The latest issue of Evolution: Education and Outreach contains a review of two books about evolution written by philosophers. The author of the review is Egbert Giles Leigh Jr. You can read it for free at: Questions about NeoDarwinism: a review of two books.
The books are,
Mind and Cosmos: Why the Materialist NeoDarwinian Conception of Nature is Almost Certainly False by Thomas Nagel. New York: Oxford University Press, 2012. ISBN 978-0-19-991975-8.
Are You an Illusion? by Mary Midgley. New York, NY: Routledge. 2014. ISBN 978-1-84465-792-6.
Both of these books challenge the idea that random mutation and natural selection can explain the world we see around us today.
The reviewer responds with a defense of natural selection from an adaptationist perspective.
I think Nagel and Midgley are wrong but for different reasons. I think that the history of life is the culmination of many random and accidental events and it could easily have gone in different directions [see Replaying life's tape]. I also think that lots of modern features are epiphenomena and not adaptations. Consciousness, to the extent that it actually exists, is one of them.
Nevertheless, Leigh's review is interesting and informative and I urge you to read it if you are interested in knowing why philosophers attack evolution. It helps us understand, once again, where philosophy is going wrong.
Today, while searching for articles on junk DNA, I came across a review of Nessa Carey's book published in The American Biology Teacher: DNA. The review was written by teacher in Colorado and she liked the book very much. Here's the opening paragraph,
The term junk DNA has been used to describe DNA that does not code for proteins or polypeptides. Recent research has made this term obsolete, and Nessa Carey elaborates on a wide spectrum of examples of ways in which DNA contributes to cell function in addition to coding for proteins. As in her earlier book, The Epigenetics Revolution (reviewed by ABT in 2013), Carey uses analogies and diagrams to relate complicated information. Although she unavoidably uses some jargon, she provides the necessary background for the nonbiologist.
The author of the review does not question or challenge the opinions of Nessa Carey and, if you think about it, that's understandable. The average biology teacher will assume that a book written by a scientist must be basically correct or it wouldn't have been published.
That's not true, as most Sandwalk readers know. You would think that biology educators should know this and exercise a little skepticism when reviewing books. Ideally, the book reviews should be written by experts who can evaluate the material in the book.
Now we have a problem. The way to correct false information about genomes and junk DNA is to teach it correctly in high school and university courses. But that means we first have to teach the teachers. Here's a case where professional teachers have been bamboozled by a bad book and that's going of make it even more difficult to correct the problem.
The last paragraph of the review shows us what influence a bad book can have,
As a biology teacher who enjoys sharing with students some details that go beyond the textbook or that challenge dogma, I enthusiastically read multiple chapters at each sitting, making note of what I cannot wait to add to class discussions. “Junk DNA” may be a misnomer, but Junk DNA is an excellent way of finding out why.
Oh dear. It's going to be hard to re-educate those students once their misconceptions have been reinforced by a teacher they respect.
We've been having a discussion on another thread about ID proponents. Are some of them acting in good faith or are they all lying and deceiving their followers?
I have similar problems about many scientists. I've been reading up on pervasive transcription and the potential number of genes for noncoding, functional, RNAs in the human genome. As far as I can tell, there are only a few hundred examples that have any supporting evidence. There are good scientific reasons to believe that most of the detected transcripts are junk RNA produced as the result of accidental, spurious, transcription.
There are about 20,000 protein-coding genes in the human genome. I think it's unlikely that there are more than a few thousand genes for functional RNAs for a total of less than 25,000 genes.
Here's one of the papers I found.
Guil, S. and Esteller, M. (2015) RNA–RNA interactions in gene regulation: the coding and noncoding players. Trends in Biochemical Sciences 40:248-256. [doi: 10.1016/j.tibs.2015.03.001]
Trends in Biochemical Sciences is a good journal and this is a review of the field by supposed experts. The authors are from the Department of Physiological Sciences II at the University of Barcelona School of Medicine in Barcelona, Catalonia, Spain. The senior author, Manel Esteller, has a Wikipedia entry [Manel Esteller].
Here's the first paragraph of the introduction.
There are more genes encoding regulatory RNAs than encoding proteins. This evidence, obtained in recent years from the sum of numerous post-genomic deep-sequencing studies, give a good clue of the gigantic step we have taken from the years of the central dogma: one gene gives rise to one RNA to produce one protein.
The first sentence is not true by any stretch of the imagination. The best that could be said is that there "may" be more genes for regulatory RNAs (> 20,000) but there's no strong consensus yet. Since the first sentence is an untruth, it follows that it is incorrect to say that the evidence supports such a claim.
It's also untrue to distort the real meaning of the Central Dogma of Molecular Biology, which never said that all genes have to encode proteins. The authors don't understand the history of their field in spite of the fact they are writing a review of that field.
Here's the problem. Are these scientists acting in good faith when they say such nonsense? Does acting in "good faith" require healthy criticism and critical thinking or is "honesty" the only criterion? The authors are clearly deluded about the controversy since they assume that it has been resolved in favor of their personal biases but they aren't lying. Can we distinguish between competent science and bad science based on such statements? Can we say that these scientists are incompetent or is that too harsh?
Furthermore, what ever happened to peer review? Isn't the system supposed to prevent such mistakes?
The Mysterious World of the Human Genome
by Frank Ryan
William Collins, an imprint of Harper Collins, London UK (2015)
ISBN 978-0-00-754906-1
This is just another "gosh, gee whiz" book on the amazing and revolutionary (not!) discoveries about the human genome. The title tells you what to expect: The Mysterious World of the Human Genome.
The author is Frank P. Ryan, a physician who was employed as an "Honorary Senior Lecturer" in the Department of Medical Education at the University of Sheffield (UK). He's a member of The Third Way group. You can read more about him at their website: Frank P. Ryan.
Last night's debate between Lawrence Krauss, Stephen Meyer, and Denis Lamoureux was very entertaining. I finally got to meet Stephen Meyer in person. (My photographer wasn't very good at focusing.)
There were some interesting exchanges during the debate. I want to talk about one of them.
Krauss tried to hammer Meyer on the "ID is not science" issue using quotes from a judge based on things said by lawyers in the Dover trial.1 Krauss tried to dismiss ID by saying that it never makes predictions but Meyer countered effectively by pointing out that ID predicts that most of our genome is functional and claiming that the prediction was confirmed by the ENCODE study.
The ID position is that Darwinists predicted that our genome would be full of junk while Intelligent Design Creationists predicted that most of our genome would be functional. ID was correct and Darwinism was wrong, according to this story.
Both Lawrence Krauss and Denis Lamoureux accepted the "fact" that ENCODE was right and most of the DNA in our genome has a function. Krauss was also hampered by his misunderstanding of evolution. It's obvious that he accepts the Richard Dawkins view of evolution so he tried to accommodate the ENCODE results by saying it's what you would expect of natural selection. This is the Richard Dawkins position.
Krauss tried to downplay the issue by saying that ID had not predicted what those functional parts of the genome would be doing but this was a weak rebuttal.
The facts are these ....
"Darwinists"—those who claim that natural selection is the only game in town—were opposed to the idea that most of our genome is junk. They still are.
Today, the majority of experts believe that most of our genome is junk in spite of the ENCODE publicity campaign from 2012.
The ENCODE Consortium has backed off it's original claim and now agrees that they misused the word "function." Some of them blame the media for distorting their position.
The ID "prediction" has been falsified.
A competent biologist would have known all this and could have challenged Meyer's statement. A biologist would have then demanded that Meyer explain how a genome that is 90% junk fits with Intelligent Design Creationism.
I talked to Denis Lamoureux after the debate to let him know that he was wrong about ENCODE and he was very gracious. I promised to send him more information. A genome full of junk DNA poses no threat to his version of Theistic Evolution.
Lawrence Krauss is an expert on cosmology but he's very weak on biology. I know it's common for physicists to think they are experts in everything but that's just not true. It was demonstrated in last night's debate.
1. This is a bad strategy. It's better to accept that ID proponents are doing science but just doing it very badly. Meyer ignored the issue of whether ID counted as science. He just presented the scientific case for ID and forced Krauss to respond to his "evidence."
Today's the day we find out "What's Behind It All?" The decision will be announced at the University of Toronto (Toronto, Ontario, Canada) by Lawrence Krauss when he educates the audience at Convocation Hall starting at 7 pm. Stephen Meyer (Intelligent Design Creationist) and Denis Lamoureux (Theistic Evolution Creationist) will also be there to learn the answer. (Spoiler Alert: the answer is "nothing.")
It's not too late to buy tickets. Email me if you want to join some of us for dinner before the event.
The event is being sponsored by Wycliffe College at the University of Toronto. This is an Anglican College that trains people to become Anglican Ministers (among other things). The college is the prime mover behind this series of events and it deserves a great deal of credit for the effort. Co-sponsors include the Centre for Inquiry, Canada and three Christian groups.
Those on the Darwinist, materialist, atheist side of the debate that we follow here aren't normally very good at listening and responding to scientific perspectives at variance from their own. They are much more interested in condemning and ridiculing -- which has got to be a poor strategy for them if they want to persuade anyone.
With that as the background, as we noted already, it's refreshing that arch-atheist cosmologist Lawrence Krauss has agreed to participate in a public conversation with Discovery Institute's Stephen Meyer, joined by theistic evolutionist Denis Lamoureux. That will be March 19 at the University of Toronto's Convocation Hall. We're looking forward to it -- and here's the even better news. You won't have to be in Toronto to enjoy the discussion. The event will stream live here at Evolution News.
I'm not a fan of TED talks. Comedian Will Stephen has figured them out and he gives a perfect example of everything that's wrong with a TED talk. Watch "How to sound smart in your TEDx Talk."
I was reading up on non-coding RNAs and came across this recent paper.
Bhartiya, D., and Scaria, V. (2016) Genomic variations in non-coding RNAs: Structure, function and regulation. Genomics 107:59-68. [doi: 10.1016/j.ygeno.2016.01.005]
Abstract: The last decade has seen tremendous improvements in the understanding of human variations and their association with human traits and diseases. The availability of high-resolution map of the human transcriptome and the discovery of a large number of non-protein coding RNA genes has created a paradigm shift in the understanding of functional variations in non-coding RNAs. Several groups in recent years have reported functional variations and trait or disease associated variations mapping to non-coding RNAs including microRNAs, small nucleolar RNAs and long non-coding RNAs. The understanding of the functional consequences of variations in non-coding RNAs has been largely restricted by the limitations in understanding the functionalities of the non-coding RNAs. In this short review, we outline the current state-of-the-art of the field with emphasis on providing a conceptual outline as on how variations could modulate changes in the sequence, structure, and thereby the functionality of non-coding RNAs.
The University of Toronto publicity department is making a big deal of Rachel Harding. She's a post-doc in the Structural Genomics Consortium (SGC). She works on Huntington's disease.
Faculty of Medicine researcher Rachel Harding will be the first known biomedical researcher to welcome the world to review her lab notes in real time. The post-doctoral fellow with U of T’s Structural Genomics Consortium (SGC) is also explaining her findings to the general public through her blog. She hopes her open approach will accelerate research into Huntington’s disease.
“This should drive the process faster than working alone,” Harding says. “By sharing my notes, I hope that other scientists will critique my work, collaborate and share data in the early stages of research.” Her research at SGC is funded by CHDI Foundation, a non-profit drug-development organization exclusively dedicated to Huntington’s disease. Both organizations aim to accelerate research by making it open and collaborative.
Her approach is intended to leverage the experience of a community of scientists. Individual researchers often still work in relative isolation and then publish only their positive discoveries, usually years after the experiments were actually done. Thus, scientists often pursue similar ideas in parallel and miss many opportunities to learn from each other’s mistakes.
She has started by publishing raw data and play-by-play details of her first effort on the CERN open digital repository Zenodo. She also posts regular updates on her blog Lab Scribbles, where she includes an experimental summary written in lay terms.
It's been over 35 years since I first starting thinking and talking about electronic (computerized) lab notes1 and it's been over twenty years since I first heard discussions about putting them online. I seriously doubt that Rachel Harding is the first biomedical researcher to put lab notes on the web. I'm also very skeptical about her keeping up the practice for very long.
Not only is it boring and tedious to write your lab notes in a word processing program but it's kinda embarrassing to post everything you do in the lab. At least it would have been for me. I made lots of mistakes and there are lots of R-rated words and phrases in my notes.
Let's keep an eye on this experiments to see how it goes. So far there are four items on the Zenodo website. The first is a Word document containing a few brief notes from Jan. 6, 7, 9, 11 and 25. There are brief notes posted on Feb. 6 and two on Feb. 11. I hope this isn't the extent of her lab notes.
The blog is Lab Scribbles. There are a few posts. It's interesting but I'm not sure anyone is going to read it even if you're interested in Huntington's.
Has anyone else experimented with open lab notes?
1. I still have a few floppy disks with those attempts from about 1981. Unfortunately, I don't have a machine that can read them.
The first drafts of the human genome sequence were published in 2001. There was still work to do on "finishing" the sequence but a lot of the International Human Genome Project (IHGP) team shifted to work on the mouse genome. The FANTOM Consortium and the RIKEN Genome Exploration Groups (I and II) published an analysis of mouse transcripts in December 2002.
Okazaki, Y., Furuno, M., Kasukawa, T., Adachi, J., Bono, H., Kondo, S., Nikaido, I., Osato, N., Saito, R., Suzuki, H. et al. (2002) Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420:563-573. [doi: 10.1038/nature01266]
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 ‘transcriptional units’, contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense–antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.
Postgenomics is a compendium of twelve scholarly articles by philosophers and sociologists who write about the implication of the human genome sequence and subsequent work on interpreting the results. The volume is edited by Sarah Richardson, a professor in Social Sciences (History of Science) at Harvard University (Boston, Massachusetts, USA), and by Hallam Stevens, a professor of History at Nanyang Technology University in Singapore (Singapore).
The first essay is by Stevens and Richardson and it outlines the goal of the book.
One of the biggest problems with the Intelligent Design Creationist movement is their attempt to corral all creationist under the same big tent. This leads to a situation where Young Earth Creationists are afforded the same level of respect as those who accept common descent and an ancient Earth.
It means that dissent within the ID community is strongly suppressed in order to maintain the illusion that they all agree on the basics (i.e. goddidit). This leads to ridiculous situations where Young Earth Creationists defend Stephen Meyer's attack on the Cambrian explosion in Darwin's Doubt when they don't even believe that the Earth is 500 million years old!
There's no consistency in the arguments from ID proponents so it's almost impossible to have a serious discussion of the science behind their claims. I've criticized ID proponents for not applying critical thinking to their own movement. They almost never dispute each other's ideas for fear that it would weaken their movement.
That fear is justified, but what they fail to realize is that the movement doesn't deserve any respect at all if they don't apply the same standards to their own views that they demand of others.
To their credit, a few members of the movement have started to change this long-standing attempt to silence dissent within the movement. I think they realize that the respect they crave will only come from kicking a few people out of the tent.
One of those people is Vincent Torley. He has posted an excellent discussion of Denton's structuralist views on Uncommon Descent: Denton vs. Moran on structuralism. I don't agree with everything Torley says but I congratulate him for his courage in thinking critically about Michael Denton's position.
It will be interesting to see if the Intelligent Design Creationist movement can deal with critical thinking. I'm watching the comments on the blog post.
Here's a video where Michael Denton describes his view of biology. The main point is that he cannot think of a way for evolution to produce the "hierarchy of nature." Therefore goddidit there must be some other explanation.
Darwinism, honestly regarded, should lead you to expect not an ordered, increasingly inclusive hierarchy of life but more like a disordered...smear of diversity. Such expectations are frustrated by reality. As biologist Michael Denton explains, life presents itself as a tiered formation marked by novelties or homologs. These taxa-defining novelties, such as the pentadactyl limb, are not lead up to by a series of forms increasingly like the final version.
That's strike one. Worse for Darwinism, it's typically the case that there is no way even to imagine how the novelty could be lead up to in such a manner. Strike two. Watch and enjoy.
Has a scientific explaination of the universe replaced the need for God as cause of its origins? Could life on our planet exist apart from divine intervention? Is there evidence for a designer?
On March 19th, three big thinkers, well-known in their various fields, will be together for the first time, on the stage at the University of Toronto’s Convocation Hall discussing God, science and the universe:
Lawrence M. Krauss World-renowned Theoretical Physicist
Stephen C. Meyer Cambridge educated author and intelligent design advocate
Denis O. Lamoureux Science and Religion professor from the University of Alberta
Questions like these will be posed to the panel:
How did the universe originate?
Does God play any role in the cosmos?
What is the relationship between science and religion?
You are invited to live-stream this event via YouTube at your venue free of charge. Once you register as an event host, Wycliffe College and our partners will be happy to provide you with promotional and follow-up material to help make your event a success.
As evidenced by our sponsors, this is an opportunity that spans the diverse interests and questions of the scientist, the scholar, the layperson, the young and the old, and the Atheist, Agnostic and Christian. Our goal is to be a catalyst in starting conversations around our country on issues of faith and their intersection with broader society.
Join thousands in Toronto and around the globe to take part in this rare and exciting opportunity.
Most of you are familiar with the long-term evolution experiment (LTEE) run by Richard Lenski. One of the cultures in that experiment evolved the ability to use citrate as a carbon source. Normally, E. coli cannot use this carbon source under aerobic conditions but the new strain not only utilizes citrate but can grow in cultures where citrate is the only source of organic carbon.
A large statue of Charles Darwin was installed in the main foyer of the London's Natural History Museum in 1885—just a few years after Darwin's death. It was removed in 1927 and replaced by a statue of Richard Owen who was no fan of Darwin.
The museum came to its senses in 2009 and put the statue back in it's original position. (It had been in the cafeteria in the basement.) Read the story at: Moving Darwin.
Owen was the man who founded the museum and he was also known for his support of structuralism—the idea that basic body plans cannot be easily explained by evolution. Structuralism is the new buzzword among Intelligent Design Creationists. They don't understand the concept but they're certain it refutes evolution and supports goddidit.
Watch Paul Nelson combine his lack of knowledge of evolution and evolutionary theory with misinformation (i.e. lies) and a little bit of false developmental biology then stir the pot with a large dose of god-of-the-gaps to produce a smooth argument that refutes evolution.
There's lots of other stuff going on in this talk. I was especially amused by the discussion of methodological naturalism at the end. Paul Nelson argues that science is blind to all the evidence of a creator because the "rule" of science is that it can't even consider that evidence.
I'll say one thing about this talk: it's very clever. It would take a book to show that Paul Nelson is wrong about everything and the explanations would be far too complicated for the average creationist. For them, it's easier to believe that Paul Nelson is telling them the truth and evolutionary biologists are too stupid to understand their own discipline.
Otangelo Grasso has posted a transcript of the talk. Thank-you Otangelo.
The draft sequences of the human genome were published fifteen years ago. The International Human Genome Project (IGHP) published its draft sequence in Nature on Feb. 15, 2001 (Lander et al., 2001) and Celera Genomics published its draft sequence in Science on Feb. 16, 2001 (Venter et al., 2001).1
For me the timing was perfect since I was scheduled to give a Journal Club talk on March 16th and you could hardly ask for a better topic.
Antonin Gregory Scalia (March 11, 1936 – February 13, 2016), justice of the Supreme Court of the United States, died a few days ago. This creates a crisis in American politics because they have a strange set of Constitutional requirements guaranteed to maximize the probability of crises every time they need a new Supreme Court justice.
Scalia's death reminded me of the dissenting opinion in EDWARDS V. AGUILLARD (June 19, 1987). This was the case that invalidated Louisiana's "Balanced Treatment for Creation-Science and Evolution-Science Act." Stephen Jay Gould was puzzled by the dissenting opinion so he wrote a wonderful essay to explain Justice Scalia's Misunderstanding.
It's worth reading the entire essay but here's the conclusion,
Following this theme, Scalia presents his most confused statement in the written dissent:
Creation science, its proponents insist, no more must explain whence life came than evolution must explain whence came the inanimate materials from which it says life evolved. But even if that were not so, to posit a past creator is not to posit the eternal and personal God who is the object of religious veneration.
True indeed; one might be a creationist in some vernacular sense by maintaining a highly abstract and impersonal view of the creator. But Aristotle's unmoved mover is no more part of science than the Lord of Genesis. Science does not deal with questions of ultimate origins. We would object just as strongly if the Aristotelophiles of Delaware forced a law through the state legislature requiring that creation of each species ex nihilo by an unmoved mover be presented every time evolution is discussed in class. The difference is only historical circumstance, not the logic of argument The unmoved mover doesn't pack much political punch; fundamentalism ranks among our most potent irrationalisms.
Consider also, indeed especially, Scalia's false concept of science. He equates creation and evolution because creationists can't explain life's beginning, while evolutionists can't resolve the ultimate origin of the inorganic components that later aggregated to life. But this inability is the very heart of creationist logic and the central reason why their doctrine is not science, while science's inability to specify the ultimate origin of matter is irrelevant because we are not trying to do any such thing. We know that we can't, and we do not even consider such a question as part of science.
We understand Hutton's wisdom. We do not search for unattainable ultimates.
We define evolution, using Darwin's phrase, as "descent with modification" from prior living things. Our documentation of life's evolutionary tree records one of science's greatest triumphs, a profoundly liberating discovery on the oldest maxim that truth can make us free. We have made this discovery by recognizing what can be answered and what must be left alone. If Justice Scalia heeded our definitions and our practices, he would understand why creationism cannot qualify as science. He would also, by the way, sense the excitement of evolution and its evidence; no person of substance could be unmoved by something so interesting. Only Aristotle's creator may be so impassive.
Who was Saint Valentine? Nobody really knows very much about the Saints Valentine (there were about a dozen of them). The whole idea of romantic Valentine's day seems to have been invented by Geoffrey Chaucer1 sometime around 1380.
It seems like people in England just wanted to enjoy a bit of debauchery fun on February 14th so they connected their frolics with a Roman Catholic saint in order to get the permission of the church! Pretty clever, eh?
Readers of this blog will know that I'm a fan of Evolution by Accident. I don't think that the history of life can be explained in strict Darwinian terms (i.e. natural selection) and I think that modern evolutionary theory includes Neutral Theory and a major role for random genetic drift.
This is the view of many modern evolutionary biologists. Their work and views have been reported frequently on Sandwalk over the past ten years but you can find it in all the evolutionary biology textbooks. I'm just the messenger here. It's evolutionary biologists who have made the case for non-adaptive evolution beginning long before The Spandrels of San Marco and the Panglossian Paradigm: A Critique of the Adaptationist Programme.
This is another post about the stupidity of Intelligent Design Creationists. Stop reading if you don't need any more convincing.
Today is Darwin Day. It's the anniversary of the birth of Charles Darwin (Feb. 12, 1809 - April 19, 1882).
This is not a happy day for the Discovery Institute so they've put up a series of posts on Evolution News & Views (sic) to discredit Darwin and "Darwinism."
To understand the core weakness of the Darwinian worldview, it is important to understand what Darwinian natural selection requires. The process will work its magic, building up functional structures in organisms, only when two very strict conditions are met: First, the structure must be adaptive—that is, helpful to the organism in flourishing in its environment—and second, there must be a continuum of structures, functional all along the way, leading from an ancestor species to the descendent.
That is, the thing we are trying to explain must in some way help the creature survive, and between the creature and the creature's ancestor there must be a gradual change, each step of which is stable and enhances fitness, or success in reproduction.
Strictly speaking, that's a reasonable explanation of Darwinism as most evolutionary biologists understand it. But here's the problem. There aren't very many evolutionary biologists who are strict Darwinists these days even though there are many who tilt strongly in that direction.
Intelligent Design Creationists are promoting a structuralist view of evolution [What is structuralism?]. The idea is that the history of life as we know it was largely preordained by the initial laws of physics and chemistry. According to this view, once life got under way it was inevitable that it would eventually evolve the way it did resulting in humans or something that closely resembles humans.
Structuralism is based on the idea of intrinsic forms that severely limit evolutionary pathways. These forms are constrained, and defined, by the physics of matter and energy. Some creationists like this idea because they believe that god created the universe and fine-tuned it for life. According to their faith, once the original laws of physics and chemistry were set up it was just a matter of time before humans evolved. These creationists can make their belief in a creator god compatible with evolution as they see it.
(Let's not forget that there are many structuralists who are legitimate scientists and some of them are atheists. Structuralism is not a creationist invention.)
The conflict between structuralists and others is brought into focus by Stephen Jay Gould writing in Wonderful Life.
The blog "Conceptual Revolutions in Science" only publishes "evidence-based, paradigm-shifting scientific news" according to their home page.
The man behind the website is Adam B. Dorfman (@DorfmanAdam). He has an MBA from my university and he currently works at a software company. Here's how he describes himself on the website.
Some of you are aware of recent attacks on Richard Dawkins. This video by Brian Dalton (Mr. Deity)1 is directed at certain people who have led the attacks. Some of them are my friends but I'm having second thoughts. They should pay close attention.
I disagree with several scientific ideas that Richard Dawkins has promoted and we have discussed these disagreements in person and on the internet. I've always found him to be polite and respectful.
Michael Denton and the Discovery Institute are promoting his new book, Evolution: Still a Theory in Crisis. I haven't yet read the book. I ordered from Amazon.ca and I won't get it until March.
The essence of the fine-tuning argument is that the basic laws of physics and chemistry are so precise that even slight changes would result in a universe where life is impossible. The focus is usually on the fundamental constants such as the speed of light and the charge on an electron. I don't know enough about physics to evaluate the argument that these are fine-tuned so I have to rely on physicists to inform me.
All available evidence suggests that we are quite likely the only advanced life form in the Milky Way galaxy. Maybe our planet harbors the only life in the entire universe.
Matthew Cobb wasn't happy with the way Denis Alexander reviewed Jerry Coyne's book. Recall that Denis Alexander is a biochemist at Cambridge University (UK) and we had a little debate a week or so ago [Is there a conflict between science and religion?]. His position is that there's no conflict between science and religion because a person who believes in god can always make their views conform to the discoveries of science. I didn't accept his premise—that gods exist—so we had a discussion about whether there's any evidence to support his belief in god.
If you believe in such a being then that conflicts with science as a way of knowing because you are believing in something without reliable evidence to support your belief. Scientists shouldn't do that and neither should any others who practice the scientific way of knowing. Denis Alexander thinks there are other, equally valid, ways of knowing but he wasn't able to offer any evidence that those other ways produce true knowledge.
Matthew Cob wrote a letter to the editor in which he asked, "I wonder if Dr Alexander, or indeed any reader, could provide an example of knowledge gained through theology, and above all tell us how they know that knowledge is true?" [see Matthew Cobb battles with the faithful over my book].
Jerry Coyne discovered a Quiz on DNA. He calls is a so-so quiz on DNA. He says that one question is really, really, dumb. I disagree, I think there are several dumb questions.
I tried it and got a score of 19/19 in just under four minutes. This is misleading since you have to get every question right before continuing on to the next question. I had to anticipate what the authors wanted in order to proceed.
Try the quiz yourself before reading any further. There are spoilers below!
The Intelligent Design Creationists are promoting Michael Denton's new book Evolution: Still a Theory in Crisis. The new buzzword is "structuralism" and it's guaranteed to impress the creationist crowd because nobody understands what it means but it sounds very "sciency" and philosophical. Also, it's an attack on "Darwinism" and anything that refutes evolution has to be good.
You can watch Michael Denton explain structuralism ... it only takes a few minutes of your time.
You are probably wondering why "Darwinism" persists after the creationists have thoroughly demonstrated that it is a failed theory. Lucky for you, the most intelligent and intellectual of all Intelligent Design Creationists, David Berlinski and Michael Denton, have gotten together to explain it in a short (15 mins) podcast.
If the most brilliant Darwin critics, like David Berlinski and Michael Denton, are right, how then does Darwinism hang on? How does a failed theory maintain its grip on our science and on our culture? Why is there a sense of stalemate? On ID the Future, we posed these questions to Dr. Berlinski and Dr. Denton.
If you are interested in the conflict between Intelligent Design and science you owe it to yourself to see/hear the best they've got on their side.
You can always dream. While the evolutionist side in the Darwin debate is long on rhetoric and insults, serious debate or dialogue is woefully rare. But imagine you had the opportunity to sit down with a thoughtful, honest, well-informed Darwinist and pose one question or challenge. What would it be?
I had the opportunity to pose that question to two of the most brilliant minds in the intelligent design community -- Michael Denton and David Berlinski. Take a well-spent 15 minutes and listen to their answers -- focusing respectively on the insect body plan and the enigma of whale evolution -- recorded as an episode of ID the Future.
Berlinski wants a detailed mathematical estimate of the number of mutations required to go from a land animal to a whale. Denton wants details on the formation of insect body plans.
It's important to note that these are questions about the history of life. You could easily answer "I don't know" to both questions and it would not affect our understanding of evolution and common descent one iota. The answers have nothing to do with "Darwinism" per se and nothing to do with evolutionary theory (which is not Darwinism).
Listen to the very best minds in the Intelligent Design Creationist community ... and weep for them. This is all they've got.
Richard Dawkins published The Selfish Gene 40 years ago and Matt Ridley notes the anniversary in a Nature article published today (Jan. 28, 2016): In retrospect: The selfish gene.
I don't remember when I first read it—probably the following year when the paperback version came out. I found it quite interesting but I was a bit put off by the emphasis on adaptation (taken from George Williams) and the idea of inclusive fitness (from W.D. Hamilton). I also didn't much like the distinction between vehicles and replicators and the idea that it was the gene, not the individual, that was the unit of selection ("selection" not "evolution").
It is finally time to return to the problem with which we started, to the tension between individual organism and gene as rival candidates for the central role in natural selection...One way of sorting this whole matter out is to use the terms ‘replicator’ and ‘vehicle’. The fundamental units of natural selection, the basic things that survive or fail to survive, that form lineages of identical copies with occasional random mutations, are called replicators. DNA molecules are replicators. They generally, for reasons that we shall come to, gang together into large communal survival machines or ‘vehicles’.
Currently there are two distinct views on the origin of life. The majority of scientists think that life arose in a prebiotic soup of complex organic molecules. Most of them think this "warm little pond" was the ocean (!) and most of them have bought into the stories about asteroids and comets delivering complex organic molecules to create a soup of amino acids and sugars. Presumably, all the earliest forms of life had to do was to join together the amino acids to make proteins and hook up the nucleotides to make RNA. The energy for these reactions was derived from breaking down all the glucose in the sweet ocean.
James McGrath is a professor of religion at Butler University in Indianapolis, Indiana, USA.
He is one of those "sophisticated theologians" who dismiss modern atheists because we haven't spent years studying theology and because we haven't experienced the true existential angst of Jean-Paul Sartre. As a group, they hold to the position that the "New Atheists" are amateurs in the study of religion and their arguments can be easily dismissed.
Back in 2010, Richard Dawkins was answering questions on Reddit and one of the questions was "Out of all the evidence used to support the theory of evolution, what would you say is the strongest, most irrefutable single piece of evidence in support of the theory."
There are several ways to answer this question. Personally, I would take a minute to explain the difference between the "theory of evolution" and the history of life. I would point out that evolutionary theory includes things like Darwin's natural selection and there is overwhelming evidence proving that natural selection exists and operates today. The entire field of population genetics, which included other mechanisms of evolution such as random genetic drift, is massively supported by thousands of published papers in the scientific literature. There is absolutely no doubt at all that the current basic tenets of evolutionary theory are correct.
Confirmation bias is one of the major logical fallacies. When philosopher Chris DiCarlo and I were teaching a course on critical thinking we used to spend quite a bit of time on it because it's a very common trap. We are all guilty, from time to time, of focusing on just the evidence that confirms our belief and ignoring all the evidence that refutes it.
Some examples of confirmation bias are a bit more complicated than others and people typically mix together several different fallacious forms of argument. Here's an example from Denis Alexander's book Creation or Evolution (p. 213) that combines begging the question and confirmation bias.
Denis Alexander is a biochemist at the University of Cambridge (UK). I thought I'd share one of the stories in his book.
At the church I attend in Cambridge we baptised an undergraduate in the natural sciences who had come to a personal, saving faith in Christ from a completely atheistic background. As is usual in our church, just before being baptised she explained publicly to the whole congregation how she had become a Christian, telling us she had become convinced there must be a God while sitting through a standard biochemistry lecture, hearing the amazing story of how two meters (about six feet) of DNA are packaged into a single cell. Of course the lecturer was not talking in religious terms at all, but she described to us how the beauty of that engineering feat overwhelmed her as she listened, giving her the deep intuition there must be a God, so leading her onward in he personal pilgrimage to put her trust in this creator God through Christ. Truly natural theology at work!
That got me thinking. I've been describing chromatin and packing in my textbooks since the first version in 1987. There must have been several hundred thousand students who have read my descriptions since then.
The post is from Dec. 1, 2015—that's only one month ago so she should be aware of all the facts concerning junk DNA.
If you are going to write about a subject in your area of expertise then it's reasonable to make yourself informed, especially if you know that the subject is controversial. For some strange reason, this common sense approach seems to be ignored when discussing genomes, evolution, and junk DNA. I don't know why some researchers think they know enough about a subject when all they've done (apparently) is read a few popular press reports.
Let's look at what Bryony Graham (@byrony_g) writes to see whether she is behaving like a proper scientist should behave when writing for the general public. It's worth noting that she was on the shortlist for the 2011 Max Perutz Science Writing Award so somebody must think she's a good science writer.
The sequence of the human genome was announced on June 26, 2000 although the actual sequence wasn't published until a year later. There were two sequences. One was the product of the International Human Genome Project led by Francis Collins who said,
"It is humbling for me and awe-inspiring to realize that we have caught the first glimpse of our own instruction book, previously known only to God."
The sequence was a composite of a number of individuals.
The second sequence was from Celera Genomics, led by Craig Venter. It was mostly his genome, making him the second being to know his own instruction book ... right after God.
It took another seven years to finish and publish the complete sequence of all of Craig Venter's chromosomes. The paper was published in PLoS Biology (Levy et al., 2007) and highlighted in a Nature News article: All about Craig: the first 'full' genome sequence.
What's unique about this genome sequence—other than the fact that it's God's Craig Venter's—is that all 46 chromosomes were sequenced. In other words, enough data was generated to put together separate sequences of each pair of chromosomes. That produces some interesting data.
There were 4.1 million differences between homologous chromosomes (22 autosomes). 78% of these events were single nucleotide polymorphisms (SNPs). The rest were indels (insertions and deletions) and these accounted for 0.9 million nucleotides. Thus, indels made up 74% of the total number of variant nucleotide sequence.
In addition, there were 62 copy number variants (duplication) accounting for an additional 10Mb of variation between haploid sets of chromosomes. The total number of nucleotide differences is 13.9Mb when you add up all the indels, SNPs, and duplications. The two haploid genomes differ by about 0.5% by this calculation (total amount sequenced was 2,895Mb).
When the two copies of all annotated genes were compared, it turned out that 44% were heterozygous—the two copies were not identical.
Craig Venter's genome sequence differs from the composite human reference genome at 4,118,889 positions. Most of these were already known as variants in the human population but 31% were new variants (in 2007).
Venter has written about his genome sequence in A Life Decoded. He has variants in his APOE gene sequence that are associated with Alzheimer's and cardiovascular diseases. He has variants in his SORL1 that also make him at risk for Alzheimer's according to 2007 data. Just about everyone who gets their genomes sequenced will find variants that put them at greater risk for some genetic disease.
Massimo Pigliucci is an atheist who thinks that science and religion are compatible because they rule in different domains. He takes a very narrow view of "science"— one that excludes the work of historians and philosophers who are presumably using some other way of knowing. (He doesn't tell us what that is.)
I prefer the broad view of science as a way of knowing that relies on evidence, rational thinking, and healthy skepticism. This broad view of science is not universal—but it's not uncommon. In fact, Alan Sokel has defended this view of Massimo Pigiucci's own blog: [What is science and why should we care? — Part III]. According to this view, any attempt to gain knowledge should employ the scientific worldview. Historian and philosophers should follow this path if they hope to be successful. Pigliucci should know that there are different definitions and any discussion of the compatibility of science and religion must take these differences into account.
We know quite a lot about the origin of new genes (Carvunis et al., 2012; Kaessman, 2010; Long et al., 2003; Long et al., 2013; Näsvall et al., 2012); Neme and Tautz, 2013; Schlötterer, 2015; Tautz and Domazet-Lošo (2011); Wu et al., 2011). Most of them are derived from gene duplication events and subsequent divergence. A smaller number are formed de novo from sequences that were not part of a gene in the ancestral species.
In spite of what you might have read in the popular literature, there are not a large number of newly formed genes in most species. Genes that appear to be unique to a single species are called "orphan" genes. When a genome is first sequenced there will always be a large number of potential orphan genes because the gene prediction software tilts toward false positives in order to minimize false negatives. Further investigation and annotation reduces the number of potential genes.
