Most of us are aware of the ENCODE publicity fiasco. The leaders of the project made some outlandish claims about the function of most of our genome in order to attract attention and make their work seem much more significant than it really is [see Sean Eddy on Junk DNA and ENCODE].
Many scientists tried to set the record straight and they pretty much succeeded, at least in the scientific community. Most scientist now know that the case for junk DNA is a lot stronger than they thought.
Unfortunately, the criticisms didn't get much publicity and the average person is left with the impression that most of our genome has an important function, even if we don't know exactly what that function is. This means that good science writers have to work harder to educate the public about the true state of our genome.
Timothy Caulfield is a Professor in the Faculty of Law and the School of Public Health at the University of Alberta in Edmonton, Alberta, Canada. He's also Canada Research Chair in Health Law and Policy, a very prestigious award. He writes the following in today's issue of The Globe & Mail, Canada's most important newspaper [We’re overselling the health-care 'revolution' of personal genomics].
The relationship between our genome and disease is far more complicated than originally anticipated. Indeed, the more we learn about the human genome, the less we seem to know. For example, results from a major international initiative to explore all the elements of our genome (the ENCODE project) found that, despite decades-old conventional wisdom that much of our genome was nothing but “junk DNA,” as much as 80 per cent of our genome likely has some biological function. This work hints that things are much more convoluted than expected. So much so that one of ENCODE’s lead researchers, Yale’s Mark Gerstein, was quoted as saying that it’s “like opening a wire closet and seeing a hairball of wires.”
Statements like this from someone who is supposed to be knowledgeable about such issues show us that the ENCODE fiasco has far-reaching consequences. The misleading statements by Ewan Birney and others will take years to undo. It's all the more reason to criticize Nature and Science for aiding and abetting the spread of this false information.
How can we expect people like Timothy Caulfield to understand the science if the leading journals get it wrong?
[Hat Tip: Ryan Gregory, "The Bullshit Continues to Spread" on Facebook.]
Paul Nelson has been challenging the pervasiveness of adaptationism by pointing out that many evolutionary biologists promte nonadaptive evolution. See the discussion and comments on Jerry Coyne's blog website: A Marshall McLuhan moment with creationist Paul Nelson. Nelson has been accused, falsely, of claiming that some evolutionary biologists deny that natural selection is an important mechanism in evolution.
Paul Nelson doesn't deny that natural selection is a real phenomenon. He may be an IDiot (and a YEC) but he's not THAT stupid. On the other hand, one didn't have to wait too long before getting confirmation that some other IDiots really are THAT stupid.
And guess what? They are allowed to post on the main Discovery Institute blog, Evolution News & Views (sic)!!! You have to read How "Real" Is Natural Selection? by Tom Bethell ... otherwise you'd never believe me.
Here's what Tom Bethell says about natural selection.
Over at Uncommon Descent there's a recent post praising the "noted philosopher" William Lane Craig [Noted philosopher William Lane Craig responds to the American Humanist Association “Kids without God” web site]. They link to an article by Craig posted on The Washington Post website a few days ago: Humanism for children.
Here's what William Lane Craig has to say about the existence of god(s).
Udo Schüklenk is a Professor of Philsophy at Queen's University in Kingston, Ontario, Canada. His specialty is bioethics.
Udo gave a presentation at Eschaton 2012 on Myths About Atheist Values. He covered three topics ...
1. Are atheists moral? Yes
2. Does life have meaning or purpose? No, not the same kind of meaning and purpose that theists imagine.
3. Do atheists value human life? Yes.
Udo has a blog and one of the services he provides on his blog is to teach us about bioethics. Part of this service is to expose quacks masquerading as bioethicists. It's a thankless job but someone has to do it.
Fortunately, Udo concentrates on Canadian quacks so you won't be overwhelmed. There are only a few hundred, mostly doctors.
Perhaps Canada's most famous quack bioethicist is Margaret Somerville, a Professor of Law at McGill University, (Montreal, Quebec, Canada). She's best known for her opposition to same-sex marriage and she's been advertised on television and in newspapers as a bioethicist who has rational views on the dangers of legalizing same-sex marriage. (She wasn't very persuasive since same-sex marriage is legal in Canada.}1
Udo Schüklenk chaired an experts panel on end-of-life decisions for the Royal Society of Canada [End-of-Life Decision-Making in Canada: The Report by the Royal Society of Canada Expert Panel on End-of-Life Decision-Making].
Margaret Sommerville didn't like their recommendations. She claims that further legalization of euthanasia will lead to people being killed against their will.
Here's how Udo deals with that issue ... Evidence has never been Ms. Somerville's strongest point. So, without any evidence to back up her claims she declares on the Catholic website, "One of the things that's wrong with respect to Justice (Lynn) Smith's judgment (in Carter v. Attorney General of B.C.) is that she purports to review the use of euthanasia and physician-assisted suicide in the jurisdictions that have legalized it. She said there is no problem, there is no slippery slope. Well, that's simply not right factually." It turns out, in our Report on end of life decision-making in Canada we reviewed the empirical evidence on the slippery slope matter and concluded that there is no evidence that assisted dying leads us down slippery slopes to unwanted killings. Of course, we reviewed evidence, Ms Somerville is in full preaching mode.
I like this guy! He thinks that real, scientific, "evidence" is an important part of any debate.
1. We're anxiously waiting to see if her predictions about kids of gay parents being traumatized will come true.
Can you go from some simple character to a more complex feature without invoking natural selection? Yes, you can. Complex features can evolve by nonadaptive means. Just think of our complex genome and read The Origins of Genome Architecture by Michael Lynch.
Want a more simple example? Read the latest post by PZ Myers: [αEP: Complexity is not usually the product of selection]1.
This is an important point. You can't just assume, without question, that a complex trait must be an adaptation and must have arisen by natural selection. That applies to molecular complexes and also to complex behavior.
1. See The Evolution of Enzymes from Promiscuous Precursors for supplementary information.
In my opinion, science is a way of knowing characterized by a requirement for evidence, healthy skepticism, and rationality. "Knowing" refers to something called "universal truth" because knowledge has to be more than just something that an individual believes is true.
I'm not aware of any other way of knowing that has produced something we can reliably classify as "knowledge" by any reasonable criteria. From time to time I've asked for examples but nobody has been able to provide any example of "universal truth" (i.e. knowledge) that has been reached by any other process.
Today Barry Arrington of Uncommon Descent decided to enlighten us [Science is Good, But Not That Good].
Consider history for example. We know with a high degree of reliability that Abraham Lincoln was the president of the United States in 1863. I did not arrive at this knowledge through scientific means. I know it because someone told me, and they in turn learned it from someone else, who in turn learned it from someone else back to the actual people who witnessed first-hand a man who called himself “Abraham Lincoln” sitting in the White House in 1863 and acting for all the world like he was the president of the United States.
Consider geography. I have never been to Russia, but I am quite certain that Moscow is the capital of that country. I did not arrive at this knowledge through scientific means either.
If timothya will stop and think a moment, he will realize that practically everything he knows he knows because someone told him, not because the truth of the proposition has been confirmed by science.
I guess that settles it. If lots of people tell you that god exists then it must be true. Epistemology is finished and the demarcation problem is solved.
Lots of people tell me that Intelligent Design Creationists aren't very bright. 
None of the Sandwalk readers rose to to challenge of identifying a really good evolutionary psychology paper [The Best of Evolutionary Psychology].
However, Jerry Coyne tries to (partially) defend evolutionary psychology and he offers the following paper as evidence that the field is not entirely worthless.
Confer, J.C., Easton, J.A., Fleischman, D.S., Goetz, C.D., Lewis, D.M.G., Perilloux, C., and Buss, D.M. (2010) Evolutionary Psychology: Controversies, Questions, Prospects, and Limitations. American Psychologist 65:110–126. [doi: 10.1037/a0018413]
The main problem with the adaptationist approach is identifying adaptations. Is something really an adaptation or are there other explanations? Part of the answer involves providing evidence that the behavior has a specific genetic component.
I don't think those problems are satisfactorily addressed in this review in spite of Jerry's recommendation. If this is the best the field has to offer then it's in real trouble.
Here's an example from that paper of the "best" kind of science.
The science of confirming and falsifying hypotheses, of course, is typically more complex than these examples indicate. Often a hypothesis is embedded within a larger theoretical network. For example, one evolutionary prediction is that women will prefer men as potential mates who express a willingness to invest in them and their offspring (Buss, 1995). This is derived from the hypothesis that in paternally investing species, females will use cues to a man’s willingness to invest as a criterion for mate selection. In turn, this hypothesis is derived from parental investment theory, which posits that the sex that invests more in its offspring will be the choosier sex when selecting mates (Trivers, 1972). Finally, the logic behind parental investment theory is derived from inclusive fitness theory (Hamilton, 1964a, 1964b), the modern formulation of evolution by natural selection. As in all realms of psychological science, the evaluation of each evolutionary psychological hypothesis, as well as the broader theories within which they are embedded, rests with the cumulative weight of the empirical evidence.
I've always been puzzled about the evolutionary significance of mate selection in humans. Whenever I look at genealogical records I'm impressed by the fact that almost all men and women who reach maturity seem to find a mate. This jibes well with my personal experience since all of my friends who wanted to live with a partner succeeded in finding one. I wonder how powerful these mate selection criteria can be if there aren't significant numbers of people don't succeed in mating. Where are the ugly mean and women who couldn't find a mate?
I understand that there are studies showing that men and women in different cultures will prefer certain physical characteristics in their mates. What I don't know is whether this actually translates into mate selection when the time comes to form a stable partnership (e.g. get married). It doesn't seem like it to me otherwise almost all wives would look like Marilyn Monroe.
If women are the choosers then why aren't there lots of single men who will never have children even though they want to? Where are the losers in our societies? How common were they in the past?
What about hypothesizing that we all dream about the appearance of the ideal mate but that when it comes time to make a choice we put our emphasis on other characteristics (e.g. availability)? Maybe our preferences aren't really adaptations at all? Was that one of the hypotheses that was considered or do evolutionary psychologists jump immediately to adaptive story-telling?
Last week's molecule was allantoin, the breakdown product of uric acid that's found in the urine of mammals. Other animals can degrade allantoin to more simple compounds but mammals have lost the genes for this pathway. The winners were Paul Clapham and Jacob Troth [Monday's Molecule #194]. They should contact me by email.
This week's molecule is a ubiquitous and essential molecule in all species. Give the common name but be sure you don't confuse it with other, very similar, molecules.
Post your answer as a comment. I'll hold off releasing any comments for 24 hours. The first one with the correct answer wins. I will only post mostly correct answers to avoid embarrassment. The winner will be treated to a free lunch.
There could be two winners. If the first correct answer isn't from an undergraduate student then I'll select a second winner from those undergraduates who post the correct answer. You will need to identify yourself as an undergraduate in order to win. (Put "undergraduate" at the bottom of your comment.)
My friends and I were talking about the purpose of education over dinner on Saturday night. This video criticizes one side of the issue; namely, the idea that the purpose of education is to prepare you for a job. It should not be the goal of education.1
1. But it may be a collateral benefit.
[Hat Tip: Veronica at Canadian Atheist.]
A brief summary of what went on in Ottawa Nov. 30 - Dec. 2, 2012 from Atheism TV.
[Hat Tip: Veronica Abbas at Canadian Atheist.]
I claim that the top three criteria for good science reporting are: Accuracy, Accuracy, and Accuracy. Everything else falls into fourth place or lower, including the presentation style.
There have been a number of TED (or TEDx) talks on science that fail the top three criteria [TED: Alexander Tsiaras, "It was hard not to attribute divinity to it" ] [The Trouble with TED].
Apparently the high command at TED has woken up to the fact that they are being bamboozled by pseudoscientists. Phil Plait of Bad Astronomy alerts us to a letter that they recently sent out to all TEDx organizers [TEDx Talks: Some Ideas Are Not Worth Spreading]. (I love his title!)
Here's a copy of the letter: A letter to the TEDx community on TEDx and bad science. And here's the opening praragraphs—you should read the entire letter because it contains a lot of information about how to recognize bad science.
Hello TEDx Community,
In light of a few suspect talks that have come out of the TEDx movement — some of which we at TED have taken action to remove, some being examined now — and this recent thread on Reddit [http://www.reddit.com/r/science/comments/1444lm/the_ted_name_is_being_dragged_through_the_mud_in/], we feel it is important to reach out to all TEDx organizers on the topic of bad science and pseudoscience.
Please know this above all:
It is your job, before any speaker is booked, to check them out, and to reject bad science, pseudoscience and health hoaxes.
Vetting your speakers is hard work, and can lead to uncomfortable moments. But as TEDx organizers, your audience’s trust is your top priority, over and above any other personal or business relationship that may have brought this speaker to your attention. It is not your audience’s job to figure out if a speaker is offering legitimate science or not. It is your job.
The consequence of bad science and health hoaxes are not trivial. As an example, Andrew Wakefield’s attempt to link autism and vaccines was exposed as a hoax last year. But while his work was being investigated, millions of children went without vaccines, and many contracted deadly illnesses as a result.
We take this seriously. Presenting bad science on the TEDx stage is grounds for revoking your license.
Apparently TED will take down videos that spread pseudoscience. That explains why I was having so much trouble finding examples.
I reviewed Shapiro's book, Evolution: A View from the 21st Century for NCSE reports. (NCSE = National Center for Science Education.) You can read it here.
James Shapiro has responded to my review in the latest issue of NCSE reports: Reply to Laurence A Moran’s review of Evolution: A View
from the 21st Century.
Shapiro seems to be really upset that NCSE would choose someone like me to review his book. He opens his rebuttal with ...
Before I saw Laurence A Moran’s book review (Moran 2012), I wrote the following: “It is a shame that NCSE chose Larry Moran to review my book; not because of anything he said in the review but because he is hostile to new ideas and perspectives.”
A year ago, Moran posted a piece entitled “Physicists and biologists” on his Sandwalk blog [Physicists and Biologists1]. In this post, he ridiculed the enthusiasm I expressed in the book for physicists coming into evolutionary studies and bringing new skills and new ideas.
Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism and ecology. That’s just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.
What a great way to make new friends for evolution science—equating physicists with creationists and calling them “equally ignorant”!
One of the Saturday morning sessions at Eschaton 2012 was on science education. Eugenie Scott started off with a survey of various states (in the USA) that are passing laws promoting creationism. In my presentation I tried to explain the scientific facts that we know for sure then I described an example of Intelligent Design Creationist stupidity showing that they really have no idea what they are talking about. See: Breaking News: IDiots Don't Understand Genomes or Biology. PZ Myers finished of with a depressing summary of the state of science education in the USA.
In my talk I explained that I preferred a broad definition of science, one that emphasizes science as a way of knowing. My definition encompasses the activities of everyone who seeks knowledge and that includes people working in fields outside of the traditional science disciplines.
Eugenie Scott prefers a more restricted definition of science, one that refers to the activities of biologists, chemists, physicists, and geologists. Eugenie thinks there are other ways of knowing and she supports the idea that the actions of scientists are constrained by the rule of methodological naturalism.
I met many interesting people at Eschaton 2012 in Ottawa. One of them was Ian Cromwell who gave a talk about racism on Sunday morning. Ian thinks that the skeptic/atheist movement ought to pay more attention to racism and he made his point by teaching us how to recognize zombies and racists.
Ian has a degree in statistics and epidemeology from Queen's University (Ontario, Canada) and he now works in Vancouver (British Columbia, Canada). He has a blog called The Crommunist Manifesto on Freethought Blogs. His blog deals mostly with racism issues.
Here's a video of a recent talk he gave in Vancouver (Part 1 of 5).
I really enjoyed Ian's presentation except for one small comment he made. He said something like, "There's no meaningful distinction between human races." When I asked him about this after his talk, he seemed to defend the proposition that human races don't exist. The comments on his blog suggest that we could have a productive discussion about the meaning of the word "race." See: #Eschaton2012: some additional reflections where he says ...
The thesis statement of my talk: that skepticism can and should be applied to the topic of race, seemed to strike the crowd as pretty non-controversial, which was nice. The lion’s share of the questions in the subsequent panel went to me, suggesting to me that the topic of race is one that is underexplored but sorely wanted within the skeptical/freethinking movement. There was an exchange with Larry Moran after my talk was over that I anticipate will turn into a brief back-and-forth between our two blogs as we sort out the biological underpinning of race and what those mean in the real world.
My position is that the term "race" is used frequently to describe sub-populations of species, or groups that have been genetically isolated from each other1 for many generations. By this definition, races exist in humans just as they do in many other species.
The genetic evidence shows clearly that Africans form a distinctive, but somewhat polyphyletic, group that differs from the people living outside of Africa. Amongst the non-Africans, we recognize two major sub-groups; Europeans and Asians. I see no reason why these major sub-populations don't qualify as races in the biological sense. lease read: Do Human Races Exist?.
I don't think that denying the existence of races is going to make racism go away. Nor do I think that accepting the existence of biological races is going to foster racism.
1. Genetically isolated does NOT mean there's no gene flow between the groups. Is there was none, they would be different species. Please don't use the silly argument that the existence of hybrids disproves the concept of human races.
One of the remarkable things about kooks is that they are incredibly resistant to learning from their mistakes. James Shapiro gives us a fine example in one of his latest articles on The Huffington Post where he tries to convince us that the old definition of "gene" has outlived its usefulness. According to Shapiro, "DNA and molecular genetics have brought us to a fundamentally new conceptual understanding of genomes, how they are organized and how they function."
Really? While we all can agree that there's no definition of "gene" that doesn't have exceptions, we can surely agree that some definitions work pretty well. I've argued that defining a gene as, "a DNA sequence that is transcribed to produce a functional product" works well in most cases [What Is a Gene?].
Let's see how James Shapiro handles this problem.1 He says,
The identification of DNA as the key molecule of heredity and Crick's Central Dogma of Molecule Biology [Crick 1970] initially seemed to confirm Beadle and Tatum's "one gene -- one enzyme" hypothesis.
I've already explained that Shapiro doesn't understand the Central Dogma of Molecular Biology even though he quotes the Francis Crick papers that explain it correctly [Revisiting the Central Dogma in the 21st Century]. I also made this point in my review of his book: Evolution: A View from the 21st Century.
