the IDiots who make them look silly. When they do that, they may find that more of us are willing to have a serious discussion about science.
David Klinghoffer is one of the names I mentioned in an earlier post when I identified leading ID proponents who have no clue about the science they are opposing. Others are Denyse O'Leary, Barry Arrington, Phillip Johnson, Casey Luskin,1 David Klinghoffer, Paul Nelson, John West, and William Lane Craig. These people represent the face of the ID movement and that's how we're going to judge Intelligent Design Creationism unless they clean up their act. (We also judge it by the people who post comments on blogs and Facebook and by those politicians who support it in the public sphere.)
Klinghoffer posts on Evolution News & Views (sic)—a site that doesn't allow comments. His latest post is a classic example of the problems that the ID movement faces: Here's Why We Answer Some of Our Less Cogent Critics.
As you can see, he avoids the issue I raised in favor of an ad hominem attack. Wouldn't it be nice to see a scientific debate between Michael Behe and David Klinghoffer on the meaning of evolution? Not going to happen as long as ID is primarily a religious movement.
1. Casey Luskin can't decide how old the universe is but he leans toward Young Earth Creationism. Yet he's a leading spokesman for the "science" of intelligent design.
The history of DNA repair is well-known. Here's a quote from "Early days of DNA repair: discovery of nucleotide excision repair and homology-dependent recombinational repair" by W.D. Rupp in 2013 (Rupp, 2013).
This article describes events related to the first papers published in the 1960s describing nucleotide excision repair (NER) and homology-dependent recombinational repair.
Here's are the relevant papers.
Setlow, R.B., and Carrier, W.L. (1964) The disappearance of thymine dimers from DNA: An error-correcting mechanism. Proc. Natl. Acad. Sci. (USA) 51:226–231. [Full Text]
Boyce, R.P., Howard-Flanders, P. (1964) Release of ultraviolet light-induced thymine dimers from DNA in E. coli K-12. Proc. Natl. Acad. Sci. (USA) 51:293–300. [Full Text]
Pettijohn, D, and Hanawalt, P. (1964) Evidence for repair-replication of ultraviolet damaged DNA in bacteria. J. Mol. Biol. 9:395–410. [PubMed]
