#6 of Our Top Stories of 2019: Polar Bear Seminar

first_imgAnswering Objection 2: Did Behe accurately estimate the number of polar bear genes that experienced damaging mutations? When Behe calculated the number of polar bear genes that experienced adaptive yet degradative mutations, he closely followed the methodology of Liu et al. (2014). Even critics admitted that Behe’s upper estimate of the number damaged polar bear genes was reasonable under Liu et al. — 14 out of 17, or 83 percent of highly selected genes probably experienced damaging mutations. As for Behe’s lower estimate, here too he closely followed Liu et al. — and followed their methodology more closely than his critics. Unlike Liu et al., these critics excluded from their lower estimate all cases where the computer program predicted a mutation was “possibly damaging.” (Even in those cases, the mutation was predicted to be damaging but was called “possibly damaging” to recognize the possibility of false positives.) Behe followed Liu et al.’s methodology and accurately calculated that the minimum number of degraded genes in polar bears was 11 out of 17, or 65 percent. You can read more about this here and here. Answering Objection 3: Did Behe omit contrary information from the chart? Behe’s blog post responding to Objection 2 only showed a portion of the damaging mutation chart from Liu et al., but Behe did this for good reason: The table is large (49 lines x 8 columns), and for clarity he wanted to present only the data that was required to refute the critics. In this case, critics had challenged Behe’s estimates of the number of polar bear genes that experienced damaging mutations. The chart data Behe presented was sufficient to show he was correct. One critic even admitted Behe “isn’t lying exactly” since he was just showing the “relevant information.” In a reply to the critics’ complaints, we reprinted the full table and showed why none of the data Behe left out contradicts his thesis. Some of it represented results that predicted mutations were damaging — data that clearly supports Behe! The remainder entailed mutations that were predicted to be “benign” — but this does not contradict Behe either: Behe’s “devolution” model is only challenged by “constructive” mutations, but he fully allows that benign or neutral mutations are common and even form “the bulk of changes at the molecular level,” as he writes in Darwin Devolves. Congratulations to Science Magazine for an Honest Portrayal of Darwin’s Descent of Man Behe gives many examples supporting his thesis, but the first ones offered are polar bear genes. About 20 genes in polar bears show strong evidence of adaptive mutations, and a computer analysis of those mutations by a 2014 paper in the journal Cell by Liu et al. found that “a large proportion (ca. 50%) of mutations were predicted to be functionally damaging.” This, Behe argues, confirms his thesis that adaptive mutations tend to be degradative.  Evolution #6 of Our Top Stories of 2019: Polar Bear SeminarCasey LuskinDecember 27, 2019, 4:33 AM TagsAPOBblood streamCell (journal)cholesterolcomputer analysisDarwin Devolveshigh fat dietLiu et al. (2014)medical literatureMichael Behemutationspolar bearPolar Bear SeminarPolyPhen-2Shiping Liu,Trending Photo at top: A polar bear instructs a trio of knowledge-hungry walruses, by Caterina Sanders via Unsplash. “A Summary of the Evidence for Intelligent Design”: The Study Guide According to the computer study, one of the polar bears genes most strongly predicted to have experienced damage is APOB, a gene that helps regulate cholesterol in the blood. Liu et al. (2014) predicted that mutations in APOB helped polar bears deal with a high-fat diet from eating seal blubber. The question at issue is whether mutations in APOB and other highly selected polar bear genes degraded or enhanced their molecular functions. The Critics RespondBehe’s critics responded with four main objections: Objection 1: They criticized using the computer program to conclude that a gene was probably damaged. They argued the program could not detect biochemical damage because all it detects is changes to how the gene operates or phenotypic damage — but it cannot detect whether those changes were harmful or beneficial to a gene’s function at the biochemical level. Thus the objection came in two parts: (a) They claimed that when damage is detected by the program, that means “phenotypically damaging, not biochemically damaged” because “Polyphen does not attempt to predict ‘biochemical damage.’” (b) They argued that Behe misread a table in Liu et al., which over 40 times predicted a mutation was “damaging,” because “damaging in this table does not mean damaging.” Instead, they said, all the program is actually detecting is a “change in function.”  Recommended Objection 3: Some critics complained about a chart from Liu et al. that Behe showed, in part, in a blog post. The chart showed when mutations were predicted to be damaging or when they were predicted to be “benign.” These critics argued that Behe omitted important data from the table reporting benign mutations, and was therefore “deeply misleading,” “intentionally leaving out evidence that is contrary to his position,” and “deceptive to doctor the chart.”  Email Print Google+ Linkedin Twitter Share Casey LuskinAssociate Director, Center for Science and CultureCasey Luskin is a geologist and an attorney with graduate degrees in science and law, giving him expertise in both the scientific and legal dimensions of the debate over evolution. He earned his PhD in Geology from the University of Johannesburg, and BS and MS degrees in Earth Sciences from the University of California, San Diego, where he studied evolution extensively at both the graduate and undergraduate levels. His law degree is from the University of San Diego, where he focused his studies on First Amendment law, education law, and environmental law.Follow CaseyProfileWebsite Sharecenter_img Jane Goodall Meets the God Hypothesis Objection 4: Behe’s critics also focused specifically on APOB, arguing that Liu et al. and a news article about the paper did not conclude the gene was damaged. They even claimed that the mutations “likely enhance the function of apoB” which they presumed is simply to remove cholesterol from the blood. As one critic put it, mutations in APOB “improved one of its activities, namely the clearance of cholesterol from the blood.” Critics further claimed that we misread Liu et al. since “the authors do not expect the polar bear APOB to be broken or damaged” and “There is no evidence for Behe’s claim that APOB is degraded or diminished in polar bears.” Those who claimed that Liu et al. concluded APOB was predicted to be damaged were accused of “lying.”In Reply to the CriticsWe responded to each objection in detail:Answering Objection 1a: Does the program examine biochemical damage? We pointed out that the computer program is precisely designed to detect biochemical damage. The technical documentation for PolyPhen-2 explains that it predicts when a mutation is “likely to destroy the hydrophobic core of a protein, electrostatic interactions, interactions with ligands or other important features of a protein,” and predicts when a mutation is “affecting protein stability or function.” That’s biochemical damage. (For our discussions, see here, here, or here.)  Email Print Google+ Linkedin Twitter Share Objection 2: Behe’s critics claimed that he exaggerated when estimating the number of polar bear genes that Liu et al. had predicted experienced damaging mutations.  Answering Objection 4: Did APOB experience damaging mutations? Liu et al. reported that five mutations in APOB were “predicted to be functionally damaging.” One of those mutations received the program’s highest possible score — 100 percent likelihood — for predicting damage. Critics accused us of “quote-mining,” so we asked them to provide language from the paper indicating otherwise — that APOB mutations were not damaging. They could not do this. Instead they put words into the mouths of the authors, citing statements from the paper and from a news article that were silent about whether APOB mutations enhanced or degraded its function. While the paper certainly predicts that mutations in APOB help polar bears cope with a high-fat diet to effectively reduce cholesterol, it simply did not speculate about the exact mechanism by which this happens. Curiously, critics who argued that mutations “likely enhance the function” of APOB did not acknowledge key language from the paper which admitted: “It remains an enigma how polar bears are able to deal with such lifelong elevated levels of cholesterol.” Likewise, they failed to note that a news article about the paper stated: “It’s not clear exactly what the gene variants [of APOB] do for the polar bears.” If we don’t know the exact function of APOB in polar bears or how it helps them cope with a high-fat diet, how can we know that its function was enhanced? We can’t. Absent empirical studies of exactly what APOB does, the best evidence about the impact of APOB’s mutations is from the computer analysis which strongly predicted that it experienced damaging mutations. For details, see here, here and here.  Requesting a (Partial) Retraction from Darrel Falk and BioLogos Editor’s note: The staff of Evolution News wish you a Happy New Year! We are counting down our top ten stories of 2019. If you haven’t done so yet, please take a moment now to contribute to our work in bringing you news and analysis about evolution, intelligent design, and more every day of the year. There is no other voice, no other source of information, like ours. Thank you for your friendship and your support!The following article was originally published here on May 6, 2019.Recent months have witnessed a debate between Michael Behe and his supporters, on one hand, and Behe’s critics on the other, over arguments in his book Darwin Devolves about mutations in polar bear genes. The discussion has now come to end. Having heard what critics have to say and having responded extensively, we believe the evidence comes down decisively on Behe’s side. Barring startling new revelations from the research community, nothing more needs to be said for now. But because this conversation has been intense, technical, and complex, it seems fitting to offer a concise summary. (Along with apologies if, like us, you are suffering from a bit of polar bear fatigue.) Find the full Seminar here.Behe’s CaseBehe’s main thesis in Darwin Devolves is that adaptive mutations tend to degrade or diminish functions at the molecular level.  Origin of Life: Brian Miller Distills a Debate Between Dave Farina and James Tour Answering Objection 1b: Can the program ever reasonably predict that a protein was probably damaged? We also pointed out that the computer analysis gives a very good probabilistic estimate that the protein’s function was damaged, not simply changed. The program looks at the substituted amino acids and assesses whether they have similar chemical properties to the residues at the same position in a suite of other known homologues of that protein in other species. If they don’t, it’s safe to assume that the function of the protein is going to begin to diverge from the original function. The program can directly analyze and predict whether mutations affect protein’s stability or core function — crucial factors for assessing whether its function was damaged. The result, given in probabilistic terms, indicates when the protein’s native function is most likely being biochemically degraded and damaged. In Darwin Devolves, Behe appropriately described the program’s results as showing when a mutation was “likely” to be damaging. (We explained this here and here.) New evidence answering Objection 4: Degradative mutations in APOB can lower cholesterol:  Most critics assumed that the function of APOB is to remove cholesterol from the bloodstream, and that polar bears cope with a high fat diet via mutations that enhance this function. They thought this made it difficult to believe Behe’s prediction that degradative mutations in APOB help reduce cholesterol. As a final point, a body of medical literature proved Behe could be right. Studies of APOB in humans show that one of its functions is to load cholesterol into the bloodstream, and that mutations that degrade this function can lead to lower cholesterol levels. In other words, degradative mutations in APOB could plausibly help polar bears deal with their high fat diet. As we explained here, functionally damaged apoB proteins can indeed lead to less cholesterol in the blood.Mysteries remain: What exactly does APOB do in polar bears? And if it is helping reduce cholesterol (as most everyone believes), why do polar bears still have such high cholesterol, and how exactly do they cope with that? No one knows for sure what APOB is doing in polar bears and exactly how its mutations or mutations in other genes help polar bears cope with a high fat diet. But genetic analyses strongly indicate that many APOB mutations were damaging to its function, and there are plausible models by which damaging APOB can reduce cholesterol. All of this is enough to show that Behe’s arguments about APOB and devolving polar bear genes are backed by evidence and hold merit as a plausible model. Enough NowSo Behe’s position has come out looking very strong. Of course, all scientists know we must be open to revising our views based upon future discoveries. We presently lack direct empirical studies of how exactly APOB functions in polar bears and how polar bears cope with high cholesterol. Perhaps studies will be done in years to come casting new light on those questions. For that matter, perhaps one day polar bears will talk, dance, watch TV, ice-skate, and drink Coca-Cola, as in the famous commercials. Who can say what the future holds?That’s enough now. So take a deep breath, relax, and watch some polar bears: A Physician Describes How Behe Changed His MindLife’s Origin — A “Mystery” Made AccessibleCodes Are Not Products of PhysicsIxnay on the Ambriancay PlosionexhayDesign Triangulation: My Thanksgiving Gift to Alllast_img read more

UPDATE: Hudong-Zhonghua nets LNG tanker order

first_imgHudong-Zhonghua Shipbuilding confirmed that it had signed a contract with BG to build four 174,000 cbm LNG tankers.“With GTT No.96 E-2 membrane-type cargo tanks, these vessels are 290m in length, 46.95m in breath and 26.25m in depth,” the Chinese shipbuilder said in a statement.The LNG vessels will be owned by a consortium consisting of BG, CNOOC Energy Technology and Services, China LNG Shipping, Teekay LNG Partners and BW’s LNG investment arm, according to local media reports.Local media in China have also reported that the Export-Import Bank of China will lend $400m for the construction of the LNG tankers.The tankers are expected to transport LNG from BG’s QCLNG project in Australia[mappress]LNG World News Staff, July 4, 2014; Image: HZ-Shipgrouplast_img read more

‘Boom-bust’ warning for top commercial firms

first_imgTop commercial law firms must become more flexible and less reactive to cope with the boom-bust pattern of global markets over the next 10 years, a report by consultants Jomati has suggested. Introducing variable rather than fixed costs, creating links with legal process outsourcers (LPOs), and setting up internal LPO-style businesses will be essential to dampen the effects of unpredictable markets, according to the report, New Frontiers: Law Firms in 2020. The report said: ‘As the building up of global capability grows over the next 10 years, and the investment in people, IT, office space and support staff grows for transactional teams, so will the risk of a dangerous cost over-shoot. A bust for a one-office firm is bad enough; a bust for a firm with corporate associates in 20 offices is going to hurt significantly more.’ Meanwhile, competition from Chinese law firms, which are already hiring senior lawyers from major UK and US firms and are becoming increasingly skilled, could lead to fee competition across Asia, the report predicted. Jomati principal Tony Williams, a former managing partner at magic circle firm Clifford Chance, said: ‘We often talk about global law firms as if they are finished products. The truth is, the development of global law firms is just beginning.’ Top lawyers and general counsel from the ‘baby boom’ generation will retire over the next 10 years, leaving a skills gap at senior management level, the report warned. At the same time, global law firms will increasingly have to be stocked with senior lawyers with a deep understanding of emerging markets, it suggested. Population changes will create a ‘pull effect’ on banks and corporates, which will in turn look to lawyers for advice, the report said. Predicted population growth of 10% in the US in the lead up to 2020 could signal more domestic legal work for mid-tier US firms, and increase the value of what is already the world’s most valuable legal market, the report found. It added that Japan’s stagnant economy could force companies to restructure and expand aggressively abroad, bringing related work for lawyers. An increasing number of high net- worth individuals will also bring more private client work, and in particular a need for advice on tax avoidance, the report suggested.last_img read more

Former NBA Star Kenny Anderson Gives Back in His ‘Basketball Showcase’

first_img Related TopicsKenny Anderson NEO HS Staff By Don DiFrancesco​​Former NBA star Kenny Anderson has taken on a number of challenges in his life, both on and off the court. But he recently completed his first season as the head coach of men’s basketball at Fisk University and things were beginning to look up—for both the school and the coach.In late February however, he suffered a stroke at his home in Florida and was briefly hospitalized. Fortunately for Anderson, his wife, Natasha—an administrator in the healthcare field—recognized his symptoms and he was treated promptly. He is expected to return to Fisk, an HBCU (historically black college or university) in Nashville, Tennessee in time for the 2019-2020 basketball season.To be sure, Anderson, 48, is receiving excellent medical care. But a decidedly different form of therapy has brought a smile to his face in recent weeks. In May he traveled to Cleveland to help kick off the inaugural “Kenny Anderson Basketball Showcase,” a two-day program for high school players looking to demonstrate their skills to college coaches in the Division 2, Division 3, NAIA, and Junior College ranks.The tournament was the brainchild of local coaches Ian Cunningham and Reggie Harwell. They had been looking for a way to enable players to get needed exposure without requiring them to pay the exorbitant fees normally charged for such events. Cunningham had viewed a documentary film on Anderson’s life and felt a spiritual connection to the basketball legend. So he made some phone calls the next day. And his sincere passion for the project was enough to convince Anderson to participate!Thanks to the unceasing efforts of Cunningham, Harwell, and friends, 40 high school students gathered at The Edge Sports & Arts Academy in Twinsburg on the evening of May 31st to meet each other and to receive some inspiration from Anderson and others. The following day they competed in a series of games at The Edge, culminating in a final contest with the day’s top 16 performers as selected by a committee of coaches.Jaidon Lipscomb, a recent graduate of Pickerington Central High School in the Columbus area, was named the Most Valuable Player of the tournament.Finding sponsors to help with the costs, and putting in the many hours of work required to pull off such an event was no small feat. But Cunningham and Harwell considered it a labor of love and a true blessing. They are looking forward to year two of the showcase, giving even more student athletes the opportunity to continue their basketball and academic careers at the next level.And Mr. Anderson? He is progressing nicely and credits his “Ohio basketball therapy” with playing an important role. The latest report is that a couple of the players he met in Twinsburg may be joining him in Nashville this fall. And what a blessing THAT would be for all concerned!By Don DiFrancesco​​last_img read more

Cundy heads for Devonshire loan

first_imgHe joins the Grecians ahead of the 2019/20 campaign, linking up with his new teammates for their pre-season schedule.Cundy is a new arrival in BS3, having made the move from Bath City in June. The defender joined the Robins on a two-year deal, with the option of a further year.last_img