Friday, April 28, 2017

How much does it bother me that people believe in gods?

I came across a Quora question not too long ago, Does it bother atheists that people believe in God?. Here's my answer.


The Out Campaign: Scarlet Letter of AtheismIt does bother me that people believe in gods, but the extent to which it bothers me depends very much on the specifics of how the person acts.

Look, most of my friends are Christians. And for the most part, we only discuss religion a bit, and have a live and let live attitude. As long as people are reasonable and tolerant, religion isn't the type of thing that gets me up in arms. But even then, it still bothers me some. I mean, I think back to when I was still a Christian, and all the cognitive dissonance I experienced, the fear of Hell (especially for others besides myself), the Catholic guilt, the wrestling with secular ethics vs. Biblical rules, etc. It may have taken me a few years to get to this point, but I'm happier now as an atheist than I was as a Christian, and I'd like for others to have that. But, I also don't want to be that guy that's always arguing and being pushy about beliefs. So here's a list of examples stepping through different types of believers and how I feel about them.


Type of Believer: Tolerant believer who keeps their religion private and doesn't impose on others
My Feelings: This bothers me on the same level as people who believe in urban legends, or who root for different sports teams from me. They're wrong about the nature of reality, and I would like to help them see the world more clearly, and recognize that the Steelers are the one true... sorry - wrong topic
Level of Opposition: Good natured discussions over beer (though I hardly ever bring it up, waiting for others to broach the subject)


Type of Believer: Somewhat tolerant believer, but who lets their religious beliefs influence the way they vote (particularly if they vote against women's rights or LGBT rights, or think global warming can't be real because God wouldn't let it happen)
My Feelings: Well, now your religious beliefs aren't as private anymore, since they're having real world effects. So, now I do feel more justified in trying to get you to change your mind.
Level of Opposition: More heated discussions over beer, Possible end of friendship depending on how they treat individuals


Type of Believer: Door to door proselytizers
My Feelings: Hoo boy. I love debate, and I have strong opinions on religion, and you actually came to my house with the purpose of talking about religion, so here we go.
Level of Opposition: Debate for as long as they're willing to stay at my house


Type of Believer: Parents who withhold real medical treatment from children in favor of faith healing
My Feelings: I don't personally know anyone like this, but I know they're out there. The case of Makayla Sault was a heartbreaking, recent example. Children shouldn't have to suffer or die for the religious beliefs of their parents.
Level of Opposition: Push for laws to outlaw this type of child abuse


Type of Believer: Intolerant believer, who lets their religious beliefs influence the way they vote and how they treat individuals (particularly women, the LGBT community, and people outside their faith)
My Feelings: Yeah, now they're definitely into the strong negative effects of religion, and I don't just feel justified to try to change their minds, but see it as a moral duty to society.
Level of Opposition: Strong debate, definitely not going to be friends


Type of Believer: Creationist/Evangelical/Fundamentalist Preachers/Leaders
My Feelings: You're not just misleading yourself, but misleading all the people who follow you. And these brands of religion are usually the more close-minded branches that lead to negative effects, so I'm definitely going to speak up.
Level of Opposition: Pointed blog entries and Quora answers


Type of Believer: Intolerant Religious Politicians
My Feelings: We have a First Amendment for a reason. Government and religion aren't supposed to be intertwined. It really, really bothers me when politicians pass religiously based laws, or give preferential treatment to certain religious institutions.
Level of Opposition: Pointed blog entries and Quora answers, Vote for opponent


So, that's how I feel about it. We live in a free, multicultural society, where people have the right to believe anything they want. As long as religious people are tolerant of others and don't use religion as a reason to discriminate or make bad decisions, the most they'll have to fear from me is talking about religion over a beer every once in a while. However, if a person's religious beliefs are having harmful, real-world consequences, then I'm going to speak up.

Thursday, April 13, 2017

Answering Quora - Why are you not preparing for the tiny possibility of a literal Hell?

A few months ago, I came across a question on Quora, Why are you not preparing for the tiny possibility of a literal Hell?. Here's my answer.

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I don't prepare for the Christian Hell for the same reason I don't prepare for this afterlife:

Egyptian Book of the Dead

The ancient Egyptians believed there were seven gates the deceased must pass through on their way to the Field of Reeds, and each of those gates was guarded by some type of supernatural creature. The only way past was to recite the appropriate spell for each one. If you made it past all them, then your heart was judged on the scale of Maat:

Scale of Maat

Your heart had better match the feather of truth, or else Ammit will devour your soul. If you pass that test, then you get to go on and enjoy the afterlife.

If all that was true, that would be pretty important for your eternal afterlife. Would it make sense to memorize all the spells to recite at the seven gates? I mean, even if there's only a tiny possibility of it being true, what's a few hours worth of memorization compared to eternity?

Or do you, like most people, dismiss the Egyptian afterlife stories as just ancient superstition, and consider the 'tiny' possibility they might be true to actually be a negligible, virtually non-existent chance? Perhaps it's interesting, but no, it's not even worth devoting a few hours worth of time to memorize spells that you will never use, ever again, except perhaps as some interesting bit of trivia at cocktail parties.

That's how non-Christians feel about the Christian Hell. The whole religion is so obviously not true. The 'tiny' chance that Hell might be real is on par with the 'tiny' chance that fairies may exist - i.e. virtually no chance at all. Why worry about such obvious superstition? And even if you were going to worry about it, why pick that superstition in particular? There are lots of proposed possibilities for the afterlife. If you really wanted to be safe, you'd have to prepare for all of them.

Images from Wikipedia - Book of the Dead

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Related Entries:

Wednesday, April 5, 2017

How Bad are Unpronouncable Chemical Ingredients in Food?

I ran across a new line of frozen lunches the other day, SmartMade by SmartOnes. One of the key selling points on the box is 'Made with real ingredients you can pronounce'. This seems to be a common attitude among people who don't understand chemistry as well as they could. But how bad for you are foods made up of all these strange sounding chemicals?

For example, here are the ingredients to a treat I eat nearly every weekend:

Ingredients for Weekend Treat


And here are the ingredients to an energy drink I drink nearly every day:

Ingredients for Energy Drink


Should I be worried about all those chemicals?

.
.
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Okay, it was a trick question. I cropped those images to hide what types of food they were. Here are the original, uncropped images, made by James Kennedy, showing what the foods were (click to go to source):

Egg Ingredients


Coffee Ingredients


Mr. Kennedy has a whole series of these types of images (as well as posters of them for download and for sale).

The whole point is that everything we eat is made up of chemicals. Living things, especially, are this whole complicated cocktail of chemicals. And most of those chemical names sound very foreign to those of us who don't study them on a regular basis. But that doesn't make them dangerous.

When certain chemicals are added to processed foods, it's done in a very controlled way. Instead of the cocktail of chemicals you get from natural foods, they're adding very specific ingredients, in tightly controlled quantities. There's nothing inherently dangerous about not being able to pronounce those chemicals, unless you think we should be avoiding eggs because they contain arginine and eicosatetraenoic acid.

Tuesday, April 4, 2017

Website Update - Top 10 Page List for February & March 2017

Top 10 ListWell, I fell behind again. I missed doing this list after February, so today is a two-fer.

There was only one newcomer between both months, but it's an entry I like a lot myself, Response to Kent Hovind Video - Bird Evolution. It really highlights how bad and misinformed creationist arguments can be. In fact, I'd even just included it on my new page, Recommended Reading - Evolution.

Speaking of, you may have noticed a new link in the side bar, Recommended Reading. I figure that with as many entries as I've written over the years, certain particularly informative ones just kind of get lost in the mix, so it might be useful for newcomers to have a list of some of those entries to start off with. There are also two sub-pages, one of which I already mentioned, Recommended Reading - Evolution and Recommended Reading - Religion.

Anyway, here are the top 10 most visited pages from this site for February and March:

Top 10 for February 2017

  1. Origin of Arabic Numerals - Was It Really for Counting Angles?
  2. Tank Game - QBasic Source Code
  3. Response to Global Warming Denialist E-mail - Volcanoes and Global Cooling
  4. Autogyro History & Theory
  5. Response to E-mail - 1400 years of In-breeding
  6. A Skeptical Look at MBT Shoes
  7. Retroactive Soapbox Entry- Fed Up with U.S. Public, Part II
  8. A Skeptical Look at Bio-Identical Hormone Replacement Therapy
  9. Response to E-mail - Are America's Hunters the World's Largest Army?
  10. Gamera Human Powered Helicopter


Top 10 for March 2017

  1. Origin of Arabic Numerals - Was It Really for Counting Angles?
  2. Response to E-mail - 1400 years of In-breeding
  3. Autogyro History & Theory
  4. Retroactive Soapbox Entry- Fed Up with U.S. Public, Part II
  5. Response to Kent Hovind Video - Bird Evolution
  6. Debunking an E-mail on Charities
  7. Response to Global Warming Denialist E-mail - Volcanoes and Global Cooling
  8. Tank Game - QBasic Source Code
  9. A Skeptical Look at Bio-Identical Hormone Replacement Therapy
  10. Response to E-mail - Are America's Hunters the World's Largest Army?

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

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.

Wednesday, March 22, 2017

Understanding Evolution - Development of Eyes

Well, I just had an answer 'disappeared' on Quora. Since I kind of liked it, I'm going to repost it here, to make sure it's still easy to find. 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 the full story of what happened to my Quora answer, it wasn't anything malicious - it was the result of Quora's policy of merging similar questions. I had already answered one question, If theory of evolution is true, why aren't there more semi-evolved species with hands coming out of their skulls or other half-baked monstrosities?, and even adapted it to an entry on this site, Understanding Evolution - Origin of Limbs. Well, someone went and asked a similar question, If evolution is true, why aren't there millions of creatures out there with partially developed features and organs?. I wrote up an answer, looking at it a little differently than I had the first time. When someone noticed that both questions were similar, they merged the questions. Since Quora's policy is to only have one answer per user per question, when the questions were merged, they took my most popular answer and kept that. So, my newer answer more or less disappeared, and is basically only available by direct link or through my profile.

For a slightly different perspective, to quote my summary from my other answer, "evolution doesn't have foresight or a plan. For that matter, it's not a conscious entity at all, even if anthropomorphizing sometimes helps to explain it. Evolution only works through small incremental changes, and each of the changes has to be beneficial if the organisms are going to survive and pass those changes on to future generations. Every organism alive, past and present, is in a sense the end result of all the evolutionary history leading up to it. But in another sense, as long as they don't go extinct, evolution never stops, so every organism is also a transitional form to whatever its descendants might be."

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