The details behind the story of how bacteria mutated in order to grow bigger and better by eating oranges, instead of sugar. Last week, we talked to a member of the Long-Term Evolution Experiment, Dr. Zachary Blount. He and his colleagues followed 75,000 generations of bacteria competing for a limited food resource — sugar — and described many different kinds of genetic changes in 57 different genes. Creationists and ID-proponents dismiss this as “simply breaking genes.” In this episode, we take a very deep-dive into the story, and show how this is actually a prime example of evolution proceeding through gene duplication, progressive modifications, and the building up of new regulatory pathways and metabolic functions. How it is that well educated anti-evolutionists, especially the biochemists among them, can only see this as destructive and detrimental either says something about them being biased and misled … or deceptive!? Before we asked Zach to give us the details, we provided some background introductory information: evolution often involves duplication of stretches of DNA, followed by modifications which eventually lead to new functions, while leaving the original copy intact. This is NOT “breaking the gene” we give a crash course on how bacteria extract energy from glucose (see the color image attached below) evolution often happens in three steps: (1) prepare for new function (or “potentiation”) – changes occur which by themselves don’t appear to affect function, but they set the stage for something else (2) get the new function (or “actualization” or “instantiation” – the “something else” suddenly appears as a new function, although usually in a very weak and inefficient form (3) refine the new function – tweaking and optimization Bacterial metabolism of glucose through biochemical conversions (buckets) involving other molecules such as acetate, citrate, and succinate, producing energy molecules (the green “E”s in the figure). A potentiating mutation (#1, highlighted in pink) allows acetate to escape the process, thus accelerating the flow of glucose through the top half). An actualizing mutation (#2, highlighted in yellow) allows the OCEAN of citrate that the bugs are swimming in to now flow into the process, making it possible to grow on citrate in the presence of oxygen when glucose levels drop. [nb: this chart simplifies the story to the point of being inaccurate, but at least a non-expert can follow it!]] With that introduction in place, we then got deep into the details of this story: after 30,000 generations and 16 years, mutant cells had gained the ability to grow on citrate in the presence of oxygen (something that their non-mutated cousins couldn’t do) although the LTEE had found many other mutations that occurred in all 12 test-tubes, this one new function only happened in one of the 12 [and this is still true even today!]; this raises raises big questions regarding evolution, and became Zach’s research project (had to test 44 trillion cells to get some of the answers!!!) they went back to their “Frozen Fossil Record” (see last week’s post), and learned that mutations happened a year prior which weren’t detectable because the advantage was miniscule. BUT IT WAS THERE!  And it could then be refined (which it did by 33,000 generations) some changes enabled the bugs to take up much larger amounts of glucose, but at the “expense” of pooping out acetate, which later became a new food source through a new loophole that connected to citrate other changes that “Potentiated” … set the stage to use citrate as a food source the “Actualization” step was a duplication of a citrate transporter gene that was put under the regulation of glucose levels (the original copy was left in place and still regulated by oxygen levels … in other words, NOT BROKEN!!); now citrate uptake and metabolism can happen when glucose runs out! Like the Energizer Bunny, these mutant bugs now just keep on going when their non-mutated cousins are slowing down and dying ID-proponents, especially their biochemists, should be able to see this as an increase in function, information and complexity, but they PERSIST in dismissing this as “just breaking genes” or asking ignorant questions like: “did they see any examples of entirely new nanomachines?” (again, see last week’s episode) Contrary to the Creationist party line, this is precisely an example of small changes which accumulate and eventually become a new function. Evolution may be “clever” and innovative, but often it won’t be elegant; we talked about bizarre and inelegant designs like the anatomy of the recurrent laryngeal nerve, or the biochemistry of a photosynthetic enzyme in plants called rubisco; in the same way, this new re-design of citrate metabolism is also a “clunky” design, but it lets these mutants grow and thrive while their non-mutant cousins go extinct the new citrate-using bugs at generation 75,000 are growing better and better on the citrate/succinate microenvironment they’re creating (niche creation), but at the same time, are getting worse at growing on glucose (their ancestral resource). They are becoming a new species … becoming ecologically specialized! As always, tell us your thoughts on this topic … Find more information about our guest, Dr. Zachary Blount at his university profile page and his own lab’s web-site. Learn more about the LTEE itself, including descriptions of the team members and lists of their publications, at their webpage. You can also watch a video in which Dr. Blount regales Dr. Richard Lenski on the latter’s 60th birthday, and recounts the whole history of the LTEE. If you enjoyed this episode, you may also like the mini-series of episodes we did focusing on Intelligent Design and its misrepresentation of science. Episode image by Andrew Kirkham. Thanks Andrew! To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

Two very different interpretations of the same set of data: one from Creationists and ID proponents, and the other from the scientists actually doing the work. Here, we talk to one of the latter. A frequent talking point for creationists and Intelligent Design proponents in their anti-evolution rhetoric is a ground-breaking scientific project referred to as “the Long-Term Evolution Experiment.” Almost forty years ago, Dr. Richard Lenski began studying bacteria competing for limited energy resources (sugars) — generation after generation — looking for any genetic changes which gave any kind of advantage in that competition. His group have recently reached 76,000 generations, and documented many dozens of genetic mutations: rearrangements of regulatory pathways, elimination of genes which were no longer needed, introduction of new metabolic functions, shuffling of genetic information. In the process, there has been an incredible increase in fitness. This is much like someone deciding to train for a marathon — losing layers of fat, toning up muscles, revising their diet, replacing their normal wardrobe with ultra-light clothes and expensive runners, shaving seconds off of their run-time, increasing their stamina — and in the process, becoming a lean, mean running machine. Nonetheless, creationists and ID proponents persist in diminishing the LTEE findings to just “breaking genes” and losing information. After a brief introduction to the LTEE and the primary variables that they were monitoring (oxygen; fuel sources), we then talked to Dr. Zachary Blount, a member of the LTEE team who is continuing and broadening that research program, building on the findings and strategies of the LTEE. Points that we discussed included: the history of the LTEE: its founder, leaders, goals, and basic methodology twelve different “test tubes” of populations were kept separate, in order to see how the ancestral populations might try different evolutionary strategies they’ve now reached 76,000 generations; every 500 generations, they’ve frozen samples of the bugs so they can do follow-up experiments and/or recover from technical mistakes without having to start all over at the beginning …. they refer to this collection of samples as their “frozen fossil record” aerobic versus anaerobic metabolism (meaning with versus without oxygen) of glucose and another fuel source called citrate why did the experimenters add citrate to the medium in the first place? years later, the cells suddenly acquired a new ability to grow on the citrate in the presence of oxygen, something that their original bacterial ancestors were unable to do exactly how/why does metabolism of citrate change in the presence/absence of oxygen what were the “stressors” being imposed on the cells … answer: no “stress” or “stressor,” but rather simple competition for limited resources (fuel sources) what were the original goals of the LTEE project? the “randomness” of genetic variation mutations are not just simply individual “point-changes” in the base sequence of the DNA base, or individual amino-acids in the whole protein sequence; they can also include movements/insertions/deletions of whole segments of the DNA (thousands of bases at a time), duplication of large segments, and other forms of gene rearrangements the 12 separate populations of the ancestral bugs mutated in different directions and in somewhat different ways, but often landed on the same gene targets (although changing those genes in different ways) the mutated cells are much larger than the original ancestor (the researchers had expected a progressive reduction in size) the LTEE team found 57 different genetic changes …. and these were NOT simply just “breaking genes” or losing information, as creationists and ID proponents will so often say Dr. Blount then got into a very detailed and technical description of the whole citrate story, which is the one detail that creationists and ID proponents will particularly dwell upon, but we’re saving that part of the conversation for next week Scott and Luke then reflected a bit on what Zachary told us so far, and how that relates to the on-going discussion going on between creationists and anti-evolutionists: how it’s okay to be skeptical about scientific claims … to ask questions, and put the claims to the test … this is part of the Scientific Method and something that scientists do all the time; however, once those follow-up questions and tests have been answered and the claim still stands, a good and unbiased scientist accepts the claim and moves on. But creationists and ID proponents keep circling around the same inaccurate counterarguments the LTEE’s finding that 12 different populations set out on 12 different evolutionary journeys and yet often arrived at similar endpoints sounds an awful lot like life’s common ancestor spreading out to several different geographically isolated parts of the globe, exploring different evolutionary pathways and often coming up with very similar and yet fundamentally different answers (comparisons between mammals and marsupials were the specific example here) once again, the frustrating tendency of creationists and ID proponents to focus on just “breaking genes” and degradation of information; cells have a genetic toolkit which enables them to shuffle parts of genes or whole sections of DNA around; perhaps the best and most complicated example of this genetic shuffling is our immune system some might think that an evolutionary advantage of “only a couple percent” is too small to realistically provide a driving force on evolution; however, say that to an athlete who’s just trying to shave a few seconds off of an event that lasts minutes or hours … or to an investor who’s comparing stocks that make either 4% or 6% gains, or the manager’s expense fees being raised to 3% from 2.5% Luke’s intense frustration with the leaders and scholars of creationist and Intelligent Design worldviews, who are educated and smart enough to understand the science here, but who persist in misrepresenting and distorting that science (possibly intentionally so!?) As always, tell us your thoughts on this topic … Find more information about our guest, Dr. Zachary Blount at his university profile page and his own lab’s web-site. Learn more about the LTEE itself, including descriptions of the team members and lists of their publications, at their webpage. You can also watch a video in which Dr. Blount regales Dr. Richard Lenski on the latter’s 60th birthday, and recounts the whole history of the LTEE. If you enjoyed this episode, you may also like the mini-series of episodes we did focusing on Intelligent Design and its misrepresentation of science. Episode image by WikiImages from Pixabay. To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

Dr. Janet Kellogg Ray, a deeply Evangelical believer and state college professor, has long been speaking to and educating Evangelicals about their science denial Unfortunately, science denial and pseudoscience run rampant in Evangelical circles. In our previous episodes, we’ve learned about the exceptionally strong correlations between being Evangelical and: … being against COVID protection measures (vaxing, masking, social distancing) … being against evolution (particularly so about human evolution) … denying climate change … accepting the Sunday School version of the Noah’s Ark story as historical … and otherwise disagreeing on several other points which many others take for granted. Our guest today — Dr. Janet Kellogg Ray — has been teaching, speaking and writing to Evangelicals for decades about this science denial. Here, we talk about her latest book coming out next week from Eerdmans: The God of Monkey Science: People of Faith in a Modern Scientific World. Points that we covered include: science denial and pseudoscience run rampant in Evangelical circles phylogeny (creating a “family tree”) of anti-evolution arguments shows how their arguments gradually evolve, and also how Evangelicals will use the “play-book” for their anti-evolution campaign (e.g., the Scopes Monkey Trial) in their war against COVID policies, or climate change, or vaccines, or …… her first book, Baby Dinosaurs on The Ark: the mental and theological gymnastics involved in explaining or rationalizing the Noah’s Ark story, and a comment made by a Young Earther in a discussion forum about the logistical hurdles in floating that boat: “let’s not get caught up with logic when dealing with faith,” which is a perfect example of one of the things that Mark A Noll wrote about in Scandal of the Evangelical Mind. Evangelicals and Evangelicalism have become not only anti-science but also anti-intellectual, as seen in their rejection of whole categories of art, music, philosophy the Galileo Affair didn’t have the impact that the “Scopes Monkey Trial” did. Why? Biblical Criticism (introduced by Julius Wellhausenin the mid-19th century) crystalized a response in Evangelicals against science and intellectualism, leading to an embrace of Biblical inerrancy and infallibility the birth of the new Young Earth Creationism — Intelligent Design — which was presented as an “alternative science” Evolution Theory became a target for Evangelicals, who saw it as the source of all social evils (abortion; homosexuality; rape; murder; etc) science became the front in a culture war … anti-COVID measures were seen as an assault on religious rights and Christianity itself the creation of an education bubble …. Evangelicals set up their own elementary, secondary, and post-secondary institutions, and poured themselves into home schooling; also set up their own publishing houses and music industry. Answers-in-Genesis and Institute for Creation Research even warn parents not to send their kids to certain Christian schools (the ones that are friendly towards evolution teaching). This leads to intellectual and cultural siloing and cloistering. America has a very broad Evangelical demographic, including “Evangelicals” who don’t attend church Evangelicals have learned to approach/do science with pre-existing assumptions, leading to all forms of pseudoscience (ivermectin; hydroxychloroquin; Young Earth Creationism; Flood geology; Intelligent Design) because secular scientists can’t be trusted (“they’re in on it”). Evangelicals lose the ability to discern between an expert and an authority. A celebrity, athlete, family doctor or pastor can substitute for nationally and globally recognized scientists (Francis Collins), doctors (Anthony Fauci) and institutions (national and global medical boards). The YEC film Is Genesis history? features individuals with scientific degrees who defend views and interpretations completely opposite to those held by a large majority of their peers. Our previous episodes featured ID “experts” who don’t actually work in the scientific fields on which they speak, contradicting scientific experts who do work in those fields. people feel empowered by the internet to be their own experts (“doing the homework”; “following the data to where it leads”) the damage done by denying science and denigrating scientists … Evangelicals can no longer discriminate between authorities versus experts, or recognize when someone is speaking with or without expertise cherry-picking, misapplying and misquoting Scripture in defense of bizarre scientific claims the exponential development of the apologetic industry, making the Bible speak to science, and vice versa, sometimes in order to prove the existence of God science is trying to exorcise itself of teleological language (talking about Evolution as if it had agency, and intention/purpose). Intelligent Design tries to re-insert teleology back into science Dr. Ray teaches at a state [secular] university and is open about evolution: Christian students sometimes feel threatened by her (in their minds, she becomes the Hollywood-ized professor whose goal is to kill their faith). She has had to develop strategies to best teach evolution as well as a healthy Christian response/attitude to it. the damage/costs of an anti-science bubble: opportunity costs (esp. with respect to employment) and health risks (vaccines; transfusions; mental health; sex education; prolongation of the COVID epidemic because of anti-vaxers). That bubble can also actually predispose young people towards losing their faith (they’re not able to deal with the contrary evidence). does evolution have any impact on ones ability to do medicine? ….. or to do research? pro-evolution Christians need to involve themselves in confronting science denial …. get in the conversation (otherwise, you remove self from the conversation) … become relevant. As always, tell us your thoughts on this topic … Find out more about Dr. Janet Kellogg Ray and her books at her profile page at Eerdmans Publishing, or at her FaceBook page. If you enjoyed this episode, you may also like our mini-series of episodes on: Young Earth Creationism (9 episodes) Intelligent Design (8 episodes) Evangelicalism (10 episodes) a Christian response to Evolution (11 episodes) or maybe individual episodes on science denial (#27), COVID-denial and pseudoscience (#61), the Evangelical response to science (#24), a prominent social influencer whose faith was destroyed by YECism, aka “Paulogia” (#25), or another one whose faith was ruined by working for Answers-in-Genesis (#31). To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

After a seven-episode deep-dive into Intelligent Design, we finally arrive at our better informed opinion of our position on this worldview. We started this 7-part mini-series introducing the Intelligent Design proposal that many creationists hold, and also shared our position at the outset on it: at that time, we were not convinced, feeling like we should embrace it but still a bit skeptical, and not really knowing what to do. It took seven episodes — three in which we gave you, the non-expert, some conceptual foundations to follow the scientific arguments (what is Intelligent Design; how do genes work; how are proteins made), and then the interviews with two leading Intelligent Design proponents (Michael Behe; Jonathan McLatchie) and the counterarguments from three scientific experts (Nick Matzke; Matt Miller; Mark Pallen). We now feel ready to make a better informed opinion about the ID worldview. In this episode, Scott and Luke pull the threads together, compare notes, and try to make sense of the differing arguments presented. Points that we covered include: the reasons why we decided to do this deep-dive into ID, despite the warning that listeners might not be too interested the leaders in this new wave of creationism (Michael Behe; Stephen Meyer; Jonathan McLatchie) are much more highly credentialed in relevant academic fields than those in the first wave (Duane Gish; Henry Morris; Ken Ham) the leading ID proponents and the scientific experts that we brought in told very different stories!? Non-experts listening to these two groups aren’t well-equipped to discern the differences, and to evaluate which side is bringing the better information or interpretation. both Luke and Scott went into this deep-dive willing to give ID a fair chance, but both found the perspective conveyed by the ID-advocates quite unconvincing (and their modus operandi annoying), and the perspective from the scientists to be not only convincing, but even exhilarating despite the protests of its advocates, ID still comes across as God-of-the-gaps thinking the talking strategy that ID advocates tend to use is: selectively cherry-pick the scientific papers/studies they’ll consult or refer to when addressing any given issue; use technical jargon which goes far above the heads of most of their listeners; use glitzy, well-produced videos to mesmerize their audience into an absorptive state (just like watching TV at the end of a hard day); misrepresent (or misunderstand?) the opposing or contradictory scientific evidence; use a lot of hyperbole (e.g., genetic mutations cause “cataclysmic” failure of the organism). ID advocates love to bring up the “junk DNA” story as if they were the ones to set the scientific world straight on this point, but we explain why they have no more claim over this than secular scientists themselves Luke is annoyed when they tirelessly defend arguments that have been repeatedly debunked: this persistence borders on wilful ignorance …. or even deception? we wondered if the tendency towards ID thinking arises from nature (the human tendencies to perceive agency and to be awe-struck) or nurture (Sunday school upbringing; a culture that is increasingly skeptical and questions authorities; the internet encourages us to think we can be our own experts; a culture that replaces credentialed experts with celebrities, athletes, or anyone with a degree who will say what they want to hear) We also took time to respond to some questions/comments from our listeners: Skyler: ID isn’t (and can’t be) a scientific theory; Edward: what’s the difference between ID and Theistic Evolution? Nathan: what’s the difference between ID and Biologos? Nick: what are the falsification criteria for ID? (the problem is, ID advocates hide behind “we don’t know the design constraints” to shut down the conversation, just like AiG use “were you there” to do the same thing); John: ID is making God look deceptive; Mi K.: too much God-of-the-gaps argument; David: ID adherents reject the consensus opinion of a majority of experts, and instead latch on to a minority opinion anonymous pro-ID person: they know at least one scientist out there studying the flagellum who is pro-ID (Luke wonders why that person is so unheard-from); Ian: was pleasantly surprised and pleased with our episode featuring three experts describing an emerging scientific consensus on the origin of the flagellum. As always, tell us your thoughts on this topic … To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

After last week’s scientific experts cleared up much ID-rhetoric, we ask a rising star in the ID movement — Dr. Jonathan McLatchie — to respond to our reinvigorated questions, concern, and critiques of Intelligent Design After starting this mini-series with an interview with one leading ID proponent, and then hearing from a number of scientific experts who gave a different perspective on things, we now want to finish this on-going conversation with an interview with another leading ID proponent — a relatively new face — Dr. Jonathan McLatchie. With three graduate degrees in biology and evolutionary biology, he may be a rising leader in that movement. Before the interview, we gave him a list of the anti-ID challenges we’d be raising, so that we could get fully prepared and informed responses to those questions. Here are his answers, and our other points of discussion: Challenge #1: for us, ID is still just God-of-the-gaps thinking Challenge #2: ID doesn’t explain anything, it just attributes phenomena to an intelligence without saying anything about exactly how that intelligence might have done it. ID proponents often refer to this as an inference to the best explanation, but is it really just an inference to the best attribution? Challenge #3: where does the science go after the attribution has been established? Does ID make testable predictions which actually advance scientific knowledge? as always happens in discussions with ID proponents, “junk DNA” came up as one of ID’s greatest scientific advances Challenge #4: ID proponents often make reference to astronomically huge numbers when refuting evolutionists (“the chances of that happening spontaneously are one in 10 with eighty-nine zeroes behind it“) …. again, this just betrays God-of-the-gaps thinking Challenge #5: ID proponents are always attacking “Darwinism.” We need to move away from simple Darwinian mechanisms and recognize that genetics has moved far, far beyond simple point mutations; we now know about large-scale movements and reorganizations of DNA what exactly does “Darwinism” mean to an ID proponent? we started to wade a bit into the evo/devo world (a term for evolutionary developmental biology, which pertains to how a single-celled embryo organizes itself into a multi-cellular fetus) Challenge #6: ID proponents often resort to hyperbolic appeals to “cataclysmic failure” and “death” and “extinction” in order to push back on discussions of genetic mutations and rearrangements being the creative engine of evolution; they only see genetic changes as harming a given protein/function, and avoid or ignore the possibility that a genetic change might morph that function into a new one (a process referred to as exaptation) gene duplication with modification is the R&D department of the cell as ID proponents often do, Dr. McLatchie quoted from a small select group of scientific studies which supported his pro-ID or anti-evolution point(s), while not accounting for the much larger number of scientific papers which come to the opposite conclusions (“cherry-picking”) Dr. McLatchie claimed that there is very little evidence of gene duplication and modification producing new functions; we countered with one example of the family of receptors that convey smell (there are thousands of these, all just a little bit different from each other), but didn’t have time to talk about visual receptors, ion channels, protein-eating enzymes, carbohydrate-eating enzymes, neurotransmitter receptors, signaling molecules called GPCRs, antibodies, ………… the list goes on and on ID proponents re-defining the adjectives “detrimental” and “beneficial” when talking about genetic mutations disparaging misrepresentations of the Long-Term Evolution Experiment; we will be talking to one of the members of that project in the next few weeks to fact-check statements from Dr. McLatchie (in this episode), Dr. Behe a few weeks ago, and from ID proponents in general Dr. McLatchie sees evolutionary mechanisms simply “degrading genetic information,” while we see this as life getting creative and trying new things, and re-purposing old ideas function becomes conflated with design; just because something has a function, this doesn’t mean it was “designed” to do that (did someone “design” an old broken brick to hold that garage door open?) strange/awkward designs (backwards wiring of the retina) and truly malevolent designs (convergence of the wind-pipe and food-pipe, or childbirth) make it hard for many of us to embrace ID; a designer working from the bottom up wouldn’t design it this way when asked why humans couldn’t have been “designed” with thicker necks having a food pipe on one side completely separate from a windpipe on the other side, the response can’t be “well, that would look weird” the accumulation of gradual changes that we see in living organisms over time (complete with genetic dead-ends and fragments of old, out-dated designs) is not consistent with the idea of a Master Designer what do ID proponents think of common descent of humans and primates (they’re quite divided on this), and how exactly do they explain speciation? why is the scientific community at large so resistant to ID-thinking? the ancient Hebrews thought the weather involved God having jars of rain, closets of lightning bolts, and breathing out the wind and the dew; today, we can set up mathematical models that only take into account gradients of temperature, pressure and humidity and predict the weather out over the next week or two exactly how would “the Designer” design things? What would this look like? Is he/she/it tirelessly tinkering away at a work-bench, or just dropping in from time to time to nudge things over key evolutionary hurdles? Jonathan’s answer included a reference to periodic injection of information content into the global pool of living organisms (“the biosphere”) As always, tell us your thoughts on this topic … Find more about Dr. Jonathan McLatchie, including upcoming public speaking engagements and writings, at his web-site. To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

Three internationally-recognized, world experts on the bacterial flagellum connect the dots regarding the evolutionary origin of the flagellum, and draw some compelling comparisons to the evolutionary emergence of the Bible! Three episodes ago, Dr. Michael Behe used the bacterial flagellum as Exhibit A in his defense of the Intelligent Design proposal. Last week, we heard Dr. Nicholas Matzke, who actually does cutting edge research on the flagellum, give his understanding of the bacterial flagellum, with comparisons to claims frequently made by the ID community. In this episode, we hear three world-leading scientific experts on the flagellum discussing the latest scientific data on an amazing evolutionary journey which seems to explain the origin of the flagellum. Those three are Drs. Matthew Baker (University of New South Wales, Australia), Mark Pallen (University of East Anglia, UK), and Nick Matzke (University of Aukland, New Zealand). Some of the technical points they discussed include: how to make direct measurements of individual flagellum motors freshly isolated from a test tube of bacteria why is there so much interest in the bacterial flagellum ….. why have so many researchers using such high-tech equipment studied this thing? the flagellum is not just one unchangeable thing (as ID proponents will often suggest); instead, the broad scientific community agrees that there are MANY different kinds of bacterial flagella (hundreds of thousands), each with different genetic sequences, and some of which seem to be missing parts, and yet still work for their hosts at the heart of two bacterial nanomachines there is a third nanomachine called “the type III secretion system” whose function is to squirt out proteins; the one in the flagellum squirts out the proteins that make the long propellor whip, while the one in “the injectosome” squirts out the toxins that the bacteria uses to capture its prey these are two examples of machines built on top of machines – Mark referred to it as “a modular system” there is yet another bacterial nanomachine — “the “ATP-synthase” — whose function it is to generate energy molecules called ATP; given how fundamental this function is, ATP-synthase is probably one of the oldest of cellular machines there are many striking similarities (genetic; structural; functional) between ATP-synthase and the type III secretory system, which suggests a common ancestral origin; in other words, those two very different enzymes seem to have both descended from yet another earlier enzymatic precursor there is some reason to suggest that the precursor for the type III secretory system (and for ATP-synthase) might have been related to one that modifies RNA, an enzyme called RNA-helicase; one of those reasons is the fact that all three are made up of six globular proteins that form a ring wrapped around a central filament of protein (in the case of the type III secretory system) or a filament of RNA (in the case of RNA-helicase), and all three spin like rotary motors as they do their job the type III secretory system is NOT a devolved bacterial flagellum (as ID proponents will often claim) Altogether, the evidence starts to point to a possible scenario involving a recurring theme of gene duplication with subsequent modification of the copies, followed by selection for a useful function: an ancient primordial gene for an enzyme that comprised a rotary motor that spins around some filament was duplicated those two primordial gene copies morphed and diverged such that one specialized for RNA (the helicase) and the other specialized for proteins (becoming a generic protein pump) somewhere in that transition, one of those two new genes duplicated, and the resulting copy started to code for a rotary engine that ran in reverse and latched onto a protein to drive it to generate ATP (ATP synthase) the gene for the generic protein pump was duplicated and the copies began to specialize for pumping certain subsets of proteins … one for flagellar proteins (thereby becoming a propellor, the bacterial flagellum) …. and the other one for toxins (thereby becoming a weapon, the injectosome) Parts of this story are more speculative than others, but the emerging picture is looking quite clear that the bacterial flagellum is the product of a long evolutionary journey. That hypothesis then prompts new research questions which flesh out the details of this evolutionary journey. There was an extended conversation about how genes/proteins can change/morph over time and take on entirely new functions …. and how this phenomenon is precisely paralleled by the evolution of language (the words loyal, legal, and lawful all have a common ancestral origin), and even of the Bible itself! I asked our guests to comment on Michael Behe’s claim that secular scientists themselves are doing the scientific work of Intelligent Design by “doing their experiments from a Design perspective without calling it that.” Admittedly, it’s pretty hard for scientists to say anything about evolution without using wording such as “this protein/trait is designed to enable the animal to XYZ” or “this organism evolved toward being able to XYZ.” This is goal-oriented language … wording that conveys purpose, meaning, direction, guidance … otherwise known as “teleological” language. One response to this assertion was that it can also be “sloppy language,” just like humans have the tendency to refer to Earth as “her” or to a truck as “him.” I also asked our guests if it is possible to meet the ID proponents in the middle by saying that there is indeed “a designer”, but that designer is the cell itself (which orchestrates the genetic changes) and evolutionary pressures (which select out the good stuff). One guest replied provocatively, but entirely legitimately, that if ID proponents insist on personifying “the designer” by referring to him/her/it as intelligent, then how do they explain the flagellum being so well designed to move the bacterium around through the human host’s body in order to mediate such nasty, devastating, destructive disease outcomes. Interesting conversation indeed! As always, tell us your thoughts on this topic … Find more information about our guests at Nicholas Matzke’s profile, Mark Pallen’s profile, and Matthew Baker’s profile. Episode image by Arek Socha from Pixabay. To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

A scientist who specifically studies the bacterial flagellum using some of the most cutting-edge research tools clears up a few myths and misconceptions. Much of Dr. Michael Behe’s defense of Intelligent Design rests on claims made about the bacterial flagellum. It certainly has become his signature, and one could even say it’s become the symbol or mascot of the ID movement (like the polar bear became for the global warming movement). Some of his claims are often challenged by opponents of ID. To shed some light on the subject, we reached out to several scientists who actually work with the bacterial flagellum (Behe does not). Here, we speak to Dr. Nicholas Mitzke, who gives us a basic introduction to this bacterial machine, demystifying it and clearing up some misconceptions that have been built up around it. Points that we discussed included: misconception #1: the flagellum is not just one unique thing that cannot be altered in any way without completely losing its function. There are in fact thousands of different versions of the flagellum, each with differences in their amino acid sequence (which necessarily means their gene sequence was changed), and some of them are even missing certain protein parts, and yet all of these altered versions retain their function. misconception #2: the flagellum did not in fact arise through a series of intermediate steps, each intermediate being non-functional, before finally becoming a functional machine. Instead, we’re now getting glimpses of its evolutionary journey through various stages of different functionality. proteins in general can evolve, changing amino acid sequences in many ways, and yet retain their original shape, and therefore full function how the rotary engine in the flagellum converts chemical energy into a rotational movement; it uses an acid battery that spins an “electric” rotor the flagellum is made of multiple copies of 20 proteins; 99% of the flagellum is the long whip (tens of thousands of copies of one particular protein); the other 19 proteins are at the base of the flagellum, forming one machine that creates the flagellum (the “type III secretion system”) and another machine that rotates the flagellum (the motor). misconception #3: given the statement above, the type III secretion system is NOT a “devolved” flagellum misconception #4: cellular machines (like the flagellum) do not need a mechanic to assemble the different parts into a functional machine (a misconception based on our familiarity with human-made machines). Instead, cellular machines can make themselves!? Self assembly!!! [we talked about this in detail in episode #131] misconception #5: the flagellum motor does not work through pistons, gears, fan-belts, and other such moving parts (as might be misconstrued by the frequent references to the flagellum being “like the outboard engine of a boat”). Instead, they work through a series of simple shape-shifts … the protein parts just bend a bit this way or that, causing other subtle shape-shifts in their neighbors. we introduced another bacterial machine called the ATP-synthase, because this will become a key star in next week’s episode about the evolutionary origin story of the flagellum. It’s basically two small machines combined into one: an ion pump, and an energy molecule factory. we heard a very condensed version of that evolutionary origin story, one that links three very different bacterial machines (the type III secretion system, ATP synthase, and the flagellum), in order to whet listener’s appetite for next week’s episode. This story is very much like someone encountering a complete stranger, noticing some absolutely striking resemblances in facial features, and finding out that the stranger is a cousin/sibling they never knew about. As always, tell us your thoughts on this topic. To learn more about our guest expert, visit his faculty profile page. If you enjoyed this episode, make sure you’ve listened to our interview with Michael Behe (or listen to it again, now that you’ve been informed). Also, if you haven’t already heard the other episodes in this mini-series, you might benefit from our basic introductions to how genes and proteins work. Episode image by Raman Oza from Pixabay. To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

Most people don’t know: the genome is a formatted database with read/write memory systems which can reorganize itself to produce new species. This is a re-release of an episode we put out almost two years ago. In the episode that preceded this re-release, and which set the stage for this interview, we had given a thumbnail sketch of genetics as most people understand it. We distilled that common understanding into five basic statements, and showed how most people think new species (or new cellular machines, like flagella) somehow arise from genetic mistakes and accidents. And we said we would be talking to Dr. James Shapiro, a world-leading geneticist with 60 years of experience in the field and who co-leads a large group of world-leading scientists working to correct this fundamental misunderstanding of genetics and evolution, in order to fact-check that common understanding. It turns out, it’s not just outdated, but deceptively wrong! Here’s what he told us about those five basic statements. Fasten your seat belts! (1) it’s all about DNA: who you and your children are is all completely determined by your DNA; Your brain cells, muscle cells, blood cells … and all the other cells of your body … have exactly the same DNA; and yet they’re so very unique in many ways! What makes them different from each other — and you from anybody else — is determined largely by another molecule: RNA. (2) DNA is a long molecule which gathers together many genes, like beads on a string, which code for the proteins that your body is made of; Only a very small fraction of your genome (the total collection of all your genetic material) codes for proteins; just a few percent in fact. Most of the rest of your DNA codes for RNA molecules which regulate the entire genetic machine. Also, any given “gene” (discrete chunk of information) is not like one of those beads on the string: instead, it has bits and pieces scattered all over your genome. (3) cells do everything they can to protect those genes from any kind of change; In fact, your cells have built-in mechanisms which do the exact opposite of that: they actively change the organization of your DNA, in response to evolutionary pressures, by: – moving large chunks from one position to another, even between chromosomes (recombination and reorganization); – moving large chunks between completely different species (“horizontal transmission”, in contrast to the standard “vertical transmission” from your parents); – combining the genomes of two different related species to produce a new third species (hybridization) or produce an entirely different kind of organism (the origin of the mitochondria and chloroplast); (4) UV light and mutagenic chemicals cause random mutations in the DNA, which can alter the function of the proteins they encode; Cells have very good error-correcting mechanisms which undo those kinds of mistakes, as well as those made when the “photocopier” (the DNA-duplicating machine) goes on the fritz; (5) those random mutations accumulate over time, producing individuals with new characteristics (e.g., blood type; hair color) and eventually … a new species; The occasional random mutations which might make it through the error-correcting mechanisms referred to in #4 above are completely unable to explain the origin of major changes in a given species (new “phenotypes”), let alone the origin of entirely new species. How much more wrong could we have been? This new and improved understanding of genetics and biological evolution opens up new ways to defuse the debates which keep coming up when creationists push back on the Theory of Evolution. Or on the evolutionary origin of the bacterial flagellum! As always, tell us what you think … If you want to hear our summary of the common [mis]understanding of genetics, and the backdrop for this interview, check out Episode #69. As a bonus, that episode also explored nine reasons why some people push back on the whole idea of evolution (in some cases, because they just don’t properly understand genetics and evolution). To find more about Dr. James Shapiro and the group of scholars he co-leads seeking to bring awareness to this new understanding of genetics, go to The Third Way of Evolution. Episode image from Pixabay (and modified). To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Back to Recovering Evangelicals home-page and the podcast archive

Dr. Michael Behe, a biochemist and Intelligent Design proponent, gives us his perspective of ID, and responses to several counterarguments against ID. To start off our deep-dive into Intelligent Design, we wanted to talk to a knowledgeable representative of that movement. Dr. Michael Behe, a biochemist who has been waving that flag for three decades now, and Senior Fellow at the Discovery Institute (“ID Headquarters”), was a great choice for this first conversation. In addition to exploring a variety of biochemical and physiological concepts, our main goal was to get his response to several counterarguments against Intelligent Design which we hear often (and resonate with). Our points of discussion included: he’s not a Young Earth Creationist … he does accept human evolution from an ancestor we share in common with the apes; as an Intelligent Design proponent, he believes that the evolutionary steps had to have been guided (not random or undirected) “irreducible complexity” refers to a system/machine which has multiple parts and requires ALL of those parts to maintain its original function [our response: “sure, but it CAN be changed or reduced to do other functions”] his often-used analogy for irreducible complexity is a mouse-trap cells are made up of nanomachines which are made out of many parts, all of which are essential or the machine no longer works (“so they’re irreducibly complex”); his often-used example is the bacterial flagellum motor (BFM) he argues that this irreducible complexity can not be accounted for by Darwinian mechanisms counterargument #1: you can indeed take away certain parts, and what remains can still be quite functional, albeit perhaps not as a flagellum motor (or mousetrap). The BFM can be stripped down to a much smaller number of parts leaving another bacterial machine (the type III secretory system) which has a completely different function (it’s involved in squirting proteins out of the cell, rather than in giving the cell mobility). Also, many of the individual parts of the BFM can serve other functions on their own. counterargument #2: ID proponents tend to limit the discussion to “Darwinian” evolutionary mechanisms — random, undirected mutations of single base pairs — and avoid a more modern understanding of genetics which includes large-scale genetic changes which are orchestrated by the cell (duplication; reorganization; shuffling of whole sections of DNA; recombination; horizontal gene transfer; epigenetic changes) counterargument #3: if we’re going to attribute changes to a Designer, what do we do about examples of bad design (not just strange or clunky design …. but actually horrible design which produces indiscriminate suffering and death) counterargument #4: ID is not science. It doesn’t propose hypotheses that can be tested. It doesn’t explain the phenomenon (the mutation or new genetic trait), it only attributes the phenomenon to a Designer who worked in a mysterious way that we might never understand and for reasons that we can’t see counterargument #5: ID is more religion than science, and forces people to choose between the two (in a zero-sum fashion) there is another entirely different bacterial nanomachine called ATP-synthase which has jaw-dropping genetic and structural similarity to the type III secretory system at the heart of the BFM, but has yet another completely different function (it makes energy molecules, rather than squirt out proteins or give the cell mobility). This similarity might give clues regarding the evolutionary origin of the BFM. We’re going to get into this in much more detail in a couple weeks with experts in this area As always, tell us your thoughts on this topic … If you haven’t already heard the two episodes that preceded this one (Episode #130 and #131), you really should: they’re all part of a mini-series we’re doing on Intelligent Design, and they set the stage for this one. You may also like Episode #70, where we talked to Dr. James Shapiro (an Emeritus professor with decades of hands-on experience with genetics at several world-renowned universities) about how cells routinely move large chunks of DNA around. To find out more about Dr. Michael Behe, see his website or his page at the Discovery Institute. Episode image: Ciker Vector Free Images from Pixabay. To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive

Before hearing from Intelligent Design advocates, we thought we’d give our listeners some useful background information about how cells work …. it turns out it’s all about making shapes out of string. Before we present our interviews with Drs. Michael Behe and Jonathan McLatchie (both leading proponents of Intelligent Design), we feel we should give our listeners a quick Cell Biology 101 to explain some of the concepts that will frequently come up in those interviews, and which easily mislead non-experts. So, in this episode we’ll talk about how cells make proteins, and how it’s the sequence of amino acids (which is directly decoded from the gene sequences) which determines the 3-dimensional (3D) shape of the protein, and that in turn gives the protein its functionality. In this casual conversation, given at a NON-EXPERT level, Scott and I talked about: the string of DNA gets decoded into a long string of amino acids (we came up with two metaphors for this long string: toothpaste being squeezed out of a tube, and “Silly String” being squirted from an aerosol can at a party) that string of amino acid is called a protein; protein adopts a 3D shape that directly gives it its functionality the toothpaste / Silly String forms a long strand which flops all over itself, forming loops and folds and a completely disorganized mess; the strand of protein would also form a disorganized mess, except for the fact that the amino acids themselves begin to interact with each other and generate attractive/repulsive forces that cause it to fold and compact the loops into a particular 3D shape force #1: electrostatic attraction … a series of positive and negative charges which strongly attract each other, kind of like a sock sticking to a towel when you pull them out of the dryer, and have to peel the sock off force #2: electrostatic repulsion … a series of positive versus positive charges (or negative versus negative charges) which push each other apart, kind of like your hair standing on its end when you put your hand on a van de Graf generator at a science museum force #3: hydrophilic/hydrophobic attraction … a series of “water-loving” amino acids want to stick together (like sticking a piece of paper to a window just by making it wet); in the same way, “water-hating” amino acids want to stick together force #4: hydrophilic/hydrophobic repulsion … a series of “water-loving” amino acids and “water-hating” amino acids push away from each other (like oil and water not wanting to mix) force #5: atomic bond sharing … two amino acids both grabbing on to a hydrogen (like two people fighting over a trophy) or both becoming physically connected to a shared sulfur atom (like two people being hand-cuffed together) force #6: peg-and-socket connections …. groups of amino acids clumping together like a ball, and then inserting themselves into another group of amino acids which have formed into a doughnut shape (like buttoning up your shirt, or putting a jigsaw puzzle together) force #7: each type of amino acid holds its two arms out at different angles (both forward; or one backward and other forward; or both at 90 degrees from forward [or 60 degrees, or 45 degrees, or ….]), and as you connect these different types together (by getting them to hold hands), the angles of their arms begins to make the straight strand of protein kink up and loop in certain predictable ways we discussed how the sequence of the amino acids in the protein uses these forces and interactions to constrain the protein strand into specific and predictable 3D shapes, like: filaments, poles, tubes, beams, sheets, planks, pegs and sockets, and other shapes we did a mental exercise of creating a screw or a bolt using these forces and interactions, and also building an ion channel that you might find in a nerve cell! other intricate, complex and beautiful things can also be explained by naturalistic mechanisms: the Grand Canyon was created by simple geochemical and geophysical forces, or the beauty of a sunset against a stormy sky with a rainbow off to the side is mathematically explained by optical physics and gradients of air pressure, temperature and humidity reducing such complicated cell biology to “just chemistry and physics” doesn’t need to diminish “the Creator,” any more than showing that Leonardo DaVinci is “only” working with simple paints and a stick/brush; one is still free to invoke a Creator … or to deny the same. this raised questions about teleology and the processes being goal-directed, and science tending to be too reductionist a second VERY important topic we discussed was how these inanimate protein parts can self-assemble. Yes: SELF-ASSEMBLY! It sounds like magic, but it’s a common feature in cell systems, and it’s relatively easy to explain (we did this by having Scott jiggle a drawer full of spoons). No need for a little technician with a screw-driver and hammer in hand to put those parts together and a third VERY important topic: changes in the genetic information do not have to be simply a single change at one point in the strand of DNA or one single amino acid at a time (as YEC and ID advocates want listeners to believe). Instead, cells will commonly move and reorganize large segments of DNA at a time, coming up with entirely new combinations, which in turn leads to new genes. duplication (of parts of genes, of whole genes, or even of whole chromosomes!) accounts for the problem that YEC and ID advocates frequently raise: the original copy can still fully take care of the originally intended cell function, while the duplicated copy can go on to enhance its function, or even become adapted for a completely new purpose. Yes, you CAN have your cake and eat it too! duplication and re-shuffling of genetic information explains the evolution of proteins (we showed how easy it is to change a spoon/shovel into a knife/axe, or a stiletto/poker, a fork, a hammer). The immune system routinely takes this shuffling/re-building to a whole new level. coaptation: a protein can remain intact and serve more than one function, even in entirely different systems, or it can be slightly modified to now serve a new function As always, tell us your thoughts on this topic … If you enjoyed this episode and/or if you want to learn more about the genetic aspects of this discussion, you should check out Episode #70, where we talked to Dr. James Shapiro (an Emeritus professor with decades of hands-on experience with genetics at several world-renowned universities) about how cells routinely move large chunks of DNA around. Episode image by Milada Vigerova at Pixabay. To help grow this podcast, please like, share and post a rating/review at your favorite podcast catcher. Subscribe here to get updates each time a new episode is posted, and find us on Twitter or Facebook. Back to Recovering Evangelicals home-page and the podcast archive