Here's a video of my talk at Eschaton 2012 in Ottawa (Dec. 1, 2012).
Showing posts with label Evolutionary Biology. Show all posts
Showing posts with label Evolutionary Biology. Show all posts
Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012
The folks over at Evolution News & Views (sic) have selected the ENCODE papers as the Number 1 evolution-related story of 2012. Naturally, they fell for the hype of the ENCODE/Nature publicity campaign as you can see from the blog title: Our Top 10 Evolution-Related Stories: #1, ENCODE Project Buries "Junk DNA".
Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...
Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists!
I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.
Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...
Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.
Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists!
I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.
Carnival of Evolution #55
Welcome to 2013 and to Carnival of Evolution #55, and Happy New Year to everyone from Genome Engineering. Have you made any New Year’s resolutions this year? Apart from the oft repeated ‘This year I will write my novel’, here are some of my New Year’s resolutions for 2013.There's no host yet for the next Carnival of Evolution (February, 2013). If you want to volunteer to next month or for March, April, or May, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before but repeat hosts are more than welcome right now! Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.
New Year’s Resolution number one: Deliver Carnival of Evolution on time
Okay – broken that one already – sorry. Hope it was worth waiting for. Now onto the rest.
Ann Gauger Describes the Intelligent Design Creationist Version of Population Genetics
In lieu of Saturday morning cartoons, I offer this video. David Klinghoffer likes it [The Awkward Secret that Plagues Population Genetics and Darwinian Evolutionary Theory]. Enjoy.
Texas Wants to Protect the IDiots in Universities
The elected members of the Texas legislature are well aware of this discrimination against stupidity so they've taken steps to stop it. Bill HB285 "Relating to prohibiting discrimination by public institutions of higher education against faculty members and students based on their conduct of research relating to intelligent design" should do the trick, if it becomes law.
Here's the key provision,
An institution of higher education may not discriminate against or penalize in any manner, especially with regard to employment or academic support, a faculty member or student based on the faculty member’s or student’s conduct of research relating to the theory of intelligent design or other alternate theories of the origination and development of organisms.I suppose it was inevitable that politicians in Texas would finally recognize that their children might flunk out of university.
Fallout from the ENCODE Fiasco Makes It into the Globe & Mail
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.]
Do Some IDiots Actually Question the Existence of Natural Selection?
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.
Read more »
On the Evolution of Complexity
Want a more simple example? Read the latest post by PZ Myers: [αEP: Complexity is not usually the product of selection1.
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.
The Best of Evolutionary Psychology According to Jerry Coyne.
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?
James Shapiro Responds to My Review of His Book
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.”Read more »
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”!
The Best of Evolutionary Psychology
There seems to be general agreement that many of the papers in evolutionary psychology are less than stellar examples of the best that science has to offer [see Evolutionary Psychology as Maladapted Psychology ]. One way to decide on the overall value of a discipline is to look at its best works rather than its worst. In the past I've often asked for examples of the very best papers in evolutionary psychology. Such requests are usually met with embarrassing silence but Gad Saad once took up the challenge: The Great, Profound, and Valuable Works of Evolutionary Psychology. It's not a very impressive list. Since the discussion about evolutionary psychology is heating up again, it's time to send out another request. What are the very best papers in the field—the ones you are proud to point to whenever any criticizes evolutionary psychology? PZ Myers also wants to know [αEP: Shut up and sing!. John Wilkins would also like some examples since he's just launched a series of posts defending evolutionary psychology [Evopsychopathy 1. Conditions for sociobiology].
Read more »
Sean Eddy on Junk DNA and ENCODE
Most people now know that ENCODE did not disprove junk DNA (with the possible exception of creationists and a few kooks).
Sean has written a wonderful article for Current Biology where he explains in simple terms why there is abundant evidence for junk (i.e. nonfunctional) DNA [The C-value paradox, junk DNA and ENCODE] [preprint].
Here's a quotation from the article to pique your interest.
Recently, the ENCODE project has concluded that 80% of the human genome is reproducibly transcribed, bound to proteins, or has its chromatin specifically modified. In widespread publicity around the project, some ENCODE leaders claimed that this biochemical activity disproves junk DNA. If there is an alternative hypothesis, it must provide an alternative explanation for the data: for the C-value paradox, for mutational load, and for how a large fraction of eukaryotic genomes is composed of neutrally drifting transposon-derived sequence. ENCODE hasn’t done this, and most of ENCODE’s data don’t bear directly on the question. Transposon‑derived sequence is generally expected to be biochemically active by ENCODE’s definitions — lots of transposon sequences are inserted into transcribed genic regions, mobile transposons are transcribed and regulated, and genomic suppression of transposon activity requires DNA‑binding and chromatin modification.
The question that the ‘junk DNA’ concept addresses is not whether these sequences are biochemically ‘active’, but whether they’re there primarily because they’re useful for the organism.
1. More importantly, he's an alumnus of Talk.origins.
Carnival of Evolution #54
I hope everyone enjoyed their holiday dinosaur this Thanksgiving, and thank you joining me in this delightful excursion out into the wide wonderful world of ideas and expressions in evolution.As it turns out, I did enjoy eating dinosaur on Thanksgiving but it was so long ago (Oct. 8) that I've forgotten what it tasted like.
Enjoy your tour of Mt. Improbable!
The next Carnival of Evolution (September) will be hosted by Genome Engineering. If you want to volunteer to host others, contact Bjørn Østman. Bjørn is always looking for someone to host the Carnival of Evolution. He would prefer someone who has not hosted before. Contact him at the Carnival of Evolution blog. You can send articles directly to him or you can submit your articles at Carnival of Evolution although you now have to register to post a submission.
John Wilkins Defends Evolutionary Psychology
In an effort to correct this problem, John has decided to defend evolutionary psychology [Eww, I stepped in some evolutionary psychology and other crap]. I posted a comment explaining why he was wrong.
Those of you who are fans of this
He needs you.
PZ, Poutine, and the End of the World
Other highlights included his two talks. The one on Saturday morning was about the sorry state of science education in the United States. That was depressing.
PZ's talk on Saturday evening was at the Canadian Museum of Natural History, just around the corner from the hotel. There were about 200 people in the audience. He tackled a very difficult topic, the role of chance in evolution. Naturally he covered random genetic drift but most of his talk was about coalescent theory because he wanted to explain some recent results from the sequence of the gorilla genome (Scally et al. 2012).
The authors of that paper report that, "In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other." PZ explained why this is exactly the result you would expect. (See his blog post at: A tiny bit of knowledge is a dangerous thing.)
He also pointed out that the Intelligent Design Creationists got all excited about this result, thinking that it overthrows the theory of evolution and proves the existence of God. (I exaggerate slightly, but you get the point!) What this means if that the IDiots really don't understand evolution.
While we don't expect everyone to see immediately why 30% of our genes could be more similar to gorilla genes than to chimp genes, we do expect those who criticize evolution to have a better understanding. Instead, what we see is that those "experts" who post at Evolution News & Views (sic) don't even have an introductory college level understanding of evolution. Their ignorance of evolution produces some remarkably stupid posts on that blog—the website of the Discovery Institute.
I made a similar point in my talk except that I focused on the IDiot's lack of knowledge of mutation [see Breaking News: IDiots Don't Understand Genomes or Biology].
PZ took on a challenging task but he succeeded better than I could have imagined. While the audience didn't follow all of the explanation, they could see that it was based on solid evidence and theory. Many of them learned for the first time about chance in evolution and that's a plus, in my opinion.
Now let's work on the IDiots.
Scally, A, Dutheil, J.Y., Hillier, L.W., Jordan, G.E. et al. (2012) Insights into hominid evolution from the gorilla genome sequence. Nature 483:169-175. [PubMed]
Elisabeth Lloyd: Gould and adaptation: San Marco 33 years later
This is a talk by Elizabeth Lloyd from a conference in Italy last May on "Stephen J. Gould’s Legacy: Nature, History, Society." Thanks to Ryan Gregory for posting all the videos [Stephen Jay Gould conference in Italy — full series of talks].
Lloyd explains the problems with the adaptationist approach to the logic of research questions using a case study on the evolutionary origins of female orgasm. She points out that Gould & Lewontin were right 33 years ago when they called attention to the adaptationist bias and that things haven't changed very much.
This is an excellent example of a philosopher of biology, Elizabeth Lloyd, making a substantial contribution to science and the philosophy of science
Lloyd explains the problems with the adaptationist approach to the logic of research questions using a case study on the evolutionary origins of female orgasm. She points out that Gould & Lewontin were right 33 years ago when they called attention to the adaptationist bias and that things haven't changed very much.
This is an excellent example of a philosopher of biology, Elizabeth Lloyd, making a substantial contribution to science and the philosophy of science
Ann Gauger Says Random Mutation Can't Possibly Account for Observed Evolution
There's a lot of discussion about this video on the Biologic Facebook page [Biologic Institute]. Some commenters (e.g. Nick Matzke) raise the issue of neutral mutations and Gauger responds (not very well). This is one of the main problems with the current IDiot propaganda. They confuse the probability of specific, single nucleotide, beneficial, mutations at a specific binding site—which have a low probability—with the total number of possible mutations at thousands of different sites, any of which could have an effect on development. Many of the mutations could have been neutral giving rise to an enormous amount of standing variation in the population. (This makes it much more likely that you will get multiple mutations.)
Don't forget we're looking at a specific outcome (evolution of Homo sapiens from a common ancestors over 6 million years). There were thousand and thousands of other possible outcomes that could have given rise to intelligent beings (maybe smart chimps?) who would eventually spawn Intelligent Design Creationists.1 We don't know the total number of possibilities but it certainly isn't just one (1). Our species is a lottery winner and we all know that specific lottery winners are highly improbable.
1. I wonder if there are any possible pathways that would have given rise to truly intelligent beings and no IDiots?
Is It Science?
I've been having discussion with several of my friends and colleagues about whether the activities of the Intelligent Design Creationists count as "science." My position is that much of what they do is science, especially when they criticize existing scientific explanations. It may not be very good science but that's not the question. After all, there are atheist scientists who don't do much better.
One argument is that simply criticizing current theories doesn't count as science unless you can also offer a plausible, scientific, competing model. I don't think that's a requirement. Here's an example we can discuss ...
One of the latest posts on Evolution News & Views (sic) is an article by Casey Luskin criticizing the old Urey-Miller experiment by pointing out that their origninal conditions didn't mimic the conditions on the primitive Earth [On the Miller-Urey Experiment, Wikipedia Offers a Citation Bluff]. He goes on to say that scientists still haven't shown convincingly that amino acids (and other molecules) could have formed spontaneously on Earth. Furthermore, the "chirality problem" hasn't been solved.1
Luskin correctly points out that a Wikipedia reference misrepresents the science it reports.
Is this (Luskin's article) scientific? Isn't criticism of current models and hypotheses an example of how science is supposed to work?
One argument is that simply criticizing current theories doesn't count as science unless you can also offer a plausible, scientific, competing model. I don't think that's a requirement. Here's an example we can discuss ...
One of the latest posts on Evolution News & Views (sic) is an article by Casey Luskin criticizing the old Urey-Miller experiment by pointing out that their origninal conditions didn't mimic the conditions on the primitive Earth [On the Miller-Urey Experiment, Wikipedia Offers a Citation Bluff]. He goes on to say that scientists still haven't shown convincingly that amino acids (and other molecules) could have formed spontaneously on Earth. Furthermore, the "chirality problem" hasn't been solved.1
Luskin correctly points out that a Wikipedia reference misrepresents the science it reports.
Is this (Luskin's article) scientific? Isn't criticism of current models and hypotheses an example of how science is supposed to work?
1. I agree that the spontaneous formation on Earth of significant amounts of amino acids, carbohydrates, and, especially, nucleotides, is extremely unlikely. That's why I support "Metabolism First." I disagree about the chirality problem—I think we have a good explanation.
The Most Spectacular Mutation in Recent Human History
I'm not going to tell you what it is. You'll have to read his article. But here are a few hints.
- The mutation is only common in Europeans. Asians and Africans get along just fine without it.
- It's not clear whether the mutation confers selective advantage. There's some evidence that it does but it's difficult to understand why.
- There are several different mutations that produce the same phenotype and it's not clear which one of them is the "most spectacular."
- The article claims that the mutation appeared 10,000 years ago but that's probably not true.
- The mutation has nothing to do with walking upright, opposable thumbs, big brains, or the ability to talk. Apparently those mutations are either much less spectacular or they don't qualify as "recent."
[Photo Credit: How to Milk a Cow]
[Hat Tip: Mike the Mad Biologist]
Evolution and Design
Arrington claims that there are only three positions in this debate.
In summary, there are three positions in play here.This isn't correct. I support the 4th position; namely ....
(1) The traditional theist observes the overwhelming appearance of design in living things and is content to conclude that things are they way they appear to be, i.e., that living things appear to be designed for a purpose because they are in fact designed for a purpose.
(2) The atheist admits that the appearance of design in living things is overwhelming but asserts that the appearance of design is an illusion and in reality natural law and random chance combine to produce a result that only appears to be designed.
(3) The Barr-type theistic evolutionist admits that the appearance of design in living things is overwhelming but asserts — like the atheist — that the appearance of design is an illusion and in reality natural law and random chance combine to produce a result that only appears to be designed. The TE then goes one step further by asserting that the explanation of the illusion of design is itself an illusion, because the randomness of evolution is in fact directed.
(4) When you step back and look at the big picture, living things do not appear to be designed and they do not appear to have a purpose. While there may be some features of living things that have been honed by natural selection, they are the exception, not the rule. Even those features with a strong illusion of design look much less designed when you examine them closely.
When I talk about Evolution by Accident I intend that to be an attack on Intelligent Design and also an attack on the Dawkins' view of evolution.
Subscribe to:
Posts (Atom)
