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]
Some of you might recall that I gave a presentation at a Café Scientifique in Mississauga (Ontario, Canada) [Café Scientifique]. It was a lot of fun and there were many interesting people at the meeting.
The new season continues on Monday, October 26h with a meeting at 7 pm at The Franklin House, 263 Queen St S., in Streetsville, Mississauga (Ontario Canada) [see Meetup]. Come and join us for a discussion about teaching critical thinking in Ontario schools. My friend Chris DiCarlo is the speaker.
Come hear TVO 2008 Best Lecturer winner Christopher DiCarlo talk about “Introducing Standard Critical Thinking Skills to Ontario High Schools”.
The topic follows Dr. DiCarlo's efforts over the last five years or so to personally lobby the Ministry of Education and various School Boards in an effort to start a pilot project which introduces both teachers and students to the value of basic Critical Thinking skills. The Pilot Project began in September, 2014 with the Upper Grand District School Board. The first year of the project was a great success. It is now entering its 2nd phase which involves the development of video footage and written materials for Learning Modules which will be made available to all teachers throughout Ontario and eventually, Canada. These modules can be used for any grades, though they are intended for grades 9 and 10 in order to introduce these skills as early as possible in High School. The eventual plan also includes the development of a stand-alone course for Grade 12.
Dr. Christopher DiCarlo is a philosopher, educator, and author. He currently teaches in the Faculties of Philosophy at the University of Toronto and Ryerson University. He is also a lifetime member of Humanist Canada and an Expert Advisor for the Centre for Inquiry Canada.
He has been invited to speak at numerous national and international conferences and written many scholarly papers ranging from bioethics to cognitive evolution. His latest book entitled: How to Become a Really Good Pain in the Ass: A Critical Thinker’s Guide to Asking the Right Questions was released worldwide by Prometheus Press in August, 2011 and is currently in its fifth printing and is a best-seller in the U.S.
He is currently working on his latest book tentatively entitled: Flying Without A Pilot: A Determined Look at the Future of Ethics, Law, and the Value of Human Behavior.
In April, 2008 he was awarded TV Ontario’s Big Ideas Best Lecturer in Ontario Award for his lecture “The Relations of Natural Systems”.
In August, 2008, he was honoured with the Canadian Humanist of the Year Award from the Humanist Association of Canada.
Dr. DiCarlo is the Director of Critical Thinking Solutions, a consulting business for individuals, corporations, and not-for-profits in both the private and public sectors. He is also the developer of the first Pilot Project in Canada to introduce Standardized Critical Thinking skills into the Ontario Public High School curriculum which has begun in the Upper Grand District School Board.
Lately I've been reading a lot of papers on genomes and I've discovered some really exceptional papers that discuss the existing scientific literature and put their studies in proper context. Unfortunately, these are the exceptions, not the rule.
I've discovered many more authors who seem to be ignorant of the scientific literature and far too willing to rely of the opinions of others instead of investigating for themselves. Many of these authors seem to be completely unaware of controversy and debate in the fields they are writing about. They act, and write, as if there was only one point of view worth considering, theirs.
How does this happen? It seems to me that it can only happen if they find themselves in an environment where skepticism and critical thinking are suppressed. Otherwise, how do you explain the way they write their papers? Are there no colleagues, post-docs, or graduate students who looked at the manuscript and pointed out the problems? Are there no referees who raised questions?
Listen to Jonathan McLatchie's explanation of irreducible complexity and why it represents a problem for the "neo-Darwinian paradigm." Keep in mind that he has been asked to do this by a Christian pastor on an Christian apologetics podcast. I wonder why?
McLatchie claims that an irreducibly complex system consist of a number of subfunctions where the removal of one subfunction renders the whole system nonfunctional. He implies that such systems can't be explained by evolution. Do all ID proponents agree? If we can show you a reasonable evolutionary explanation of the evolution of a single irreducibly complex system, using McLatchie's definition, would that refute his claim that such systems present a challenge to evolution? How about if we show you two examples? Three?
Because science is defined by its methodology, any attempt to discredit a field such as Intelligent Design by casting aspersions on the motives of its leading practitioners completely misses the point. No matter what their motives might be, the only question which is germane in this context is: do Intelligent Design researchers follow a proper scientific methodology, and do ID proponents support their arguments by appealing to that methodology? The answer to this question should be obvious to anyone who has read works such as Darwin’s Black Box, The Edge of Evolution, Signature in the Cell and Darwin’s Doubt. Intelligent Design researchers and advocates commonly appeal to empirical probabilities (which can be measured in the laboratory), mathematical calculations (about what chance and/or necessity can accomplish), and abductive reasoning about historical events (such as the Cambrian explosion) which bear the hallmarks of design.
This is a video from One Minute Apologist. Really, I'm not kidding. There actually is a man called Bobby Conway who is the One Minute Apologist.
He became a devout Christian when he was 19 and subsequently went off to Bible school then got a Doctorate of Ministry in Apologetics from Southern Evangelical Seminary. He's now a Ph.D. candidate in the Philosophy of Religion department at the University of Birmingham (UK). I'd love to be on his thesis committee but I'm not a philosopher. Maybe they'll invite John Wilkins to serve as external reviewer at the thesis defense?
The theme of his videos and website is ...
We provide quick, credible answers to apologetic questions that resource people with a hunger to defend their Christian faith.
Here's an interview with Jonathan McLatchie where McLatchie tires to pretend that ID is a legitimate scientific investigation that has nothing to do with creationism. Keep in mind that he's doing this while being interviewed by a Christian Pastor in a Christian apologetics video. Watch the video, it's only one minute.
The CBC poll-tracker website shows the Liberal Party in the lead with 37% of the vote. The Conservative Party is polling at 31% and the New Democratic Party trails at 22%.
In close elections it is extremely difficult to project those numbers into seats because there are many close races and the number of people sampled in each riding is quite small. Nevertheless, ThreeHundredEight and CBC have been making seat projections since the campaign began.
Here's the latest seat projections as of yesterday ...
If these projections are accurate then the Liberals will win the most seats but will be far short of a majority. Justin Trudeau will become the next Prime Minister of Canada and Stephen Harper will be gone.
The main uncertainty is voter turnout. A lot of Liberal voters are uncertain about who to vote for and many of them will be first-time voters, if they vote. The Conservative vote, on the other hand, is pretty solid and Conservative voters are very likely to vote today. Most of the Conservative vote is concentrated in rural ridings that are guaranteed wins for the Conservatives. It is still possible for the Conservatives to win enough close races to finish on top with the most seats.1
The NDP vote is soft and dropping. The biggest change in the past few days is the seat projections in Quebec where the NDP won 59 seats in the last election. (A big surprise.) As of today, CBC is projecting that they will only win 34 seats. All three of the other parties are projected to gain seats but the Liberals gain the most. The battle in Ontario was reduced several weeks ago to mainly a fight between Liberals and Conservatives. (There are a few ridings where the Liberals and NDP are neck-and-neck.)
It's interesting that the three-way race in British Columbia hasn't changed very much in a long time. The latest projections have the Conservatives slightly ahead with 16 seats to 13 for the Liberals and 12 for the NDP. (Plus one seat for the Green Party.) There are several scenarios where the overall winner will be decided by the vote in British Columbia. It could be a long night.
The result in the Greater Toronto Area (GTA) was decided weeks ago. The Liberals are going to capture almost all of the seats. The only secure victory for the Conservatives is Thornhill, and the only projected victory for the NDP is Toronto-Danforth. [See the interactive map at: ThreeHundredEight.] Olivia Chou is trailing badly in Spadina-Fort York.
In my area, Mississauga-Brampton, every seat is projected to go Liberal and many Conservative MPs are going down to defeat, including my own MP Bob Dechert. The NDP is not a factor in any of these ridings.
1. This does not mean that Harper will be able to hold on to power but it makes things complicated.
The CBC poll-tracker website tracks a number of public opinion polls and calculates a weighted average. The latest numbers have the Liberal Party winning the most votes with the Conservative Party (current government) in second place.
This is a close election so normally you would have to take these numbers with a large grain of salt but the trend over the past month is pretty obvious.
There has been a steady decline in support for the New Democratic Party (NDP) and a steady increase in Liberal support. The percentage of people who say they will vote Conservative has not changed much. It would be truly astonishing if the actual results tonight are much different than the poll results in terms of total votes. (There could be a total collapse of the NDP vote but not a reversal of fortune.)
