Wednesday, January 17, 2018

Consider counter-evidence to avoid bias

Neurologists at the Brain and Creativity Institute at the University of South Carolina (USC) Dornsife College of Letters, Arts and Science watched the brains of 40 self-declared liberal students in a functional MRI. USC neuroscientists compared whether, and how much, people change their minds on non-political and political issues when provided counter-evidence. During their brain imaging sessions, participants were presented with eight political statements that they had said they believe just as strongly as a set of eight non-political statements. They were then shown five counter claims that challenged each statement.

Participants rated the strength of their belief in the original statement on a scale of 1-7 after reading each counter claim. The scientists then studied their brain scans to determine which areas became most engaged during these challenges.  Participants did not change their beliefs much, if at all, when provided with evidence that countered political statements. But the strength of their beliefs weakened by one or two points when provided with evidence that countered non-political statements.

The study, which concluded last month, found that people who were most resistant to changing their beliefs had more activity in the amygdala (a pair of almond-shaped areas near the center of the brain) and the insular cortex, compared with people who were more willing to change their minds. “The amygdala in particular is known to be especially involved in perceiving threat and anxiety,” said USC Psychologist Kaplan, explaining that “the insular cortex processes feelings from the body, and it is important for detecting the emotional salience of stimuli. That is consistent with the idea that when we feel threatened, anxious or emotional, then we are less likely to change our minds.” He also noted that a system in the brain called the default mode network surged in activity when participants’ political beliefs were challenged. “These areas of the brain have been linked to thinking about who we are, and with the kind of rumination or deep thinking that takes us away from the here and now,” Kaplan said.

People will flexibly react to changes in their environment. If a sidewalk or road is blocked then we have no difficulty understanding that we need to consider finding a different route to our destination. But we are not consistently rationally flexible, particularly with regard to beliefs that we link to our self-identity. Instead of prioritizing best fit with the overall available evidence, we may negatively react to evidence that conflicts with our self-identity linked beliefs similar to the way we negatively react to a threat.

People tend to link their religious beliefs to their self-identity at least as much as they do their political beliefs and they also may link their religious and political beliefs together. This is one reason why we should be careful about how we go about justifying our beliefs. We need to be careful to open-mindedly allow the overall available empirical evidence dictate to us what our beliefs about how the universe functions should be. We are prone to reversing this sequence and telling the universe how it functions as if we are each master of the universe deities. The universe is not about us, so what we think should be true, or what we want to be true, or how we define our self-identity, are irrelevant.

To try to avoid this error, my advice to everyone, regardless of whether you are a metaphysical naturalist or supernaturalist, is to consider what would need to be different about our universe to convince you to change your conclusion. Too often, when I ask this question I get pushback directed against the question itself. Not all atheists are empiricists. People react negatively to the question, claiming that it is wrong to talk about an alternative universe, that it is wrong to consider other possibilities, because that is a place of falsehood. It is said that our universe is naturalistic because supernaturalism is impossible, and to even ask such a question is to accept that supernaturalism is possible and thus is a mistake. It is said that supernaturalism is a non-starter and to even entertain it as a possibility is an unwarranted concession.

My response is this: We cannot trust our intuition, or anything mostly rooted in intuition, like faith or hope, to answer the big questions about how the universe functions because the answers to the big questions are mostly non-intuitive and counter-intuitive. So it is a mistake to rule out anything a-priori or to rely only on logic not anchored in evidenced. It is often inconsistent for some assertion to be simultaneously true and false. Therefore it is reasonable to conclude that given that X (naturalism) is true it is probably also the case that the opposite of X (supernaturalism) is impossible. But the impossibility of X being false when it is true is not a proper justification for concluding X is true, we still must justify our conclusion regarding X. To justify the conclusion that it is impossible for X to be false, we paradoxically should consider what is missing that would be required to properly justify a conclusion that X is false.

A-priori ruling out even identifying what qualifies as missing evidence favoring alternative conclusions is bad epistemology. Fairly considering what is needed to justify a conclusion entails also considering what would be needed to justify a contrary conclusion. Our justification for reaching a particular conclusion about how the universe functions is incomplete if we cannot identify missing justifications for concluding otherwise. When a conclusion is consistently supported by an abundance of highly diversified, interconnected, and direct empirical evidence it becomes unlikely that the available evidence will change so drastically as to favor the contrary conclusion, so we need not worry that our beliefs will be unstable if we allow the evidence to dictate. When a conclusion is inconsistently supported by rare, narrow, unconnected, and indirect non-empirical evidence then we should not have a strong commitment to that conclusion. Either way, there is no harm in identifying what evidence is missing that would change our conclusion if it was found.

Academic endeavors like science are publicly funded and some Senators and Representatives are prone to threaten to cut funding if they think scientific outputs interfere with their preferred political ideology. Elected school boards make decisions regarding educational curriculums, and elected governments decide if they fund private schools that set their own curriculums. Theism is a popular and often strongly held belief and educators and scientists fear popular antagonism if science is perceived as being anti-theistic. Theists falsely claim that science has a built in bias favoring naturalism, that science has a built-in self-dependency upon naturalism, and therefore science cannot fairly adjudicate the naturalism versus supernaturalism question. Some educators and scientists, many of whom are themselves theists, actively promote this false claim of bias at least in part because it is convenient as a means for avoiding provoking theists. Yes, modern knowledge favors naturalism. But our process of acquiring knowledge is not the source of this bias, the source of this bias is the nature of our universe.

People who imagine themselves living in a supernatural universe are not going to then respect a belittled empiricism that is deemed to lack the ability to challenge theism (note that most of the same theists would probably enthusiastically cite a scientific consensus that prayer works as a confirmation of God). With the false claim that empiricism has a built in bias for naturalism widely accepted it can be small additional steps to conclude that empiricism is similarly biased in multiple other contexts, that empiricism is not the best way to determine how the universe works, and that religion, wealthy business, popular entertainment, and political leaders are the most reliable sources of information about how the universe functions. Not all theists generalize away empiricism, expertise, and modern knowledge this way. But it appears that enough people generalize like this to cause mischief. Today we have wealthy businessman President Trump, maybe in 2020 it will be wealthy talk show host President Winfrey?

Sunday, December 10, 2017

An assisted dying act that merits consideration

Maryland has so far been resistant to passing a voluntary assisted end of life law. The state of Victoria in Australia recently enacted a Voluntary Assisted Dying Act law which is more elaborate and detailed than similar state laws in the United States. These laws require that the patient be diagnosed as having a remaining life expectancy of no more than six months, although Victoria's law increases this to twelve months for neurodegenerative diseases. Also, unlike here, Victoria's law has a provision to allow someone other than the patient to sign the patient's written request and to assist with administering the drugs if the patient is unable.

Victoria's law requires doctors to complete training in the end of life options law to be eligible to participate. The law establishes a Voluntary Assisted Dying Review Board to help administer the law. The initial physician receiving a verbal patient can volunteer to be the coordinating physician who makes an assessment that the request complies with the law. The coordinating doctor is sometimes required to obtain the assistance of specialists. The assessment results are given to the Board and if the coordinating doctor accepts then a second assessment begins by another doctor. A third assessment is allowed if the second assessment conflicts with the first assessment.  

If the assessments accept the request then the patient can submit a written request with two certified eyewitnesses together with the coordinating doctor as a third witness. The patient makes a final verbal request and identifies a contact person. The contact person is responsible for returning unused dispensed drugs to the pharmacy. The coordinating doctor certifies the request in writing, notifies the Board, and applies for a permit to prescribe the drugs. The Secretary of the state department of health may refuse to issue the permit if legal noncompliance is suspected.

It may be worthwhile for lawmakers submitting "end of life options" bills in states like Maryland to consider including the additional procedures and safeguards found in Victoria's law. The additions of a board, formalized written assessments, required specialist evaluation if warranted, a permit, a person designated to return unused drugs, and a 12 month availability for neurodegenerative diseases, may convince more lawmakers that the proposal merits adoption. State government employees should consider the forms included in Victoria's law for ideas when writing regulations for implementing their state's end of life options laws.

Saturday, October 21, 2017

Petition the Boy of Scouts of America to include nontheists

Message from the Secular Coalition for America:

The Boy Scouts of America Charter and ByLaws says: "The Boy Scouts of America maintains that no member can grow into the best kind of citizen without recognizing an obligation to God." No child should ever feel that they are less good, less worthy, or less capable to lead or "grow into the best kind of citizen" because they do not subscribe to religion. We know that the best kind of citizens are those who respect all people, of all faiths and no faith. The religiously unaffiliated is now the largest "religious group" in the country and our numbers are strongest among young people. We will no longer stay quiet and let organizations like the Boy Scouts tell us and our children that we cannot be moral upstanding citizens without God. With your help and your voice, we will change hearts, minds, and policy. Please help us continue to raise awareness about this issue by signing and then sharing this petition with your friends and family, especially parents who may be considering Boy Scouts of America for their children. 

Sunday, October 15, 2017

Federal judge declares higher power must be deity

U.S. District Judge Rosemary Collyer recently ruled that the House chaplain’s refusal to allow an atheist to deliver the morning prayer complies with the Equal Protection Clause.

The dispute dates to February 2015, when Rep. Mark Pocan, a Wisconsin Democrat, invited one of his constituents, Dan Barker, to deliver the invocation as a Congressional guest. The office of Catholic House Chaplain Patrick Conroy informed Barker that all guest chaplains must be “ordained by a recognized body in the faith in which he/she practices” and must present a copy of their ordination certificate as proof. He also advised that the invocation must address a “higher power.”

Barker had retained his 1975 ordination as a means to officiate at weddings to bypass discriminatory laws that restrict marriage officiants to clergy. Barker submitted his ordination certificate to Conroy’s office. He said he believes there is no higher power than “we, the people of these United States.” Conroy did not respond for almost one year, until January 2016. He then informed Barker he was denying his request to give the invocation because he had publicly announced his atheism.  

Mr. Barker, the co-president of the Wisconsin-based Freedom From Religion Foundation, consulted a lawyer and sued the Chaplain, and Speaker Paul Ryan, in May 2016. He claimed his exercise of religion rights under the Religious Freedom Restoration Act were violated. Judge Collyer concluded this argument fails: "Taking as true Mr. Barker’s allegations that atheism is his religion and assuming, but not finding, that RFRA applies to the House, the court finds Mr. Barker has failed adequately to allege a claim under RFRA because he fails to allege a substantial burden". She went on to explain that a substantial burden “exists when government action puts ‘substantial pressure on an adherent to modify his behavior and to violate his beliefs.’”  

Government authorities demand that Mr. Barker modify his belief based behavior as a condition for qualifying to participate in a government sponsored activity is a substantial demand. But the "pressure" was insubstantial in the sense that not participating in this activity is relatively easy, much easier than changing beliefs and related behaviors. This reflects the fact that the activity at issue, Congressional sponsored invocation, is itself unnecessary. Congress can perform all of its functions, and lawmakers can voluntarily pray before each session begins, without an opening prayer ritual or a paid chaplain.

Meanwhile, atheists lose an opportunity to gain publicity for themselves by giving any invocations. More significantly, and insidiously, to the extent the laws favor theism there is a resulting diffuse pressure being applied against atheism. Laws endorsing government sponsored theism communicate to the public that there are two tiers of beliefs regarding deity under the laws. There are theists who will leverage any privilege that they think they are granted, and entitled to, under the laws to act against public expressions of atheism or criticisms of theism. 

Barker also cited the U.S. Supreme Court’s 2014 ruling in Town of Greece v. Galloway, which declared that governments cannot discriminate between different beliefs when selecting who gives government sponsored invocations, to support his legal challenge. Collyer, oddly, declared that the ruling didn’t apply to Barker because the justices did not cite atheists in that particular decision. “To decide that Mr. Barker was discriminated against and should be permitted to address the House would be to disregard the Supreme Court precedent that permits legislative prayer,” the judge said.

Judge Collyer is singling out atheists for the negative purpose of refusing to apply an otherwise generally applicable civil rights protection that the Supreme Court recently reasserted. She is inserting a 'discriminate against atheists' clause into the law. Atheists lack generally applicable civil rights protections unless the Supreme Court explicitly says otherwise, according to Collyer.

Insofar as it is true that government sponsored legislative invocation is, by default, for theists only, as Collyer dubiously claims, it follows that the practice of legislative invocation itself violates the constitution for favoring theism over atheism and discriminating against atheist citizens. But legislative invocation was initiated during the first congress and declaring it unconstitutional would be difficult. Therefore, judges who are committed to the constitution and its civic equality protections should be defining legislative invocation as open to people of all beliefs, include those who believe that there is no deity to speak to. This would be easy to do and, contrary to what Collyer says, would not conflict with Supreme Court rulings.

Congress is a place where people occasionally say something that others who are present and listening disagree with, so what is the problem? An opening Congressional invocation by Dan Barker that does not cite deity is not going to infringe on anyone else's rights. Barker, not surprisingly, said he is disappointed with the ruling, complaining that it allowed the House chaplain’s ”personal biases against the nonreligious” to block him from fully participating in our government. I agree.

Sunday, October 08, 2017

The redistricting method of the future

Maryland Redistricting Reform Commission

Office of Governor Larry Hogan

Honorable members of the Redistricting Reform Commission:

Maryland law says: "Each legislative district shall consist of adjoining territory, be compact in form, and of substantially equal population. Due regard shall be given to natural boundaries and the boundaries of political subdivisions." Census tracts average about 4000 people, but in Maryland some census tracts have 24000 people. There are currently 1394 census tracts for about 5.8 million people. A Senate district is currently sized at 123,000 people +/- 4.7%. There are about 30 tracts per Senate district.

These numbers are well suited for mathematical optimization. The general idea is to define the redistricting task as sets of constraints and one or more optimization goals that are precisely defined as equations. Some optimization methods require a single optimization equation. Combining multiple optimization goals that are represented by different units of measurement can be a complication. It is possible to utilize multiple optimization goals that are represented by a common measure, such as a percentage, to avoid this complication.

The more goals there are the greater the risk that different goals will conflict with each other. The tighter the constraints the more likely that there will be no feasible solution. Therefore, it is preferable for the number of different optimization goals to be low or be selected to be non-conflicting and to take precautions that ensure the constraints are realistic.

Contiguity is a constraint. A maximum count of district boundaries crossing significant political subdivisions and natural boundaries are additional constraints. The Redistricting Reform Commission is proposing a maximum +/- 1% population variance which could be implemented as another constraint. Maximum compactness can be the optimization goal, or compactness could be combined with minimum population variance as the optimization goal.

Viable optimization algorithms for redistricting are heuristics that obtain a good result quickly. This is because redistricting optimization is technically a very difficult problem to solve given the vast number of possible solutions. Different software on different computers with different optimization algorithms will produce different results. These different results can be ranked by the optimization goals equation. This presents an opportunity to implement redistricting as a contest. Competitors can be given instructions for how to submit redistricting map proposals. The earliest submitted redistricting map that generated the highest optimization score while meeting all constraints would be automatically adopted. As an incentive the winning proposal could receive a cash award.

Compactness can be measured by boundary shape. Or by the degree to which the district spreads from a central core, called "dispersion". Or by housing patterns, which is sometimes referred to as population compactness. District tendrils are less meaningful in sparsely populated areas but more meaningful where the population is densely packed. The ratio of the proposed district's perimeter and the perimeter of a circle with the same area size is an example of a boundary shape measure of compactness.

Members of the Redistricting Reform Commission should consult with the computer science and mathematics departments at universities and colleges, particular those that offer graduate degrees in Operations Research, for expert advice. Examples of automated computer redistricting, some with free source code, are available on the Internet (,,,, and Applicable algorithms include polygonal clustering, graph partitioning, simulated annealing, and tabu search, among others. Spatial contiguity can be formulated in a mixed integer programming framework, so mathematical programming methods may also be viable.

The district boundaries after each census could be very different from the prior boundaries, which can contribute to making elections more competitive. The result of relying on mathematical optimization for redistricting will be gerrymander free and fair by the "justice is blind" standard. There is no need for a redistricting committee. A voting rights committee composed of former judges could be responsible for splitting some Senate districts into two or three Delegate districts to try to ensure compliance with the Voting Rights Act of 1965.  

Currently the Delegate districts are three member by default but with 16 one member and 12 two member districts that are not publicly explained. The Governor's Redistricting Reform Commission is recommending one member Delegate districts by default with fewer exceptions. However, one member Delegate districts give each citizen fewer representatives assigned to different committees which weakens citizens' influence over the bills. The committee votes on bills are more important than the floor votes because bills that fail in committee almost always die and bills approved in committee usually also pass when they go to floor vote. The small size of single member Delegate districts risks rendering a +/- 1% population variance constraint along with the other constraints impossible. Also, one member Delegate districts undermines Maryland's ability to demonstrate compliance with the Voting Rights Act because occasionally merging Delegate districts is unlikely to increase minority representation. 

It may be better to retain the current three member Delegate district default and require that all exceptions be justified in writing as promoting increased minority representation in accordance with the Voting Rights Act. Alternatively, mathematical optimization could draw three Delegate districts in each Senate district but with somewhat different constraints and optimization goals then were utilized to draw the Senate districts. In particular, the optimization goal could be revised to prioritize meeting the requirements of the Voting Rights Act and the constraints could be loosened for those Senate districts that have a demographic profile which introduce Voting Rights Act compliance concerns. Dividing each Senate district into three Delegate districts could be a contest for finding the best redistricting map. This would create a two phase redistricting process, Senate districts first, Delegate districts second, that will increase the time needed to complete redistricting.

Federal redistricting standards are somewhat different from the state standards.  Also, Congressional districts effect the national election and thus are no longer only about the state of Maryland. If Maryland stops gerrymandering Congressional districts while Republican states continue to gerrymander then the next federal elections results will be more favorable for Republicans. It is more likely that a General Assembly redistricting reform bill will be enacted if it is not paired with Congressional redistricting. Therefore, it would be better for the Governor's office and lawmakers to place Congressional redistricting reform proposals into a separate bill, or postpone Congressional redistricting reform until after a multi-state reform collaboration effort that crosses the partisan divide is arranged. 

Mathematical optimization is the redistricting method of the future. Reliable enabling technology is available. Maryland has people with the skills needed to implement automated redistricting. I appeal to the Commission and state lawmakers to seriously consider mathematical optimization for redistricting.

Saturday, October 07, 2017

Religion sometimes threatens civil rights and rule of law

The Justice Department claims that the free exercise of religion clause of the first amendment to our constitution includes the freedom to act as one's religion demands even when such actions curtail the civil rights of others or conflict with the laws.  This threatens the rights of countless Americans, particularly religious minorities and non-theists.  We see this in the recent executive order granting employers the option to omit contraceptive coverage from employer sponsored health insurance plans.  We see this in the recent Justice Department amicus brief supporting a baker who refused to provide a same gender couple with a marriage cake.  If free exercise of religion is not limited by civil rights protections, or generally applicable laws with good secular justifications, then where is the stopping line?  How does a judge decide that a free exercise claim goes too far?

It is difficult to fathom how a business that is owned by holders of publicly traded stock can be said to worship a deity, or posses a religious belief, let alone exercise a religion.  A way to avoid this difficulty has been to limit the applicability of free exercise claims to privately owned and "closely held" business.  In a private ownership context the business is deemed to be a vehicle through which the business owners practice their religion.  Donald Trump's recent executive order exempting businesses from including contraceptive coverage in health plans dispensed with this publicly owned versus privately owned distinction.  This will provoke lawsuits because it is so unprecedentedly broad.

The approach taken by this Republican party administration, and to some extent by the Republican party more generally, favors allowing businesses to refuse to sell products or services to, and maybe also refuse to hire or promote, individuals who do not respect whatever false beliefs, or unjustified limits on behavior, the business decides to impose on its customers or employees in the name of exercising any of the many religions. The Justice Department now appears to be arguing that a federal contractor should be able to refuse to provide services to people, including in emergencies, without risk of losing federal contracts and that organizations which were prohibited from requiring all of their employees to follow the tenets of the organization's faith should instead be able to discriminate against such employees.

An obvious problem with interpretations of free exercise of religion that privileges religious beliefs over other beliefs is that religious beliefs are themselves contradicted by religious beliefs so that there is no way to adjudicate between conflicting free exercise claims without denying someone their free exercise of their religion.  Another problem with privileging religious beliefs is that there is a lack of proper justification for the laws treating opposing beliefs differently.  If person P1 claims X is their religious belief and person P2 claims ~X is their corresponding anti-religious belief then why should the law favor X over ~X?  

We already know whose free exercise of religion will be disadvantaged if judges are required to resolve clashes between conflicting beliefs.  The free exercise of religion by employers will triumph over that of employees and customers.  Otherwise, the adherents of the smaller, less wealthy, less popular, less organized, less zealous, religion, or the religion that the judge disfavors, will partially lose free exercise of their religion. 

Free exercise is a meritorious and viable legal principle when it functions as a general protection against government repression of religions, provided that it is subordinate to civil rights equity principles and to laws that are evidenced to promote human welfare, regardless of employer, employee, or customer status.  The resulting secular laws may sometimes conflict with religiously motivated practices.  In that case the religious practices lose.  Interfering with religious practices is not a secular goal, it is a last resort from practical necessity.

It is not difficult to understand why some religious people who are convinced that their religion is both factually true and important object when their religious motivated practice is being restricted to accommodate those who have contrary beliefs or to respect secular laws. Insofar as our laws conflict with religious beliefs, those religious beliefs are arguably being disadvantaged, and therefore we should not be surprised if some people react negatively.  Secular democratic government depends, at least to some extent, and arguably to a large extent, upon the citizenry being, at least to some extent, secular.  

Accordingly, people who value secularism should argue publicly for secular government, but by itself that will not suffice.  We also need to argue more generally against religion as an arbiter of the facts about how the world works because the inability of religion to identify facts about how the world works is the reason that laws should be secular instead of religious.  If it were otherwise, if religion was a valid method for determining how the world works (if our universe was supernatural) then our laws should be religious instead of secular.

Saturday, September 16, 2017

The Big Questions in Philosophy by David K. Johnson

David K. Johnson is a professor of philosophy at Kings College in Pennsylvania who produced a Great Courses series of videos titled The Big Questions of Philosophy that sells for about $70 dollars (less for audio, more for DVD).  Some county government library systems have contracted with a company that sponsors a web site, and also an app, called kanopy.  Kanopy makes many videos available for free to people with library cards.  At least some, if not most, of those videos do not appear to be very good.  But among the many hundreds of free videos on kanopy is the entire set of 36 half hour lectures of the aforementioned course.   

He is probably not as rich, nor as famous, as George Soros whose book features five of his philosophy lectures. After watching Professor Johnson's first five lectures, and excerpts from a few other lectures, I will take a chance on him and recommend his videos.  This is the philosophy 101 course that should be included as part of everyone's basic education but not everyone receives.

Saturday, September 09, 2017

Unsafe Spaces Tour panel at American University this month

Spiked magazine is sponsoring a series of Unsafe Spaces Tour panels at different universities, including Rutgers and Harvard.  They claim they are trying to promote "the humanist case for free speech". Tickets are free.  On September 28, there’s a panel at American University (Washington, D.C.) on “Feminism, sex, and censorship on campus” featuring Nadine Strossen, Elizabeth Nolan Brown, Ella Whelan, and Robert Shibley.

Saturday, August 19, 2017

A Darwin substitute for Lamarck?

Why do animals and plants appear to be well adapted to their environments?  Lamarck had an answer that appears to make sense.  Environmental changes promote behavioral changes which promote corresponding structural adaptations in animals and plants that are transmitted to offspring.  However, Lamarck's hypothesis contradicts the prevailing theory that natural selection acts on random genetic mutations. The post Darwin discovery of genes defeated Lamarck's theory while simultaneously demonstrating the validity of much of Darwin's theory.  Yet there is still some wiggle room here for a superficially Lamarckian, non-random component within the prevailing, random mutation, framework.

Maybe natural selection acts on random mutations to produce outcomes that appear Lamarckian because environmental changes impact particular genes differently.  Particular genes can be stimulated by an environmental change.  Maybe the rate of mutation on stimulated genes increases relative to the rate in genes unaffected by the environmental change.   Because random mutations in that gene are more likely to occur more quickly than would otherwise be the case, the likelihood of a rare beneficial mutation also increases.  Natural selection then favors the rare beneficial mutation in the overall population.

When cells replicate their DNA, the replication by transcription mechanism sometimes stalls. Sometimes, when a stalled replication resumes, a gene sequence is deleted or extra copies of it are made.  A combination of factors could make these copying errors more likely to occur for those particular genes that are actively responding to environmental stresses, so that those particular genes are more likely to show copy number variation.

I read that there is some evidence that "adaptive mutation" of this sort could be occurring in microorganisms.  For example, there is more copy number variation of the copper-resistance gene CUP1 when it is stimulated by environmental copper.  When CUP1 was modified by a team of researchers led by Jonathan Houseley, a specialist in molecular biology and genetics at the Babraham Institute in Cambridge, to react to a non-toxic sugar instead of to copper, an increase in copy number variation result was again seen after the modified CUP1 gene was stimulated by that environmental sugar.  

There is substantial skepticism that adaptive mutation plays a significant role in evolution among biologists.  More and better evidence for stimulated gene localized copy number variation, and a mechanism that translates stimulation of a gene into a higher mutation rate, will be required for this speculative hypothesis to be accepted.  Efforts to prove or disprove adaptive mutation in microorganisms may accelerate as a result of the recent positive CUP1 gene results.  If biologists one day determine that adaptive mutation is true, and probably had some role in humans being one branch on the primate tree, then will more people put aside their religious beliefs and accept that humans are ancestors of microorganisms?

Sunday, August 13, 2017

Over there and over here, one difference

We collectively make our history.  Human history has its ups and downs.  Our legacy is not particularly good overall, there are many ugly events to relate.  We should not be proud of our history, it is too often shameful.  We need our history, for its pains and glories, and it's ambiguities too, as lessons.  From history we can learn about what not to do, sometimes about what to do, to locate a better future.  From the past we select what history we value when we name our airports, towns, and highways, and who we honor with memorial statues in our public places.  

Having lived my youth in the northeast, I found little difference overall following my move south to the mid-Atlantic past the Mason-Dixon Line.  The Swatztikas on the local train tressle and etched into the public school desks and library cubicles, the German language "Juden" graffiti in black paint on my high school, my immediate neighbor with a pick-up truck whose rear window was covered by a Confederate battle flag, over there.  New co-workers who made a point of telling me that they supported David Duke, the Swatztikas drawn inside a cave, on a motorcyclist's helmet, drawn on the downtown street signs, and building walls, over here.  

However, there is a difference. Here, but not there, the names of Confederate generals were part of the public infrastructure.  Those Confederate generals endorsed, and fought to preserve, commercial kidnapping and enslaving of Africans, many of whom were killed as a result, and whose ancestors live among us today.  The Civil War history was not a part of my life.  My European Jewish ancestors came here during and after WW I, fleeing the anti-semitism that later morphed into the mass murder of Jews who remained in Europe.  Yet this history, both on the Nazi and Confederate sides, kept announcing itself uninvited in odd places and contexts where it did not belong, strangely introduced and repeated by people with crayons, ink, knives, paint, flags, and words.  But with the highway and place names for Confederate war heroes here only.

The people of Charlottesville, like all towns, decide for themselves what history they want to associate themselves with.  They acted reasonably and responsibly when they decided to remove a statue of a Confederate general from their town park.  Among the decisions our local governments face, whether or not that statue resides in a park is not a particularly pressing national concern.  This is primarily a concern for the people living in those towns.

The people with torches and battle flags who thought the public display of this particular statue was so important that they traveled from all over the country to demonstrate for keeping the statue in that park have misdirected priorities.  Adding or removing a statue does not establish, change, or erase the history.   The overreaction against the removal of the statue is evidence that such statues and place names are not innocent and academic placeholders for history.  They are deemed by caucasian, and some Christian, supremacists, such as David Duke and his followers, as representing a positive history that we should emulate, as endorsing traditional attitudes and policies that we should identify ourselves with today.  Instead, towns and states should follow the positive trend of removing the Confederate war hero statues and place names.  Their essential place is in our history books.  They need not be, and should not be, the statues in our parks or our place names.

Saturday, July 22, 2017

Evidence for string theory and atheism

String theory posits that the particles and forces that physicists detect using machines are vibrating, string shaped units of energy embedded in a universe that is multi-dimensional.  Like most of science, this theory is non-intuitive and counter-intuitive to us.  Not in a million years would any philosopher, or theologian, or science fiction author, have invented string theory by reasoning primarily from their intuition, instead of from following the empirical evidence. It can be difficult, even for the scientists themselves, but especially for non-scientists like me, to grasp the concept.  The pervasively non-intuitive and counter-intuitive quality of modern theories regarding how our universe functions is important.  This tells us that we must rely on empirical evidence, and the consensus of experts when possible, not on our intuition, because our ignorant intuition is incompetent and more likely to be a counter-productive obstacle than a productive tool for understanding.

Electrons have a property called spin that either has the same, or opposite, direction as the direction that the electron travels.  According to string theory, the electron spin can flip directions in the presence of a strong gravitational field and magnetic field, such as near the event horizon of a black hole.  Theorists have concluded that in some contexts a temperature gradient can substitute for the gravitational field.

Recently, several IBM scientists, interested in exploring the possibility of deploying new types of materials for building future electronic devices for their employer, decided to test if they could observe a change in behavior of electrons in a semimetal that they were studying.  Semimetals are intermediate between conductive metals and semiconductors.  If string theory is true then a temperature gradient and strong magnetic field applied to the semimetal will break the spin symmetry conservation property of the electrons residing in the semimetal and produce a measureable current.  The IBM scientists succeeded in verifying this prediction, see Scientists Observe Gravitational Anomaly on Earth.

So what is the point of this post?  String theory, like most of modern knowledge about how the universe functions, is relevant to the theism versus atheism disagreement.  String theory, like all physics, chemistry, biology, etc., is thoroughly naturalistic.  String theory translates into mathematical equations that express the logic of physical, material, mechanical processes.  All of modern knowledge regarding how our universe functions is derived from naturalistic methods and reaches conclusions that are naturalistic.

Humanity did not begin the pursuit for knowledge preferring naturalistic methods and explanations.  We got pulled towards naturalism despite a long standing preference for supernaturalism.  This distinction is not binary, it is a continuum, and there is no measuring device.  Naturalism imposes constraints that limits options to explain and people, wanting explanation, tend to consider the naturalism constraint to be too restrictive.  Yet the naturalism versus supernaturalism contest outcome lopsidedly favors naturalism, it is not a close call.  Time and time again, at all levels of focus from the smallest detail to the largest generality, there is opportunity for either more naturalistic oriented or more supernaturalistic oriented methods to be productive, and for either naturalistic favoring or supernaturalistic favoring conclusions to be successful.  Unrelentingly, over and over again, only the more naturalistic oriented methods are productive and only the naturalistic favoring conclusions are successful.

Several hundred years ago it was reasonable for well educated adults to endorse supernaturalism.  Science eventually abandoned supernaturalism because of its track record of total failure.  Today, theists, and non-atheist agnostics also, are downplaying, ignoring, and disregarding the pervasiveness, consistency, and diversity of the evidence for naturalism.  Many agnostics and theists who can be very good at respecting and following the empirical evidence in their professional and non-professional lives, nevertheless fail, apparently unwittingly, to apply that same rational standard to this question.  If they did apply the same rational standard of attending to the overall available evidence, as they otherwise routinely do every day, instead of myopically focusing narrowly on lack of knowledge trivialities and mysteries, and carefully avoided the mistake of placing personal preference or intuition over evidence, then they would be atheists.

Sunday, July 16, 2017

Summer 2017 emails to Congress

Send your emails using the forms provided by Americans United for Separation of Church and State and/or Secular Coalition for America and/or Freedom From Religion Foundation. Or call or write letters.

The "Johnson Amendment" is the commonly utilized name for a law that prohibits nonprofit charities (religious nonprofits are automatically categorized as charities) that are financed with tax deductible contributions from endorsing political candidates.  Houses of worship (a.k.a. "churches"), their integrated auxiliaries, and conventions or associations of houses of worship, are the only nonprofits that not required to file an IRS tax form (or at least a Form 990N declaring that their income is under $50,000).  IRS Form 990 discloses basic information about a nonprofit’s expenditures and sources of revenue.  Because houses of worship are exempt from this crucial transparency requirement, the repeal of the Johnson Amendment would effectively allow houses of worship to function like invisible Super PACs and unleash a wave of religiously motivated ‘dark money’ into the political system.  Full repeal of the Johnson Amendment is the Religious Right's #1 priority.  Ask your members of Congress to safeguard this important law that acknowledges the fact that political campaigns are not a charitable activity and therefore should not be funded with tax deductible contributions (under current law, non-profits that are funded with contributions which are not tax deductible can legally support political campaigns).  Also, please ask them to eliminate the IRS Form 990 exemption for houses of worship.

The Do No Harm Act has been reintroduced in the House.  This bill would restore true religious freedom by amending the 1993 Religious Freedom Restoration Act (RFRA) to ensure that religion is not used as a license to deprive some people of their secular civil rights.  Privileging religious beliefs will continue to erode progress on civil rights until Congress draws a line in the sand.  Tell your members of Congress to restore the meaning of religious freedom as a shield to protect individuals of all faiths and no faith, not as a weapon for people to impose their religious beliefs on others who reject those beliefs, by co-sponsoring the Do No Harm Act, and thank Congressmen Bobby Scott (D-VA) and Joe Kennedy (D-MA) for introducing the bill. 

Saturday, June 24, 2017

Maajid Nawaz files lawsuit against the SPLC

The Quilliam Foundation is a counter-extremism think tank that was co-founded by Ed Husain and Maajid Nawaz, former activists in the radical Islamist party Hizb ut-TahrirQuilliam's argument is that the government should not only tackle those advocating terrorist violence, but should also focus on those who have the same views, even if they adopt peaceful meansSupporters say this is necessary to tackle the roots of terrorist violence for the long term.  Critics of the foundation accuse it of McCarthyite smear tactics, brand its claims ridiculous, and say the foundation labels vast swathes of Muslim Britain as extremist.  It can be difficult to know who is right without knowing more about the Muslim groups that Quilliam criticized.  But based on what Nawaz says and writes in general, he sounds like a reasonable, moderate, guy and not at all like an "anti-Muslim extremist" that the Southern Poverty Law Center oddly rates him to be.

He is somewhat alarmist, using the adjective "insurgency" to describe the jihadist movement in Europe, which may describe how some jihadists see themselves.  His foundation depends on funding, so there is a self-interest for him to promote fear about the threat that his foundation focuses on.  Quilliam receives funding from the conservative leaning Templeton Foundation which spends tens of millions of dollars a year to promote the popular but dubious view that exclusively naturalistic science and supernatural theistic religions are mutually consistent and supportive.  Nawaz's estimates of the overall numbers of violence prone "jihadists", and non-violent but potentially jihad violence supporting Islamists, in Britain are somewhat high but appears to be defensible.  He says there are 23,000 extremists, which is the sum of the 3,000 currently under investigation plus the 20,000 previously under investigation and still listed by the government as people of interest (some of the people accused of participating in attacks are among those on this latter list).  He estimates there are about three times as many sympathizers out of about "4 million" British Muslims, which is between 2-3% total.  

None of this qualifies him as being an extremist of any sort. Nawaz is a secularist Muslim, his expressed views are consistently anti-extremist.  People like him do not threaten the civic equality (let alone the lives) of atheists, gays, Jews, Christians, women, music band and night club attendees, or other Muslims like extremists do.  Here is the recent video of Bill Maher's interview of Maajid Nawaz.  Free speech protection is legally favored which makes it difficult for defamation lawsuits to prevail in the United States.  Accordingly, SPLC may be exonerated under the standards set in our laws, but they are guilty of defamation regardless of the lawsuit's final outcome.

Sunday, June 18, 2017

Douglas Navarick's false equivelancy

Douglas J. Navarick is a Professor of Psychology at California State University.  He is sometimes published in Skeptic magazine.  His perspective is that many atheists are not skeptical, but are instead dogmatic, and thus suffer from a similar, if not identical, pathology as the hyper-religious.  His opposition to dogmatic thinking is well-grounded, but his method of identifying dogmatic thinking is mistaken.   Navarick claims that the “Four Horsemen” of the New Atheism —Christopher Hitchens, Sam Harris, Richard Dawkins, and Daniel Dennett, share "the off putting dogmatism of the hyper-religious".  I disagree and I am going to try to explain where I think Navarick is going wrong.

Navarick argues that the evidence for ESP is greater than the evidence for abiogenesis.  He says the evidence for the former is at best weak, but the evidence for the latter is non-existent.  This is one of his mistakes.  Macroevolution is evidence for abiogenesis because they are logically related to each other probabilistically.  If macroevolution was disproved then life would be more likely to be a supernaturalistic phenomena and abiogenesis, because it is the naturalistic explanation for the start of life, would be less probable.  Similarly, if the one to one relationship between chemistry and biology was disproved then life would be more likely to be a supernaturalistic phenomena and abiogenesis would be less probable.

Navarick, like many other non-atheists, has this big blind spot.  He does not acknowledge the logical connection between macroevolution being a strictly naturalistic phenomena, life being a strictly naturalistic phenomena, and life having a strictly naturalistic origin.  All evidence for one is evidence for the latter, and vica versa, yet Navarick basis his argument on a refusal to acknowledge this.  Instead, he downplays the significance of the logical connection between physics, chemistry, and biology each being exclusively naturalistic to advance his argument that life itself is supernaturalistic.

He defines God thusly: "A willful, creative, force that transcends material reality and operates both through and independently of natural laws."  Any force that operates through natural laws would appear to us as natural laws.  To justifiably conclude otherwise we would need good evidence that natural laws by themselves are insufficient.  Contrary to what Navarick tries to argue, we have no good evidence that natural laws are by themselves insufficient.  What remains are God of the gaps arguments which are weak arguments.  If that is how God operates then God is hiding from us and therefore we should disbelieve in God.

Navarick claims that his God theory makes "a strong prediction" that efforts to create living cells will fail.  This is a good example of a weak, God of the gaps argument.  This is because we can expect efforts to create living cells to fail for other reasons that are consistent with abiogenesis being true.  In particular, abiogenesis may be a rare, and slow to occur, process.  We do not have a full understanding of the physical conditions at the time and place life began and we cannot go back in time to witness it.  There was a lot of time, water, molecules, heat, comets and meteorites, minerals, solar radiation, variations in local conditions, etc. for a rare abiogenesis process to occur once naturally, and the required combinations of events may be complex and very difficult to identify and reproduce.

He also cites the lack of evidence for intelligent life elsewhere in the universe as evidence for his God theory.  But it is not clear why his God failed to fill our universe with intelligent life, why his God relied on the cruelty intrinsic to evolution as the natural law to disguise her presence, why his God first placed us humans on this particular isolated planet and Galaxy so many billions years after the universe began, why his God would create such an expansive universe beyond what we need, the origin of his God, etc.  In contrast, there are naturalistic explanations for our not yet encountering other intelligent life.  Multi-cellular life may be much slower and less likely to evolve than single celled life, intelligent life may be too fragile to usually survive for long in our frequently harsh to life universe, the tremendous distances between galaxies and stars make it less likely we will encounter intelligent life, and our searches to date may not be looking at good signals or in the best locations.

Navarick proposes that life is an independent property that catalyzes biochemical reactions without actually participating in these reactions.  Life, he argues, thus precedes the reactions, it does not result from them.  He cites as evidence cryopreservation, where "all biochemical activity ceases ... but the cells remain alive".  Yet there is nothing about cryopreservation that is inconsistent with life consisting of biochemistry alone.  Life ceases when the biochemistry ceases due to insufficient temperature.  The biochemistry, and therefore life, resume when the minimum requisite temperature returns.  We encounter a similar phenomena of non-biological chemistry stopping, and then resuming, with changes in temperature without inferring a supernatural catalyzing force.

Navarick sounds desperate to retain supernaturalism against the odds.  As many hard skeptics do, he starts with a biased commitment to retaining the viability of supernaturalism against the evidence and then homes in on whatever excuses he can find.  From there he promotes his agnostic perspective as the most reasonable conclusion.  He acknowledges that theists and atheists can be agnostic and categorizes them as being reasonable, while claiming that gnostic theists and atheists are two equally dogmatic extremes, as if rational reasonableness is a synonym for the geometric middle ground between opposing positions.  

Navarick unfairly assumes any atheist who does not explicitly cite evidence or uncertainty, without prompting, when explaining why they are an atheist, is dogmatic.  But empiricism is not a synonym for agnosticism, defined as being "without a claim of knowledge", as Navarick claims.  Empiricism can dictate a firm conclusion.  Navarick implicitly basis his argument for characterizing many atheists as being dogmatic on denying that evidence for naturalism is pervasive, diverse, and consistent, while evidence for supernaturalism is almost non-existent.  He does not explicitly concede that his argument rests on this assumption and that his argument is therefore biased against atheism.

It is no doubt true that some atheists adopt a somewhat circular, closed minded, dogmatic approach to justifying their atheism, like Navarick claims.  Not all atheists are epistemologically sophisticated.  However, Navarick's survey results, where he catagorizes atheists as nonbelievers, agnostic atheists, or gnostic atheists, and concludes that the category that by his measure was most popular, gnostic atheists, are dogmatic, is too flawed to provide an accurate measure of the prevalence of dogmatism among atheists.

Friday, June 09, 2017

Senators Sanders and Van Hollen v. Russell Vought

Wheaton College, a Christian school, fired a political science professor for a Facebook post intended to express solidarity with Muslims. Russell Vought, the new nominee for deputy director of the Office of Management and Budget, had defended the school in an article published in January 2016 on a conservative websiteDuring the hearing, Senator Sanders repeatedly quoted one passage from that article which he found to be objectionable: "Muslims do not simply have a deficient theology. They do not know God because they have rejected Jesus Christ his Son, and they stand condemned."

John 3:18 depicts Jesus as saying: “Whoever believes in [the Son] is not condemned, but whoever does not believe is condemned already, because he has not believed in the name of the only Son of God.”  Senator Sanders characterized Vought's conclusion thusly: “In my view, the statement made by Mr. Vought is indefensible, it is hateful, it is Islamophobic, and it is an insult to over a billion Muslims throughout the world..."  Obviously, insulting under a billion people would be better.  Let's get our priorities right, Mr. Vought should pay more attention to the demographics and less attention to the anonymous author of John 3:18.  Unfortunately, Mr. Vought prioritizes John 3:18 as if it was revealed to us by an all powerful God, and some of those aforementioned billion plus people anchor their beliefs similarly on their sacred books, rendering both groups prone to take great offense too easily while also being confidently and callously offensive to each other.

Russell Vought replied to Senator's Sanders' implied accusation that he is bigoted by citing the doctrine known as imago dei. “As a Christian, I believe that all individuals are made in the image of God and are worthy of dignity and respect, regardless of their religious beliefs.”  Senator Sanders responded with incredulity that Vought respected "other religions".  But Vought did not say he respected other religions, he said he believes in respecting individuals regardless of their religious beliefs.  The question here is whether Vought's grounding his support for firing the professor in Christian doctrine is inconsistent with his assertion that his Christianity respects individual dignity without regard to religious beliefs.

What was troubling about Russell Vought's responses was his repeated assertions of religious motivations and justifications.  How about a straightforward "I believe that all individuals are worthy of dignity and respect regardless of their religious beliefs" without attaching that sentiment to his religious identity and beliefs?  But to be fair to Vought, Sanders was challenging Vought's prior religiously motivated argument, so Vought had some reason to want to defend his religious beliefs in response.

Senator Sanders' is being reasonable in not respecting Vought's reliance on John 3:18, and I share Senator Sanders' strong dislike for that religious belief.  But is Vought therefore unfit to serve as the deputy director of the Office of Management and Budget?  Senator Sanders repeatedly cited "Islamophobia" in his criticism of Vought.  Yet Senator Sanders himself was arguably exhibiting "Christianity-phobia" at the hearing.  People who keep railing one-sidedly against Islamophobia as the bigotry of the day that needs to be condemned tend to overlook an important detail: Insofar as the holy books of Islam, Christianity, or Judaism promote negative, harmful, and/or destructive, beliefs among some followers of those religions a corresponding amount of Islamophobia, Christianity-phobia, or Judaism-phobia directed against those religious beliefs is properly justified.

My own Senator, Chris Van Hollen, defended Senator Sanders, saying it’s “irrefutable” that comments like Vought’s suggest to many that he’s condemning all people who aren’t Christians. Well, yes, Vought is doing that, which reflects the negative influence of the Christian bible on his beliefs.  Senator Van Hollen then defended his Christian faith by asserting that Vought’s Christianity is mistaken: “I’m a Christian, but part of being a Christian, in my view, is recognizing that there are lots of ways that people can pursue their God.” Van Hollen then said “No one is questioning your faith ... It’s your comments that suggest a violation of the public trust in what will be a very important position.”  But why must Vought share Van Hollen's view regarding what the bible directs Christians to believe to comply with "the public trust"?  Senator Van Hollen, like Senator Sanders, failed to make a good argument that Vought violates the public trust as a result of his interpretation of John 3:18.

Senators Sanders' and Van Hollen's insistence that the nominee expressed nothing other than respect for other religions in his prior publications as a criteria for being deemed worthy of serving in federal office is inappropriate.  No one fully respects the entirety of everyone else's religious beliefs.  Maybe religious beliefs are false?  Must we respect false beliefs?  Maybe different religious beliefs contradict each other?  What does it mean to respect beliefs that contradict our own beliefs?  The equating of a lack of respect for different religious beliefs with bigotry against individuals who profess those competing religious beliefs is unfair.  

Either Senator could have expressed concern that Vought's support for imposing religious belief mandates on a professor at a Christian college intoduces doubts about whether there would be equal treatment of the employees in the department under his leadership.  Requesting that Vought provide a yes or no response on whether it would be acceptable for the department to discriminate between prospective or current employees on the basis of particular beliefs, including atheism and Islam, or other personal characteristics that some Christians condemn, such as sex outside of marriage or same gender sex, would have provided us with a measure of the nominees commitment to the public trust.  They failed to do that.

Sunday, June 04, 2017

Life, complexity, and negative entropy

Our universe started in a very low entropy state and evolves toward a very high entropy state.   Any decrease of entropy on earth is more than offset by the increase in entropy on the sun.  Does life resist, or at least slow down, the universal increase in entropy?  Some people claim it does and they may then draw conclusions about human ethics from their belief that it does.  

I am skeptical that life slows down the rate of entropy increase.  I am also very skeptical that the answer to this question has any implications for human ethics.  I am wary of getting into discussions on technical topics like this.  I am not a scientist.  But for whatever it is worth, here is my explanation for my skepticism.

For each visible photon the earth absorbs from the sun the earth radiates back to space about 20 infrared photons (earth converts visible light energy absorbed from the sun to "heat" energy that it radiates back to space).  That is a net twenty fold increase in overall entropy.  The overall energy is unchanged (ignoring changes to atmospheric greenhouse gases, etc.) because the energy of one visible photon is twenty times greater than the energy of one infrared photon.  

The amount of solar radiation that is reflected back to space is referred to as the albedo.  Ocean surfaces and rain forests have low albedos, which means that they reflect only a small portion of the sun's energy. Deserts, ice, and clouds, however, have high albedos (desert sands get hot but they still reflect more sun light back into space than grasslands). Over the whole surface of the Earth, about 30 percent of incoming solar energy is reflected back to space.  Higher albedo reduces the rate that the Earth is contributing to entropy increase.

Entropy should not be confused with complexity.  Both low entropy and high entropy conditions are uniform and thus non-complex.  The highly lumpy, highly varied, far from equilibrium, conditions that characterize complexity reach their maximum when entropy is moderate.  Life, because it depends on complexity, is impossible in very low or high entropy conditions.  Moderate entropy is the current condition of our currently complex universe.  So life is consistent with current conditions.

How does low entropy life start given that entropy increases?   One way to try to tackle this question is to focus on metabolism.  The complex chemical pathway, catalyzed by metals such as iron, that converts carbon dioxide to methane, known as serpentinization, resembles the metabolic chemical pathways in some microbial life.  Some people speculate that life may have originated via such a pre-RNA "metabolism first" route.  

Adding hydrogen atoms to carbon is referred to as carbon hydrogenation.  Carbon dioxide molecules (one carbon and two oxygen atoms) have lower entropy than methane molecules (one carbon and four hydrogen atoms).  But all known paths from carbon dioxide to methane molecules have intermediary molecules that are lower entropy than carbon dioxide.   We can depict lower entropy as a higher elevation relative to higher entropy.  This analogy of higher entropy to lower elevation allows us to represent the pull toward higher entropy as being equivalent to the downward pull of gravity.  The overall path from carbon dioxide to methane is downhill.  But an initial uphill push that still increases entropy overall is required to reach the peak and start the trip downhill.

No natural process, including metabolism, can occur unless it is accompanied by an increase in the overall entropy of the universe.  Life is not a substance or force.  Life is a process that is sustained by increasing entropy, it is an entropy generating machine. Life contributes to increasing entropy even though life itself is inconsistent with very high (and very low) entropy. A living organism is an open system, exchanging both matter and energy with its environment.

For example, an animal builds cells, tissues, ligaments, etc. This process increases order in the body and thus decreases entropy. This is the local"negative entropy" that characterizes all of life.  Animals also radiate heat into space, consume and break down energy-containing substances (i.e., food), and eliminate waste (e.g., carbon dioxide, water, etc.). When taking all these processes into account, the total entropy of the system (i.e., the animal together with the environment) increases. Although the details relevant to the calculations vary, this same result must also hold for photosynthetic plants and microorganisms.  

Life depends on, and affects, the overall increase in entropy.  Maybe the evolution of life favors a more efficient, and more entropy neutral, metabolism (for example, being sluggish and cold blooded) because that is more environmentally sustainable over the long term.  But I suspect that evolution also favors exploiting entropy increasing opportunities because that provides paths to competitive advantage (for example, active, intelligent, and warm blooded).  The more energy consumed by life the more entropy will increase because there is no possible path for life to utilize more energy without thereby also increasing overall entropy.   Increased efficiency maybe can reduce the entropy increase, but it does not alter the direction of this equation.

The decrease in albedo due to oceans, and the increase due to ice, suggests that physical features of planets, and their relationship with nearby stars, impacts the rate of entropy increase of planets independently of, and potentially more substantially than, any life that may reside on the planets.  It is not clear, at least not to me, that an overall decrease in the rate of entropy increase is an expected result, or a function, of life.  I think not.