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Friday, March 31, 2017

Friday Trump & Politics Roundup - 13

Donald TrumpThis is my semi-regular feature to post links to articles about Donald Trump along with excerpts from those articles. Trump has the potential to cause so much damage to our country and the world that it's every citizen's responsibility to keep pressure on him and our other elected officials to try to minimize the damage. To read previous entries in this series and other Trump related posts, check out my Trump archives.

It's been a few weeks since I've done one of these posts - not because Trump's been getting better, but because I've been busy focusing on other things. But like the introduction says, Trump has so much potential to cause harm, so we can't let 'Trump fatigue' let him start getting away with harmful policies and actions.


NBC News - Trump Proposes Slashing Medical Research This Year, Too

"The Trump proposals would slice $1.2 billion from a $31.6 billion NIH budget as it was laid out in the December continuing resolution. They also target health and science programs across other government agencies, including plans to:
•Take $350 million from the National Science Foundation's $6.9 billion budget
•Cut $37 million from the Department of Energy's $5.3 billion worth of science programs
•Excise $48 million from the Environmental Protection Agency's research and development budget of $483 million
•Cut in half the $101 million Teen Pregnancy Prevention program
•Reduce Food and Drug Administration staff spending by $40 million
•Cut domestic and global HIV/AIDS programs by $100 million plus cut the Presidential Emergency Program for AIDS Relief (PEPFAR) $4.3 billion budget by $242 million
•Completely delete the $72 million Global Health Security fund at the State Department and cut other global health programs by $90 million and $62 million for global family planning"


Helicopter Association International - HAI statement on President Trump's 2018 budget proposal and administration support for privatizing air traffic control

"With the release of the White House's budget blueprint, Helicopter Association International (HAI) is alarmed that the Trump administration is pursuing the transfer of oversight of air traffic control (ATC) from the FAA to a private corporate entity that will be under the control of an airline-dominated board of directors. / 'HAI members currently enjoy a good relationship with and high level of service from the air traffic control division of the FAA, which is universally acknowledged as the safest and most efficient system in the world,' said Matthew Zuccaro, president and CEO of HAI. 'It would appear that the primary rationale for this initiative is the airlines' desire to gain control of the airspace, which is not in the best interest of other aviation stakeholders. The turnover of control of the National Airspace System to the airlines represents a clear conflict of interest. As the dominant force on the proposed governing board of the new ATC entity, the airlines stand to gain the most by focusing on their particular needs.' / The helicopter industry takes comfort in the fact that the air traffic control system is under the watchful eye of Congress, and that FAA ATC daily operations are conducted by the recognized professionals within the air traffic controller community."


Industrial Equipment News - Trump Budget Causes Alarm in Appalachia: The Appalachian Regional Commission says it has created or retained more than 23,670 jobs in the past two years, but it's on the chopping block in Trump's new budget.

"The ARC began its work in 1965 as part of former Democratic President Lyndon Johnson's famous "war on poverty." In the past two years, the agency has spent $175.7 million on 662 projects that is says has created or retained more than 23,670 jobs. / That investment has paid off: In Kentucky, the commission has awarded $707,000 to the Eastern Kentucky Concentrated Employment Program, which used the money to train 670 people who now have full time jobs earning a combined $13.6 million in wages." ... "It's also targeted for elimination by President Donald Trump. / Trump's budget proposal has alarmed much of the region, including longtime Republican Congressman Hal Rogers, who represents the mountainous eastern Kentucky coal region where Trump won every county, a first for a Republican presidential candidate. / 'I am disappointed that many of the reductions and eliminations proposed in the President's skinny budget are draconian, careless and counterproductive,' Rogers said."


IFL Science - Trump's Budget Annihilates Funding For Education And Environmental Science

"President Trump submitted his budget blueprint for the upcoming fiscal year to Congress today, and as expected, it's mostly bad news for government agencies, who are having their funding drastically slashed through a series of draconian spending cuts. / The biggest swing of the axe is set to fall on the beleaguered Environmental Protection Agency (EPA), which is currently led by a climate change denier of the highest order, the agency's former archenemy Scott Pruitt. According to an analysis by Bloomberg, its budget will be reduced by 29.6 percent, with programs focusing on pollution and carbon footprint mitigation set to lose out the most. / The Department of Education (ED), headed by someone with no experience in public schools whatsoever, is also set to lose 13.6 percent of its funding. / It's worth noting that both Betsy DeVos and Pruitt are nonplussed whenever the subject of the obliteration of their agencies comes up in conversation - and that there are concrete steps being made by Congressional Republicans to abolish both of them by the end of 2018." ... "The Department of Agriculture (USDA), the federal branch of government responsible for, among other things, maintaining the food supply of the US, is set to lose 29 percent of its funding. Health and Human Services (HHS), whose job it is to protect the health of all Americans, will also lose 23 percent of its budget."


Vox - The House just passed two bills that would stifle science at the EPA

"House Republicans just passed two bills that will make it harder for the Environmental Protection Agency to use scientific research to protect health and the environment. And they've done so under the deceptive guise of 'transparency.' / Over the past two days, the House has passed the 'HONEST Act' and the 'EPA Science Advisory Board Reform Act.' On the surface, they seem noble. They use the same language scientists use when advocating for stronger research practices. / But they're 'wolf in sheep's clothing types of statutes,' says Sarah Lamdan, a law professor who studies environmental information access at CUNY. 'What's really happening is that they're preventing the EPA from doing its job.' "


Bad Astronomy - BREAKING NEWS: Scott Pruitt, head of EPA, doesn't think carbon dioxide is the main driver of global warming

"In a CNBC interview, when asked, "Do you believe that it's been proven that CO2 is the primary control knob for climate?" he replied this way: / 'No, I think that measuring with precision human activity on the climate is something very challenging to do and there's tremendous disagreement about the degree of impact. So no, I would not agree that it's a primary contributor to the global warming that we see.' / This is science denialism at a stunning level. And it's incredibly disingenuous, too." ... "That's a classic denial method of distraction, sowing confusion about one issue to downplay another. Not only that, it's utter baloney. We know for a fact that carbon dioxide is a greenhouse gas, and the main driver for the increased global warming we've seen over the past few decades. We also know for a fact that all or nearly all of that warming we've seen is caused by human activity." ... "And that is why so many scientists are up in arms over the Trump administration's bizarre and terrible appointees to science agencies, like Pruitt. They aren't just ignorant of basic science; they're openly antagonistic toward it. And that's why we must continue to speak up, make our voices heard, and do what we can to prevent these people for destroying the one planet we've got."

Related: Nature - Trump and Republicans take aim at environmental agency: EPA chief Scott Pruitt denies carbon dioxide's impact on the climate, and promises deregulation.


IFL Science - Energy Department's Climate Office Banned From Using Phrase 'Climate Change'

"In case you needed reminding, it's a bad time to be a scientist in the US. If you work for a federal research group, you've been muzzled, had your funding cut to historically low levels, and been told by a committee of anti-intellectual parrots that you're constantly lying. / Earlier this month, the word "science" was removed from the Environmental Protection Agency's (EPA) mission statement under the auspices of a man who doesn't think carbon dioxide warms the planet. Now, it seems that the Department of Energy's (DoE) climate change research office has banned the use of the phrase "climate change". / As reported by Politico, a supervisor at the DoE's Office of International Climate and Clean Energy told the staff in no uncertain terms that the phrases "climate change", "emissions reduction", and "Paris agreement" are not to be used in written memos, briefings, or any form of communication."


Bad Astronomy - When it comes to climate change, some people just want to watch the world burn

"On Wednesday, March 29, the House Committee on Science, Space, and Technology will hold a hearing entitled 'Climate Science: Assumptions, Policy Implications, and the Scientific Method'. / This hearing will be a sham. / My apologies for not mincing words, but there's no other way to say it. This Committee holding a hearing on the scientific method is like an arsonist holding a hearing on how to upgrade a fireworks factory security system. I strongly doubt the intent will be to honestly investigate climate change and scientific methodology. Instead, it will likely be an attack on the science, and lay the groundwork for further impediments to it. / This isn't hard to suss out; over the years the many sins of the Committee's majority members have been out in the open for all to see. Right after the GOP took over the House in the 2010 midterm elections, they stacked the Committee with members who deny basic science -- including such things as the Big Bang, evolution, climate science, and even anatomy (remember Todd Akin?). Their official Twitter feed commonly posts ridiculous comments..."


Scientific American Blogs - Anti-Immigration Rhetoric Is a Threat to American Leadership: Our embrace of international students and faculty has given the U.S. a leg up on all other countries in the race to lead in innovation and discovery

"America's universities are the best in the world. The quality of the students, faculty, teaching, infrastructure, the commitment to academic freedom, and the extraordinary research opportunities attract the best and brightest people from around the globe to the United States. And our nation is far better for it." ... "In all, 42 percent of the Nobel Prizes awarded between 1901 and 2015 went to individuals working/living in the United States, and nearly one third of those recipients were born outside the U.S. Our ability to attract the world's leading scientists to our universities has helped us maintain global leadership in innovation and discovery, a tremendous component of our economic strength and national security." ... "Research universities are seeing an immediate effect on the recruitment of international faculty and students. Stony Brook University has seen a decline of roughly 10 percent in international applications for graduate school this year, a figure that seems to be on a par with the decline seen at other institutions. The reasons for these declines may not be solely based on anti-immigration policies and rhetoric, but some accepted applicants to Stony Brook, especially from countries targeted by the first Executive Order, have stated explicitly that they will choose a Canadian or Australian university instead, based on the uncertainty of U.S. immigration policy and the fact that they are being singled out based on their country of origin, not on their academic credentials. And the recent suspension of expedited processing of H1-B visas, which is of significant concern to the Technology Sector, could also have a chilling effect on the ability of Universities to attract outstanding international faculty and scientists to help sustain our research and educational missions."


Scientific American Blogs - Republicans Want to Destroy Our National Parks. It's Up to Us to Save Them

"Since the election, Republicans in Congress have launched a sustained attack on America's national parks and public lands. Starting in January, they wasted no time putting in place new rules and legislation that threaten the future of our national treasures. They launched their assault on their very first day in session, and haven't stopped." ... "Republicans are determined to place our public lands in corporate hands, and Trump is happy to help them. So it's up to us. If you've ever loved our national parks, if you've ever enjoyed the wildlife in federal refuges, if you've ever taken your family to explore our heritage at national historic sites, now's the time for you to act."


Vox - 6 reasons the Trump presidency is in shambles

[On the plus side, this means Trump isn't wrecking things. On the negative side, it means nothing constructive is being accomplished by the President of the United States of America. It's a national embarrassment. However, before getting too comfortable thinking Trump isn't causing too much damage, take a look at the next article after this one.]

"Bullshitting is easy, but governing is hard: Trump's bluster and bombast, so effective on the campaign trail, has backfired spectacularly in office. / As Vox's Ezra Klein noted this week, Trump is failing on almost every front. His health care bill died -- killed by his own party. His approval rating has sunk to 35 percent. His executive orders banning immigrants from seven Muslim-majority countries were struck down by the courts. Russia-related investigations are undermining his agenda. And his administration, plagued by leaks, remains divided."


Washington Post Op-ed - The Daily 202: How Trump's presidency is succeeding

"Despite the chaos and the growing credibility gap, Trump is systematically succeeding in his quest to "deconstruct the administrative state," as his chief strategist Stephen K. Bannon puts it. He's pursued the most aggressive regulatory rollback since Ronald Reagan, especially on environmental issues, with a series of bills and executive orders. He's placed devoted ideologues into perches from which they can stop aggressively enforcing laws that conservatives don't like. By not filling certain posts, he's ensuring that certain government functions will simply not be performed. His budget proposal spotlighted his desire to make as much of the federal bureaucracy as possible wither on the vine."

Tuesday, March 28, 2017

Recommended Reading - Evolution

Tree of LifeI write quite a bit about evolution, but if you're new to this site or the subject of evolution, it might be a little overwhelming to just browse through the site and read the articles at random. So, this page offers some recommendations on entries to start off with, to give you a good foundation before moving on. I very strongly recommend reading the first four essays in the Foundation section. And if you happen to doubt evolution for religious reasons, and have seen presentations or read material from some of the more prominent creationists (e.g. Answers in Genesis, Kent Hovind, Discovery Institute, etc.), then I'd also recommended the entries from the 'Responses to Misunderstandings and Creationist Arguments' section.


The Foundation


Exploring Other Evolutionary Concepts


Responses to Misunderstandings and Creationist Arguments

The first two of these are probably the most informative. They're also rather long. I took the time to respond in decent detail to a myriad of misunderstandings and misconceptions about evolution. The third is offered as a kind of example of the bad arguments many creationists use.


Further Reading, This Site

I've written quite a bit more about evolution and creationism. You can find most of it in the following archives.

  • Science & Nature Archive
    Evolution will be mixed in here along with a variety of other science topics. These entries tend to be more straight science.
     
  • Skepticism, Religion Archive
    These tend to be focused on skepticism, so the evolution related articles mixed in here will be more in response to creationists.
     
  • My Quora Profile
    Okay, this isn't exactly this site, but I do write a bit about evolution on Quora, and only adapt some of those answers for this blog. Evolution related answers will be mixed in with all my other Quor answers.
     


Further Reading, Other Sources

I'm actually going to link to a Quora answer I wrote with those types of sources. You can also see what others suggested.

Image Source: DavidPratt.info

Recommended Reading - Religion

Religion?I've written an entire book on religion, plus a ton of other essays for this site. That's a lot to expect anybody to read, so if you want the quick introduction, this is it.


For the super quick summary, I grew up as a Christian, with a strong and sincere faith. But as I grew older and learned more about religion and the world at large, I came to realize that religion simply wasn't true, and that atheism was by far the most likely explanation of the universe. The essays below explain all of that in a lot more detail.


Introduction

For Anyone Interested in Luring Me Back Into the Fold

  • How to Convert Me Back to Christianity
    This is a list of all the issues you would have to address to get me to reconsider the validity of Christianity, and whether or not to even be a Christian if you could demonstrate that it was true.
     
  • Standards of Evidence for Religion
    This is the type of evidence that would be required to convince me of the reality of gods or religions.
     

Additional Info

I've written a lot about religion. Here are four collections.

  • My Book, online
    I tried to keep the book short enough that it wouldn't be overwhelming, but long enough to be a good, informative introduction.
     
  • Religion Archive
    Pretty much all the religious essays I've ever written for this blog.
     
  • Friday Bible Blogging Index
    This is an ongoing effort to re-read the entire Bible as an atheist. I started off pretty good, but progress has been slow for a while.
     
  • My Quora Profile
    I write a fair amount about religion on Quora, though those answers are mixed in with all my other Quora answers.
     

Recommended Reading

Old Book Bindings, from Wikimedia CommonsIf you like this site, I'd recommend just looking around and browsing. But I've written nearly 1000 blog entries so far, not to mention all my static pages, so I know that you'd only get a small glimpse of everything I've written that way. So, I figured it might be useful to highlight a few essays and pages that are particularly useful or informative.


Disclaimers & What Not

  • Putting This Blog in Perspective
    Even if you disagree with practically everything I've written on my site, realize that we could probably still get along in person. There's a lot more I do in my day to day life, but not stuff that anybody would be interested in reading about.
     
  • Official Disclaimer
    The usual - this is all my own personal opinion, and doesn't represent any of the organizations I'm associated with.
     
  • Official Commenting Policy
    Basically - BNBR: Be nice, be respectful. Also, please provide references. And no spam.
     


Collections for Recommended Reading

For these subsections, there were so many recommendations, that I broke them out into their own pages:

  • Evolution
    I'm very, very intrigued by evolution, so I write about it a lot. And if I may say so, I think some of the things I've written are pretty informative.
     
  • Religion
    So, I'm an atheist. That's still a bit of an oddity in the U.S. (particularly in my neck of the woods), so here are some essays to start you off, with links to more info.
     


Politics

I know. Opinions about politics are like a certain body part - we all have one, and they all stink. But, since this is my personal website, I get to share mine (opinions about politics, that is).


Indices for Other Collections

There are a few subjects I've covered repeatedly, so I made indices for them. Since those indices might get lost amongst the rest of my entries, here are links to all of them.

  • The Ray Comfort Index
    Ray Comfort will always hold a special place on this blog for inspiring me to start it in the first place. This index contains all the entries I've ever written about him.
     
  • The Ben Carson Index
    I've actually written quite a bit about Ben Carson over the years. This is all of it.
     
  • Friday Bible Blogging Index
    This is an ongoing effort to re-read the entire Bible as an atheist. I started off pretty good, but progress has been slow for a while.
     
  • Book Review - God- or Gorilla?
    If you're really interested in creationist claims from 100 years ago, then this is the series for you. I reviewed a 1922 creationist book in detail.
     

Image Source: Wikimedia Commons

Monday, March 27, 2017

Understanding Evolution - The Basics

This entry is part of a collection on Understanding Evolution. For other entries in this collection, follow that link.


I discuss evolution enough on this blog that I figured I ought to do a post covering the basics. Just what is evolution, and how does it work? I'm going to try to focus mainly on describing what evolution is, but since there are so many misconceptions out there, a little bit of this post is going to be clarifying what evolution isn't. I'll admit up front that this explanation is a little animal-centric, even though evolution occurs in all types of life.


Defining Evolution and Understanding DNA

DNA MoleculeAt the most basic, evolution is change in a population over time. But to understand that change, first you need to understand where it comes from.

In a way, our cells and bodies are run by our DNA and genes. DNA is a long, chain-like chemical in almost all of our cells. Along the length of that chain are special sections called genes, that act like templates for making various chemicals that our cells will use. You can think of our DNA and genes somewhat like a set of instructions for how the cells will work. If A happens, do B. If C happens, do D. And on and on. It's all of these instructions interacting together that make our cells work the way they do, and then all of our cells interacting together to make our bodies work the way they do. This even affects the way we grow up and mature. There may be some genes that work together to tell certain cells to become muscles, and other cells to grow bones, and other cells to become nerves.

By and large, whatever DNA we're born with is the DNA we'll have our whole lives. But, sometimes our cells make mistakes in copying the DNA. These mistakes are called mutations, and can change the instructions of our DNA. Mutations can be harmful, beneficial, or not even really do all that much and be neutral. Some of the most harmful mutations that can occur in our bodies lead to cancer. But most of those mutations don't affect evolution, because they only affect their owner's body, not their children. The only mutations that affect evolution are the ones that can be passed on to the next generation, the ones that occur in the specific cells that are going to come together to make a new baby - eggs and sperm. If mutations happen to either eggs or sperm, then the babies will have a slightly different set of instructions than their parents.

None of us pick and choose our DNA, or how we want it to change. We can't will ourselves to be taller, or for our children to be taller. And we can't change our DNA through actions. For example, when we go to the gym to work out, we'll get better cardiovascular health and bigger muscles, but we won't change any of our DNA having to do with muscles or health, and we certainly won't change any of the DNA in our eggs or sperm that way. So, no matter how much we work out, our children are going to get basically the same heart and muscle controlling DNA as we have. They'll start off with the same potential as we did, and if they want to be healthy and get big muscles, they'll have to go to the gym and do the work themselves.

When these changes to our DNA happen, they simply happen by chance. Like I already said, you can't pick the mutations. Your children can't pick the mutations. There's no invisible hand controlling the mutations. They're simply mistakes made at the chemical level, when cells don't quite make a perfect copy of the DNA. And we all have a handful of these mutations. Various studies (example) have found that people have anywhere from 60 to 200 of these mistakes. Thankfully, most of them are neutral and don't have much effect. And considering that we have around 20,000 genes, even 200 mistakes is a pretty small effect percentage-wise.

But, since there have been all these copying errors being made throughout all of history, it means that there are a lot of different versions of genes out there. I have a few genes different from yours. And you have a few genes different from your friends. Everybody has a slightly different set of all these different versions of genes. If you were to add up all the different variations of genes everybody has, you could figure out what percentage of the population had each variation. If you did that tally again in a hundred years, you might find that things had shifted a bit. If you kept on doing this tally, you could trace these shifts. You might even find some variations of genes disappearing completely, and some being so beneficial that they spread to everyone. That's evolution:

Evolution is the changes in the DNA of populations over time.

Here's how an actual evolutionary biologist, Douglas Futuyma, put it in the textbook he wrote on evolution:

Biological evolution ... is change in the properties of populations of organisms that transcend the lifetime of a single individual. The ontogeny of an individual is not considered evolution; individual organisms do not evolve. The changes in populations that are considered evolutionary are those that are inheritable via the genetic material from one generation to the next. Biological evolution may be slight or substantial; it embraces everything from slight changes in the proportion of different alleles [variations of genes] within a population (such as those determining blood types) to the successive alterations that led from the earliest protoorganism to snails, bees, giraffes, and dandelions.


Natural Selection

One of the main drivers of evolution is natural selection (though not the only one). As discussed above, when organisms reproduce, they don't produce perfect clones of themselves. There are almost always slight differences. On top of that, for various reasons, not all of an organism's offspring are going to grow up to reproduce themselves. We're kind of insulated from this in modern society, but just think about the nature documentaries you watch where a sea turtle will go and lay 100 eggs in one nest. If all of those babies survived to go on and have their own babies, with all the new females laying 100 eggs per nest, and all their babies doing the same thing, it wouldn't take long before the world was overrun by sea turtles. But, many species of sea turtles are actually endangered, so we know that's not happening. The vast, vast majority of those baby sea turtles won't make it. They'll be eaten by predators, hit by speed boats, killed by disease, or somehow be felled by any of the multitude of dangers out there.

That's where these differences become important. Whatever slight differences happen to be beneficial will make their owners more likely to survive and reproduce. Any differences that happen to be harmful will make their owners less likely to reproduce, maybe even causing them to die before they get the chance. This is natural selection. It's not a conscious entity. Nobody is picking and choosing which mutations are going to become more common. It's just the way things work, the inevitable result of having variation among offspring, and producing more offspring than will reproduce themselves. So, the raw material comes from mutation, while natural selection acts like a filter, passing through beneficial mutations, and weeding out the harmful ones.

Let's look at a hypothetical example, and let's start off simple. Here's a hypothetical family tree, starting with two original parents up at the top, and going down through the generations. This is exaggerated compared to most traits in real life. Evolution is a gradual process, and you won't normally see things changing this rapidly, but this is just an example to illustrate concepts

Evolution Conceptual Family Tree - Single Lineage

So, let's just assume that for whatever reason, being darker is better in their environment. Our first two parents are light colored, but they somehow managed to survive and have children. Notice that their children have variation in their color. Some children are lighter, and some are darker. But remember that mutations are random, with no intentional change in any direction. So, because darker organisms do better in this hypothetical environment, the darker children are the ones that survive, find mates, and have children of their own, while the lighter children aren't so lucky, and don't have children to pass on their lighter coloration. Each generation is like this. Children are similar in color to the parents, with a little bit of variation, with some children being slightly lighter, and some slightly darker. It's the children who were lucky enough to have the beneficial traits that go on to have their own children.

And whether or not mutations are beneficial or harmful depends on the environment. There's a textbook example on this with the peppered moth. This is a type of moth from England. It's typical coloration was light with dark speckles - peppered. It was a very good camouflage on tree bark. Then, in the 1800s, the Industrial Revolution swept through England, and pollution became so bad that trees got a coating of soot making them black. So, the white and black speckles of the peppered moth were no longer good camouflage. Well, a mutation occurred that made some moths solid black - much better camouflage on the dirty trees. And that mutation swept through the population, until nearly all of the moths were solid black. Once people started paying more attention to pollution and putting scrubbers on smokestacks and other methods to reduce pollution, the soot started disappearing from the trees, and the black moths weren't as well camouflaged, anymore. And now, the speckled moths have become much more common. There's nothing inherently better about a moth being black or being speckled - it all depends on the environment the moth is in.

Peppered Moths
Black and Speckled Peppered Moths on a Tree (Image Source: Wikipedia)


It's All About Populations

Remember, evolution is all about populations. That's important, and one of the more common misconceptions, so let me repeat it a few times. Evolution is not about individuals. Individuals don't evolve. Evolution deals with populations. Populations evolve.

So, here's a more complicated family tree. It's not just one lineage, but a whole hypothetical population (albeit a very small one).

Evolution Conceptual Family Tree - Population

If you take the time to trace each lineage, you'll see a similar pattern to the simpler diagram up above. Each time two organisms mated and had children, their children were similar in shade to the parents, but with slight variation. And it was the individuals that were lucky enough to be born darker that were the ones that survived.

You also notice that the entire population is shifting together, gradually. The second generation doesn't look that much different than the first. And the third doesn't look that much different from the second. Each generation is similar to the previous generation, and similar to all the other organisms in its own generation, and similar to the following generation. There is never a sudden jump from light to dark. There is never a single organism that's completely new and different from it's parents. Yet, the final generation is substantially different from the first generation.

That's how evolution really works, but even more gradually. Organisms are always part of a population. They will have a few different variations of genes, but they'll always be similar to their parents, and the other members of their populations, and their offspring will also be similar. It's only over the course of generations that you'll notice the changes to the population.


Speciation

So, if evolution is always about populations, and populations change together, how did life branch out the way it has? Why are there separate species? How do species form?

Well, like most everything else in evolution, speciation isn't sudden, either. It's a gradual process. The first step is that somehow, a single population must be split into two isolated populations. This is often a geographic barrier, such as sea level rise forming a new sea, tectonic activity pushing up a new mountain range, a new canyon forming, grasslands giving way to forests or vice versa, or anything else that could split a population in two. Once this happens, there are now two independent populations. Let's take a look at another diagram.

Speciation Concept Diagram

If you were to 'zoom in' on that diagram, you'd see a whole bunch of individuals, mating with each other and having children, much like the diagram from the previous section. But that starts to get complicated and confusing, so just keep in mind that these are still populations of individuals interbreeding with each other.

Before the split, there was a single population. New mutations were popping up, but because the whole population was interbreeding together, all these new mutations were getting mixed throughout the population, and individuals in each generation were very similar to all the other organisms in their own generation. So, they had no problems finding mates and continuing that interbreeding.

Then, after whatever occurred to cause the split, new mutations kept appearing in each population, but the populations are now isolated. Mutations still get mixed throughout the smaller populations, but not between the two separate populations. These differences accumulate over time, and if the populations are isolated for long enough, they will build up enough different mutations that they're no longer similar enough to each other to breed. Even if the two populations came back in contact again, they'd be new species, and individuals from one population wouldn't be able to mate with individuals from the other population.

And if this repeats over, and over, and over, you'll eventually end up with a whole, complicated tree. Here's one more diagram, but with a slight twist. All the previous diagrams had the oldest generations at the top, and moved down through younger generations. That's the way it's normally shown in genealogy, but that's not the way it's normally shown in discussions on evolution. So, here's a diagram showing this type of family tree, with the oldest ancestors at the bottom, and the youngest descendants at the top.

Evolutionary Family Tree
Image Sources: David Peters Studios with some editing on my part

With all these different lineages, they can each 'experiment' in their own direction. And if their environments happen to be different, then different mutations will be favored in different lineages. For example, one lineage might favor a particular food source. One might live in a cold environment, while another might live in balmier conditions. Some might face different predators. Some might have less access to fresh water. Etc. Etc. All these differences will accumulate over the generations in all the different lineages, leading to a great variety of adaptations.


Summary

Evolution is all about populations. Specifically, it's the changes in the DNA of populations over time. Mutations are the raw material for evolution. They're random, with no conscious intent over what they'll be. And an organism's actions in life won't have any effect on the 'direction' of the mutations. Offspring will be imperfect copies of their parents, with the variation being random. Natural selection acts like a filter, passing through beneficial mutations, while weeding out the harmful ones, which over time can cause certain genes or variations of genes to become widespread. If a single population becomes split, the new populations will no longer be able to mix up any new mutations with each other, and after enough time, they will have accumulated enough different mutations that they'll no longer be able to interbreed - they will have become two different species.

Take all these phenomena, and multiply them over the millions and millions of years that life has existed on this planet, and they have produced the astonishing complexity and variety of life all around us.

DNA Image Source: Wikimedia Commons, with editing by me.
Note: All uncredited images are original artwork by me.


Want to learn more about evolution? Find more at Understanding Evolution.

Wednesday, March 22, 2017

Understanding Evolution - Development of Eyes

This entry is part of a collection on Understanding Evolution. For other entries in this collection, follow that link.


I wrote a Quora answer that I thought was a good explanation on how complex features can develop. The answer was dropped from their main archive when the question was merged with a similar one I had already answered. Since I thought it was a good explanation, and to make it more accessible, I'm going to repost it here. I made a few minor edits, plus added a whole brand new figure to help with the explanation. Here is my answer to the question of:

If evolution is true, why aren't there millions of creatures out there with partially developed features and organs?
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To give one concrete example, let's take a look at eyes:

Mollusc Eyes
(Image Source: StephenJayGould.org - futuyma_eye.gif)

None of those eyes are hypothetical. Every single one is a diagram of an eye from an existing, living organism, all of them snails, actually, and every single one of those eyes is beneficial to its owner. And each one of those organisms is the end result of all the evolution leading up to it.

So, let's look at that first eye. It's the simplest. It's basically a light sensitive cup. Even if it doesn't let its owner form an image, it still lets those snails detect light, and the direction the light is coming from. Many, many millions of years ago, an eye very much like that was the most advanced eye that any snail possessed. But, evolution is a branching pattern. Once a population splits into two species that can no longer interbreed, there's no more sharing of genetic mutations or adaptations between the species.

So, that ancient species of snail with that cup type eye split into two species, and those split into more, and those split into more. In at least one of those lineages, by chance, the mutations appeared that made the eye more closely resemble that second eye in the diagram above. But all of its cousins species still had the simpler cup type eye. And all those cousin species with the simpler cup type eyes were still doing a good enough job of surviving and reproducing in their own niches, so they still survived. The new species with the 'better' eye probably had advantages in certain niches, especially those that required being more active, and so probably did pretty well for itself, and proliferated into its own group of species with those 'better' eyes.

Well, a similar process repeated again. At least one lineage in that new group got the mutations to make an eye with even better imaging capabilities. Its cousins with the type 2 eye still had their own niches where they survived, as did its even more distant cousins with the type 1 eye. And this repeated over and over again, until you ended up with the existing variety of snails we have today, with eyes ranging from that very simple cup eye to 'camera' eyes with lenses.

Here's a hypothetical, and overly simple, family tree of how this might have happened (you can do searches for snail phylogenetic trees to find some real ones). Imagine that the colors represent snails with a certain type of eye. Black is the original cup type eye. Blue is the type 2 eye. Red is the type 3 eye. And on through green, magenta, and cyan. Note how once a lineage evolves an eye, it's the only lineage with that eye*. For example, once the type 2 eye evolved in a single species of snail, only descendants of that species had type 2 eyes, because they were the only ones that could inherit it. It couldn't share that trait with its cousins. Also, snails with the original type 1 cup type eyes didn't all of a sudden all go extinct, and continued to evolve in their own lineages.

Hypothetical Snail Family Tree
Hypothetical Overly-Simple Snail Family Tree
Image Sources: David Peters Studios and StephenJayGould.org, with some editing on my part

And keep in mind, eyes are only one feature of snails. The living snails with the cup type eyes have still been evolving since that ancient ancestor, and have changed in other ways. They just haven't acquired the mutations that would have changed their eyes. Or more precisely, they just haven't acquired mutations to make their eyes better at resolving images. They may still have had other mutations affecting their eyes, such as light sensitivity.

So, do the existing snails with cup type eyes have a 'partially developed' organ? Well, I guess in one sense they do, because we know that an ancient animal with a similar type of eye eventually gave rise to descendants with a more complex camera type eye. But it's not 'partially developed' in the same sense as a half built bridge that can't ferry traffic. It's a perfectly functional eye that serves a purpose and is beneficial to the snail. And there's no guarantee that any of its future descendants will necessarily develop any of the more advanced eyes.

That's how it is with every organism and every feature on the organism. As long as we manage to escape extinction, we will all evolve in the future, from us humans to ants to dandelions (as populations - individuals don't evolve). Some of our existing features and organs will change. So, with the benefit of hindsight, those future organisms (at least the ones smart enough to be thinking about evolution) will be able to look back to how we are now, and recognize which of our now existing organs were only 'partially developed'.

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*Saying that common traits never appear in separate lineages is actually a little bit of an oversimplification. For traits that are more likely to evolve, they may evolve more than once in more than one lineage, in a process known as convergent evolution. However, the traits will have evolved independently, since separate lineages can't share DNA**. Additionally, the genetic basis will almost always be different, since it was separate mutations in the separate lineages that led to a similar structure. And the traits themselves may only be superficially similar. As a good example relevant to this essay, us vertebrates have also evolved camera type eyes. But, as you would expect given that we evolved them independently, the similarities are only superficial, and there are some very fundamental differences between our eyes and mollusc eyes.

**Okay, that's a little bit of an oversimplification, as well, but horizontal gene transfer is exceedingly rare in multicellular organisms.

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For a slightly different perspective, read the related entry, Understanding Evolution - Origin of Limbs.


Want to learn more about evolution? Find more at Understanding Evolution.


Updated 2018-02-07 - Simplified much of the extraneous commentary that didn't have to do with the body of the entry.

Friday, March 17, 2017

Understanding Evolution - How Humans and Apes Fit Into the Tree of Life

This entry is part of a collection on Understanding Evolution. For other entries in this collection, follow that link.


I came across a question on Quora the other day that seemed to reflect a common incomplete understanding of evolution, If it took 5 million years for today´s humans to evolve from the apes, how long time did it take for today´s apes to evolve from their origin?. There are a few issues with that question, but rather than enumerate them all here, I'll just jump into the explanation, which will hopefully make it clear as we go. The one thing I'll say up front is that we diverged from chimps & bonobos more like 6 million years ago, not 5 million.

It all depends on what perspective you want to take, and which starting point you want to go with. When people bring up the 6 million years for humans to evolve from apes, what does that really mean? Take a look at this diagram:

Hominid Evolutionary Tree
Click to Embiggen
Image Source: The Open University - Studying mammals: Food for thought


That's one probable evolutionary tree for us over that time (the exact details are subject to debate). Notice how bushy it appears. Populations kept on splitting and splitting and splitting, and most of those species ended up going extinct. We're the only surviving members of that lineage (though Neanderthals nearly made it to the present day). But, if you wanted to ask, how long did it take for humans to evolve, where would you pick as your starting point in that diagram? It just happens to start with Orrorin tugenensis, but that's only because that's where that artist decided to start it. They could just as easily have started with Ardipithecus ramidus, and you could say it took us 4 million years to evolve from that. Or, they could have skipped ahead and started at Homo habilis, and you could say that it took us 2 million years to evolve from that. Or, you can notice that Australopithecus boisei and us are pretty distant cousins on that tree. If A. boisei had managed to not go extinct, or to have left descendants that kept on evolving into some new species, there might be another ape alive right now more closely related to us than chimps and bonobos. So, then we might be saying that it took us 3 million years to evolve from apes. But it wouldn't be anything different about how we evolved - it would just be the fact that we had a still living closer cousin to compare ourselves to. (Note that that terminology is a bit misleading, as you'll hopefully understand after reading this full entry - we are simply apes ourselves.)

Here's another diagram, this time including the still surviving great apes, but not showing all the ancestors or extinct species from side branches that died out:

Ape Evolutionary Tree
Click to Embiggen
Image Source: BOSCOH.com - Milestones of Human Evolution from Paleontology & Bioinformatics


That's where the 6 million year number comes from. It means that 6 million years ago, there was a population of animals whose descendants would eventually become chimps, bonobos, and humans. It was the last common ancestor of us three surviving species. It took each of our species 6 million years to evolve from that population. But recall the branching pattern from the previous diagram. It wasn't a straight line from that population to each of us species that's still around. It split and split and split in a bushy pattern. In the lineage that led to us, only one species survived to the present - us. In the lineage that led to chimps and bonobos, those two species survived to today.

And you don't have to pick just chimps and bonobos. If you look at gorillas, our common ancestor with them was alive roughly 8 million years ago. So, it took 8 million years for gorillas to evolve from that ancestor. It took chimps 8 million years to evolve from that ancestor. It took bonobos 8 million years to evolve from that ancestor. And it took us humans 8 million years to evolve from that ancestor. Chimps, bonobos, and us share a common portion of that 8 million years. Chimps and bonobos alone share an even longer common portion. It would be similar to asking, how many generations did it take to get from your great-grandparents to you, or to your brother, or to your cousin, or to your second-cousin? In all cases, it would be three generations. For you and your brother, you'd share most of that lineage, starting with your great-grandparent, then your grandparents, and then your parents. With your cousin, you would only share your great-grandparents and grandparents. And with your second cousin, it would only be your great-grandparents. There are a lot more greats than that considering our evolutionary history, but it's the same concept. We share more of our lineage with chimps and bonobos than with gorillas. And we share more with gorillas than with orangutans. And we share more with orangutans than with non-apes.

If you want to go further and ask how long it took for apes to evolve, it really depends on how far back you want to go. Here's another diagram:

Primate Evolutionary Tree
Click to Embiggen
Image Source: ResearchGate


Now, we get into a problem of semantics. In language, apes have a name to describe them as distinct from monkeys. But we're not really a completely distinct group. To have a distinct group in classifying these types of things, all members of that group should share a common ancestor that no other group can claim in its ancestry. Apes have such an ancestor around 20 million years ago. The only descendants of that specific animal are apes. But monkeys don't have that type of unique common ancestor. There's no single ancestor of 'monkeys' that isn't also an ancestor of apes. We're not two separate groups. Us apes are really just a specialized subset of monkeys without tails. But, if your question is just when 'apes' first appeared, then like I already said, the last common ancestor of all apes was alive around 20 million years ago.

But why stop there? When biologists say that all life on earth is related, they mean it. All life on earth shares a common ancestor. If you go back far enough, you can find our last common ancestor with chipmunks (~90 million years ago), or with a triceratops (~320 million years ago), or with a goldfish (~432 million years ago), or with an apple tree (~1.6 billion years ago), or even with the streptococcus bacteria that may have given you your last sore throat (~4.3 billion years ago). So, if you want to start at the beginning, you have to figure out when our earliest, earliest single celled ancestors were alive. The problem is that it's hard to find evidence of things that nearly inconceivably ancient, but it was probably more than 4 billion years ago. So, in that sense, it's taken humans over 4 billion years to evolve. It's take starfish over 4 billion years to evolve. It's taken e. coli over 4 billion years to evolve. It's taken oak trees over 4 billion years to evolve. Etc. Etc. Every organism alive is the end result of all that evolution leading up to where it is now.

Complete Evolutionary Tree
Click to Embiggen
Image Source: evogeneao Tree of Life


So to summarize, it's taken chimps, humans, and bonobos roughly 6 million years to evolve from our last common ancestor. It's taken all of us apes as a whole roughly 20 million years to evolve from our last common ancestor. You can keep going back in our ancestry until somewhere more than 4 billion years ago to the first life, that was the ancestor of everything alive today.

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There are some really good trees of life and similar type pages to play around with. Here are a few (I already linked to one above, but it's worth repeating). They mostly include only the tips of the tree for organisms that are still alive. So, you won't necessarily be able to find an Australopithecus or a Tyrannosaurus, but even just sticking to living animals, it's a huge, huge tree.


Want to learn more about evolution? Find more at Understanding Evolution.

Wednesday, March 8, 2017

Putting This Blog in Perspective

PerspectiveI wanted to expand on something I wrote a few years ago in the entry, The Misleading Image of Bloggers. If you come and visit this blog and read my entries here, I think it would be very easy to get a misleading image of what I'm like in real life, and maybe even some misunderstanding over just how strongly I really feel about certain issues.

First of all are the topics I discuss here. I write an awful lot about religion and politics on this blog, as well as skepticism in general. Those are topics that interest me, but I know they're not topics that interest everybody, and even if they did, they're not necessarily polite topics for dinner conversation. Nobody wants to be that guy that's always starting a religious or political debate every time you hang out with them. Granted, I do like to discuss these things when they come up, but I usually wait for other people to bring them up. If you happened to meet up with me on a Friday night to go grab a beer, chances are that these topics wouldn't even come up. So, this blog gives me an opportunity to write about these issues without boring my friends.

Plus, it's not like I only think about religion and politics. Like I wrote in that older entry, "Nobody except my friends and family really cares what TV shows I've been watching, what I've been eating for supper every night, the chores I did around the house last weekend, the grades my daughter makes in school, how she did at her piano recital, or many of the other things I do or talk about on a daily basis." I write about certain topics because I do think there's an audience that will like reading about them. And even if it's not a huge audience, at least it's a bigger audience than just my wife and parents, who are just about the only people that would want to hear about all my mundane day to day experiences.

Second is how I feel about the 'opposition'. I criticize religion, creationism, conservative politics, climate change denialism, etc. And while I may at times call out certain individuals holding those positions, I don't mean to imply that all people holding those positions are bad people, nor necessarily even the specific individuals I'm calling out. All people have a multitude of views on a multitude of issues, and I seriously doubt that any one person is going to agree with me on everything. So, when I criticize creationism, for example, I'm specifically criticizing just that one belief. I don't think most creationists are bad people. I think they're just mistaken about that particular issue.*

Moreover, while I criticize religion a lot and think that on balance it does more harm than good (see the previous entry, Why Do I Spend So Much Time on Religion, for plenty of examples of the harm of religion, including fire bombings and persecuting children as witches, or a recent entry, Christian Privilege, showing the undue privilege religion receives in our culture), I don't think it's universally horrible in every aspect. Religiously motivated soup kitchens and homeless shelters do good in the world. Christmas bazaars and pot lucks can foster a sense of community. People who have had traumatic experiences can often find comfort in religious beliefs.

In addition, I hold people to different standards depending on the situation. I've already written about this in the entry, Run of the Mill vs. Big Name Creationists. Most people never had evolution presented to them well in high school biology, and don't have much reason to study it, now. As I wrote previously, "It's hard to get good and pissed off at someone who believes something and hasn't ever been shown a good reason not to believe it." But when someone like Ben Carson, a respected neurosurgeon, goes and gives a presentation to the public, or participates in public debates, then I do expect him to have done enough research to understand the issue and speak about it knowledgeably. And then there are the prominent creationists / creationist organizations like Answers in Genesis, or Kent Hovind, or Ray Comfort, who I know have been exposed to credible science, yet continue to spread their falsehoods. And even though I just used creationism for my example, that's not the only issue where I look at things this way. It applies to politics, science, and a whole bunch of other fields. I get much more upset with people who should know better but continue to spread misinformation.

In real life, I have friends of all types of religious and political persuasions. I have friends ranging from fundamentalist Christians to Muslims to agnostics and atheists, from young and old earth creationists to evolutionary biologists, from die hard Trump supporters to people who are far more liberal than me, from gun rights absolutists to people who would like to see more gun control (though no one I know of who would advocate outright bans). We get along because most of the things we do on a daily basis are talk about work, or vent about personal problems, or get together for a crawfish boil, or go out to happy hour, or help each other move, or, well, all the normal stuff everybody does.

So, if you're reading this blog, and you think I'm attacking you personally, please keep in mind that that's usually not my intent. I try for the most part to be civil and criticize ideas, positions, or policies. If I've crossed the line and written something offensive, then I apologize, and I would ask you to point it out to me so that I could address it in the future.

And keep in mind that this entire blog is only a small slice of my views - the ones I think people would be interested in reading. If you ever met me in real life, even if we disagree about these issues, there's still a very good chance we could get along just fine and find common ground in other areas.

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*As a side note on that, though, I'm not so naive and idealistic as to think that everybody is always acting honorably. I've written quite a bit about Ray Comfort on this blog over the years. I know he's been exposed to the science regarding evolution, but he repeats the same falsehoods year after year. And he still uses dishonest tactics like quote mining and selective editing to make documentaries. It gets harder and harder to believe that he's not knowingly using dishonest tactics.

Image Source: Return of Kings

The Ray Comfort Index

The Atheist's Worst NightmareI've written quite a bit about Ray Comfort on this blog. In fact, he provided me with my inspiration to start the blog, back when a guy in a flea market gave me and my wife a copy of a Ray Comfort CD. The arguments Comfort used were just so bad that I had to vent about it somewhere, so I wrote my first real substantive blog entry, A Meandering Tale About Fundamentalism.

I don't normally go out of my way looking for things to criticize about Comfort. In fact, other than just now looking it up so that I could provide a link, I can't remember the last time I've visited his website, Living Waters. But from time to time I come across something he's done or said or written that I can't pass up commenting on, so I've actually ended up with quite a few entries devoted to him. So, I figured I'd create one entry with links to everything I've ever written about Comfort, and which I plan to update with new links if I ever write anything else about him.

Ray Comfort Entries, in Chronological Order

Friday, March 3, 2017

Christian Privilege

The Out Campaign: Scarlet Letter of AtheismBrowsing Quora recently, I came across the question, Is Christian privilege real?*. The questioner stated they were in the process of reading The God Delusion and had come across this claim. But, in their view, "He speaks of religious privilege and I have done some research into it online and I still have a hard time finding where religious people are privileged. Where is this 'Privilege'?"

Now, I used to be a Christian, myself. And I never really noticed the privilege then, because I was one of the ones benefiting from it. However, once I became an atheist and a religious outsider, this privilege became painfully obvious (I suppose that's how it goes with a lot of other majority privileges).

So, for people who may be wondering just what types of privileges Christians receive, here are several examples. Some of these are personal anecdotes, while others are links to news stories. At the end of this post, I've also provided links to sources with more examples.

Public prayer is a big thing where I live in Texas. It happens at PTA meetings, Girl Scout meetings, Junior Forum meetings (yes - I have a daughter), city council meetings, Air Force holiday parties, square dances... Really, public prayer happens at just about every public meal, and more than half of organized group gatherings. And the prayers are always Christian prayers. So it's not just us atheists being subjected to prayers we don't agree with, but also all of our community's members of non-Christian religions.

Don't want to work on your religion's most important holidays? No problem if you're Christian. Christmas is a federal holiday. Easter is on a Sunday. And lots of companies actually give you Good Friday off. If you're Jewish, or Muslim, or Hindu, or anything else, well, that's what PTO is for.

Want to send your kids to a private school? We've got five of them here in Wichita Falls. Guess how many are a religion other than some form of Christianity, or even just a secular option. If you guessed zero, congratulations.

Want to go to the only local adoption agency because you and your spouse have decided to adopt. Well, you better go to church, or no adoption for you. And yes, I have friends who were turned away from this adoption center for that very reason.

I don't go out of my way to announce my atheism, but I'm not shy about discussing it when religion comes up as a topic of conversation. So many people have been dumbfounded or shocked to find out. I've had people insist that I couldn't be a real atheist, tell me they'll pray for my soul, or wonder how in the world I could even believe that. Would anyone expect that type of reaction if you mentioned you were a Presbyterian?

On a related note, my daughter learned very early on not to mention lack of belief. At a Campfire daycamp, she merely mentioned that somebody could be good without believing in God, and was bullied by several of the other kids for it, and was practically in tears by the time we picked her up. Of course, none of the kids were ever bullied for mentioning that they believed in God. So, now that she's a bit older, she's very careful about discussing religion, or the fact that her father is an atheist.

Here's a story I ran across a few years ago - Calif. City Changes Zoning Code to Allow Home Bible Study After Couple Was Fined. The quick version is that a California city had an ordinance which barred " 'religious, fraternal or non-profit' gatherings of more than three people in residential neighborhoods without a ... permit." One couple broke that ordinance, basically running a small church out of their home, with weekly Bible studies drawing around 20 people, and a Sunday service drawing around 50. When the couple was fined for this, there was a public outcry, and the city changed the law and refunded the couple the fine. But the law wasn't changed to allow any old non-profit meetings. It specifically exempted religious gatherings from requiring a permit.

Everybody knows that just about every hotel room in the U.S. has a Bible in the nightstand, usually courtesy of Gideons (which is already an example of Christian privilege right there ). Well, in hotels run by the government, that runs counter to the Establishment Clause. So, a few years ago, the Navy decided to remove the Bibles from hotel rooms that they ran. Many Christians threw a fit. I wrote about the reaction of Ben Carson in particular, A Response to Ben Carson's Comments on Navy Bible Kerfuffle. The Freedom From Religion Foundation came up with a compromise solution - having multiple religious scriptures kept at the front desk, so that any guests that requested a holy book could get one. You'd think that would have been a good solution - Nobody was being denied their religious freedom to own or carry their own holy books, Christians could still borrow Bibles if they'd forgotten to pack their own copy, while people of other religions could also borrow their holy books. Carson and many others didn't like that solution at all, and demanded that Christian Bibles be kept in the rooms. That's not just freedom, but special treatment.

Here are a few lists with more general examples:

So yes, Christian privilege is a real thing. It's just hard to see unless you're not on the receiving end.


*This entire post is adapted from my Quora answer to that original question, with some editing and reorganization.

Friday Trump & Politics Roundup - 12

Donald TrumpThis is my semi-regular feature to post links to articles about Donald Trump along with excerpts from those articles. Trump has the potential to cause so much damage to our country and the world that it's every citizen's responsibility to keep pressure on him and our other elected officials to try to minimize the damage. To read previous entries in this series and other Trump related posts, check out my Trump archives.

I know I'm quoting Vox a lot this time around. I'll try to be more diverse in sources for the next update. Also, if you're only going to look at one article, I recommend the Foreign Policy article, President Trump's Terrible One-Month Report Card.

I'll also note that I'm experiencing a bit of a problem in focus. My original intent for this series was to post just a handful of articles pointing out the worst things Trump and his administration have been up to, making sure to include concrete policy examples, not just embarrassing things like his undignified use of Twitter. The problem is, the administration has been doing so many bad things. Believe me, I have a bunch of other articles I think are worth pointing out to people, but even just limiting myself to what I have, this post is already on the long side.


Foreign Policy Article

I'm only pulling one excerpt from this article, but I highly, highly recommend reading the whole thing. If you've already used your allotted free monthly articles from Foreign Policy, you can find further excerpts at Quora.


Foreign Policy - President Trump's Terrible One-Month Report Card

"Has it really only been a month? We wish we could say that Trump surprised us, but from the minute he took the oath of office one month ago today, he hasn't: This has been the worst, most unsettling start of a new president in modern memory. ... While the drama has provided plenty of fodder for the readers (and writers) of Shadow Government, it has been very damaging to the country. But how much? It's important to step back and reflect on the top ten things we have learned in recent weeks -- and what this means for the future."


Actual Policies:

Washington Post - Justice Department will again use private prisons

"The Justice Department will once again use private prisons to house federal inmates, reversing an Obama-era directive to stop using the facilities, which officials had then deemed less safe and less effective than those run by the government. / In a one-paragraph memo, Attorney General Jeff Sessions rescinded the previous directive to the Bureau of Prisons to either reduce or decline to renew private-prison contracts as they came due." ... "Private prisons have faced significant criticism in recent years from civil liberties advocates and others. Sally Yates, who served as deputy attorney general in the Obama administration, did not mince words in August when she ordered the Department of Justice -- of which the Bureau of Prisons is a part -- to end the use of private prisons entirely by phasing them out over time. / 'They simply do not provide the same level of correctional services, programs, and resources; they do not save substantially on costs; and as noted in a recent report by the Department's Office of Inspector General, they do not maintain the same level of safety and security,' Yates wrote." ... "The private-prison industry is a formidable one, generating billions of dollars of revenue each year and giving significant amounts to politicians. The GEO Group and CoreCivic, for example, donated $250,000 to support Trump's inaugural festivities, spokesmen for the companies said. Management and Training Corp. did not, a spokesman said. Separately, the GEO Group, gave $275,00 to the pro-Trump super PAC Rebuilding America Now, according to FEC filings. One $100,000 donation came a day after the Justice Department announced it would no longer use the facilities."


Vox - Sean Spicer just said we should expect an anti-marijuana crackdown under Trump: If Spicer is right, the administration will take federal marijuana enforcement more seriously.

"On Thursday, White House press secretary Sean Spicer gave the clearest answer yet to this question: 'There's two distinct issues here: medical marijuana and recreational marijuana. I think medical marijuana, I've said before, that the president understands the pain and suffering that many people go through, who are facing especially terminal diseases, and the comfort that some of these drugs, including medical marijuana, can bring to them. And that's one that Congress, through a rider in [2014], put an appropriations bill saying that the Department of Justice wouldn't be funded to go after those folks. / There's a big difference between that and recreational marijuana. And I think that when you see something like the opioid addiction crisis blossoming in so many states around this country, the last thing we should be doing is encouraging people. There's still a federal law that we need to abide by when it comes to recreational marijuana and other drugs of that nature.' / Given all this, Spicer said, "I do believe that you'll see greater enforcement of it." (For the record, though, the research increasingly shows that relaxing marijuana laws leads to fewer opioid overdose deaths.)"

Related: 2016 Texas Republican Platform - Part 11, Crime & Drugs - I think Spicer has it backwards. Recreational marijuana should be legal. Medicinal marijuana should be treated like any other medicine, going through clinical trials and FDA approval.


Vox - "It's dead on arrival." Republicans in Congress are balking at Trump's sweeping budget cuts.

"President Trump is currently crafting a budget to send to Congress. His initial outline would boost military spending by 10 percent in fiscal year 2018. And to pay for that, he's proposing steep cuts to a bunch of other domestic agencies -- including, reportedly, a 24 percent cut to the Environmental Protection Agency and a 30 percent cut to the State Department. Suffice to say, those are wrenching changes. / But ultimately, Congress will have the final say over any budget. And key Senate Republicans are already skeptical of Trump's outline. Sen. Lindsey Graham (R-SC) told NBC that the reported State Department cuts were 'dead on arrival.' " ... "It's worth noting that last year in the House, Rep. Ken Calvert (R-CA), who chairs the committee overseeing the EPA's $8 billion budget, only wanted to cut the agency's funding by 6 percent and freeze staffing at current levels of 15,000. He told E&E that he'd have to wait for more details before weighing in on Trump's proposals."


Vox - It's official: the Trump administration will "pull back" from investigating police abuses: Obama's Justice Department uncovered horrible abuses at police departments. Trump's attorney general said they'll "pull back" from such investigations.

"Over the past several years, the US Department of Justice played a key role in exposing abuses from local police departments, exposing everything from unjustified shootings to a broader pattern of racism in a police force. But on Tuesday, Attorney General Jeff Sessions confirmed that all of that work will come to an end -- saying that the Justice Department will "pull back" on civil rights lawsuits and investigations against police." ... "Trump argued that the administration's policies have fostered a broader anti-police sentiment, enabling more crime and violence against cops. And he suggested that he would allow police to be even more aggressive than they are today. " ... "These are only three of many more investigations by the Justice Department, ranging from Chicago to New Orleans. Time and time again, the Justice Department found big problems: a pattern of excessive use of force, racial bias, outright discrimination, and more. / These police departments were enormously troubled. The cities' residents were outright terrorized by police departments that were far more interested in looking "tough" with higher arrest numbers or collecting budget revenue for their local governments than improving public safety. Yet we would have never known about just how bad these problems were without the deep, months-long Justice Department investigations."


Scandals / Ethics / Big Picture

CNN - Trump rips media, repeats 'enemy of the people' line

[These attempts to discredit the media are actually one of my biggest immediate worries about Trump. It's one of the first steps of authoritarians - eroding faith in the very institutions that could hold them accountable.]

"President Trump mocked and disparaged the news media on Friday in a speech at the Conservative Political Action Conference, repeating his attack that much of the press represents 'the enemy of the people.' / 'I want you all to know that we are fighting the fake news,' Trump told attendees. / 'A few days ago, I called the fake news the enemy of the people, and they are,' he added, referring to a tweet last week. 'They are the enemy of the people because they have no sources. They just make them up when there are none.' / He also said reporters 'shouldn't be allowed' to use unnamed sources."


CNN - White House blocks news organizations from press briefing

"CNN and other news outlets were blocked on Friday from attending an off-camera White House press briefing that other reporters were hand-picked to attend, raising alarm among media organizations and First Amendment watchdogs. / The decision struck veteran White House journalists as unprecedented in the modern era, and escalated tensions in the already fraught relationship between the Trump administration and the press."


Vox - Bush ethics lawyer: Trump's Russia scandal so far is "much worse" than the early stages of Watergate

"The facts now in this investigation are much worse than the facts in the early stages of Watergate, which was a simple break-in ordered by midlevel campaign officials -- not by the president. Here we have facts that are much worse: We have a foreign power that has orchestrated a break-in. It's a much worse situation than the outset of Watergate." ... "I have been a Republican for decades, and the one thing that Republicans and Democrats should have in common is concern about our national security. And in particular the attempts by Russia over the decades -- going back to the 1920s -- to subvert our government by supporting extremist groups like the American Communist Party, or now white supremacist groups. / This is not a Democratic and Republican issue, and figuring out who in our government is cooperating with the Russians is of the utmost importance. We certainly don't need a McCarthy-type witch hunt, and this shouldn't be abused for political purposes, but it's a critically important issue, and Democrats and Republicans can be united on this. And I certainly don't think the Republican Party should become a pro-Putin party. If it is, we are going to have sort ourselves out."


Scientific American Blogs - How to Defeat Those Who are Waging War on Science

"President Trump's decision to constrain and muzzle scientific research signals an important milestone. The War on Science has shifted into high gear. This is a fight for our future, and scientists as well as citizens had better prepare for what is coming next. / At his confirmation hearings last week, the new EPA Administrator Scott Pruitt unveiled the new language of this war--a subtle, yet potentially damaging form of science skepticism. Manmade climate change, he says, is 'subject to continuing debate.' There is reason to be concerned about methane released by fracking, but he's 'not deeply concerned.' And research on lead poisoning is 'not something [he has] looked into.' / These might sound like quibbles compared to the larger cultural and political upheavals happening in America today, but collectively, they add up to something big. / The systematic use of so-called 'uncertainty' surrounding well-established scientific ideas has proven to be a reliable method for manipulating public perception and stalling political action. And while certain private interests and their political allies may benefit from these tactics, the damages are something we will all have to face." ... "At its heart, the War on Science is often an attempt to de-regulate industry and weaken environmental laws. Stifling science--especially on topics like climate change, toxic pollution, unsustainable agriculture, and animal welfare--is part of a ploy to undermine these safeguards, and to cast doubt on inconvenient scientific truths, all in the service of profits and power. / It's time to call out this merciless greed and ignorance. The short-term gains of a few corporations and individuals must no longer rise above our national interests, our long-term economic competitiveness, and most importantly, our individual safety, health and wellbeing. / So, let's not be timid. Let's call things as they are. / America has a choice to make. A choice between advancing civilization or bringing it down. A choice between knowledge and chaos. / Now, everyone must choose which side they are on."


Vox - 3 winners and 2 losers from President Trump's first address to Congress

"But Trump is harder to pin down than his predecessor -- for better and for worse. He is infamously prone to repeating the opinion of whoever spoke to him last, and the public is forced to resort to Kremlinological interpretations of his statements and those of key aides like Steve Bannon and Stephen Miller, along with leaks of behind-the-scenes infighting. / Tuesday night's speech was Trump's chance to clarify what he stood for and issue clear directives for what Congress should do on Obamacare, tax reform, infrastructure, and immigration. It was his chance to bring his party in line behind a specific, common agenda. / And ... none of that happened. Instead, you got a repeat of his usual greatest rhetorical hits."

"A fair read of the evidence is that immigration probably doesn't hurt US workers at all, and that even if there is damage, restricting immigration further is a ham-handed and inefficient remedy. The fact that there's still strong opposition to immigration despite this is not surprising. It just indicates that the opposition to immigration has, as in Trump's case, traditionally been motivated mainly by a desire to preserve the majority culture and a fear of demographic change, and has little to do with economics. / But the shift to economics is important for what it portends for policy. Because all immigrants, legal or not, are supposed to have these negative effects on native workers, Trump is laying the groundwork for a crackdown not just on the undocumented population but on legal immigration in the future. That's been a longstanding priority of Bannon and Miller's, and this speech was a strong indication that it's now Trump's."


Vox - Donald Trump is dangerous when he's losing: Trump's failures at governing feed his illiberalism.

"A few weeks back, I wrote a piece about Donald Trump titled "How to stop an autocracy." The essay began with the premise that Trump has a will to power and a contempt for the basic norms and institutions of American democracy, and then explored how to limit the damage. The answer, basically, was that Congress needs to do its damn job. / But after I wrote it, smart people argued the piece was built atop a mistake. Trump might have the will to power, but he doesn't have the discipline for it. Grim scenarios suggesting his presidency would grow too strong missed the likelier scenario that it would be extremely weak." ... "And then I talked to Ron Klain." ... "Klain had a theory that combined Trump's authoritarian impulses and troubled White House management in a way I found hard to dismiss. In Klain's view, it's Trump's dysfunctional relationship with the government that catalyzes his illiberal tendencies -- the more he is frustrated by the system, the more he will turn on the system. / 'If Trump became a full-fledged autocrat, it will not be because he succeeds in running the state,' Klain said. 'It's not going to be like Julius Caesar, where we thank him and here's a crown. It'll be that he fails, and he has to find a narrative for that failure. And it will not be a narrative of self-criticism. It will not be that he let you down. He will figure out who the villains are, and he will focus the public's anger at them.' "


Vox - After a new wave of anti-Semitic attacks, White House appears skeptical about anti-Semitism

"President Trump spent weeks conspicuously staying quiet about a wave of anti-Semitic incidents across the US before finally describing them last week as 'horrible and painful.' / He should have stopped there. Instead, he is now hinting the attacks might be a "false flag" operation carried out by his political opponents to make the White House look bad." ... "Shapiro later told journalists that Trump called the bomb threats and desecrations 'reprehensible,' but then seemed to indicate the threats might not be exactly what they seemed. Trump continued his comments by noting that the threats and vandalism might instead be an attempt to 'make others look bad.' " ... "In a statement distributed to the press, Rabbi Jack Moline, president of the Interfaith Alliance, said the president's comments were 'outrageous and irresponsible.' / Moline maintained that the president's comments and Scaramucci's tweet together represent an utter failure to comprehend the recent surge in violent rhetoric and attacks directed at Jews, Muslims and other religious minorities.' "

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