Answers NOT in Genesis #3: disinformation to critique a comic strip?

Answers in Genesis once again deploys gobbledy goop pseudo-science to misinform their flock about real science. In the article, which critiques a Doonesbury cartoon about bacteria acquiring resistance through mutation, they write:

…what about those experiments where some bacteria developed a resistance to substances over time due to mutations in their genes? Such mutations, which are mistakes in the genes, result from a loss of information (such as the loss of a control gene which regulates the pumping of the substance into the cell). Again, this is the opposite of evolution, which requires an increase in information if it were to occur.

First, there seems to be a fundamental misunderstanding about what a “mutation” even is. Very simply, a mutation is a change (caused by chance, by environment, by radiation, by replication errors, by many things) in a gene. Most of the time, the change is neutral and replicates slowly through the population, to remain or die out. Sometimes the mutation reduces the chance that that bacteria will survive and produce offspring. While we might have an opinion about that change, there is no “Loss of Information” here; it’s just a change. Some mutations are fatal and the individual dies without leaving offspring. Some mutations allow the individual to produce offspring and the mutation may continue in the population at a low level (and possibly combine with future mutations). Some mutations help the individual produce many offspring and that mutation flourishes and – over time – will become “normal” for the species (i.e., evolution).

Bacteria are a great example because they exist in such huge numbers and cycle through hundreds, thousands, millions of generations in a relatively short time. This gives longer-living observers (us) a chance to observe how a mutation effects the greater population.

Here’s a simple experiment: put a single species (“kinds”) of bacteria into a hundred test tubes. introduce a small amount of antibiotic into each one – just enough to harm but not eliminate the test tube population. Wait a few weeks or months, and examine the contents of each test tube.

If the creationists are right, you’d expect to see a small number of “answers” to the antibiotic stress, and these would be the a result of the variations already in the population. To have a hundred different “answers” would be impossible, since statistically that would require that the entire genome consist of just variations of resistance to the antibiotic stress. (I think I’m being conservative here – anyone with the statistical prowess to verify?)

If the scientists are right, you’d expect to see a large number of solutions, perhaps including a distribution as to ‘styles’ of response (since some single-point mutations are more likely to happen then others.)

So what do you get? (This, by the way, is what science means by “testing a hypothesis”.) If you have to ask, maybe I’ll save the answer for another post.

Now, for laughs, mix all the test tubes together and continue the antibiotic stress.

If you’re a creationist you’d expect the “best performer” of the hundred test tubes take over the population, and that’s it (since we’ve teased out the “best” gene in the experiment above). If you’re a scientist you’d expect, well, lots of things: you’d expect the “best performer” to do well, but not necessarily. You’d also expect to observe further mutation as time goes by.

So what do you get? Again, if you have to ask I won’t tell you.

Second, what’s this “loss of information” kick the creationist crowd seems to be so in love with? Quoted by trolls on forums, by ditto-heads on talk shows, and in supposedly “informative” articles like this one, I hear the phrase “loss of information” over and over again. This is a very red herring, since “loss of information” has no meaning in Real Science, unless it’s about a graduate student’s computer crashing the night before the thesis is due. The way it seems to be defined among the creationist pseudo-scientists is, “Something Good” = “Information”, and “Something Bad” = “Loss of Information”.

But let’s say Real Life is actually like that (it isn’t). OK so a “bad mutation” causes Sickle Cell Anemia (SCA). That’s bad, right? Loss of information? After all it’s a “harmful” mutation so it’s Loss of Information definitely. But wait a minute! It turns out that SCA protects certain populations against malaria. In other words, having SCA in the population is a Good Thing when malaria is a problem. OK, so now it’s “Added Information” where there is malaria but “Loss of Information” where there is no malaria.

If that doesn’t make sense, there’s a good reason: The “Added Information” canard in creationism is just a bunch of BS; it makes for nice scienterrific-sounding media-bites, and wows the Faithful, but it has no meaning in the context being used by the creationists.

OK, strip out their misleading definition of mutations. Now omit the meaningless “Added Information”/”Loss of Information” pseudo-babble. And you get… well you get nothing since that’s all there was to the article.

Answers NOT in Genesis #2: Origins of Life and creationist propaganda-babble

Once again, Answers in Genesis purposely confuses the issues surrounding evolutionary science, this time in their article Natural processes—can they explain the origin of life? by staff writer Pam S. Sheppard

This “confusion” is one of many arguments used by creationists. Instead of addressing the science, they misrepresent it badly, then construct a phony argument against the misrepresentation. Other strategies include quote mining – creating long lists of out-of-context and thereby misleading quotes by scientists, focusing on areas of research as “problems” (or criticizing early research for being incorrect, yet ignoring later research) and of course the good old ad hominum argument: say something nasty about a person doing real science.

Note that any organization using arguments like these says a lot about the organization itself; that they have no foundation in rational argument so they must obfuscate instead. I can condone making errors like these in, say, heated argument, or in an email exchange where much context is assumed. But to use these techniques as strategy is not acceptable. I find it utterly perplexing that AIG pursues this course. What is the value of arguments won by lies?

The article mostly follows the work of Mike Riddle, an ex-marine and now a “consultant” on evolutionary issues in schools helping (apparently fundamentalist) parent groups select “appropriate” biology textbooks for their children. Riddle dismisses some texts as including “content long since disproven such as the peppered moth and Haeckel’s embryos.”

First, the peppered moth is NOT disproven. Though there are some objections to the early experiments, the fundamental processes that the experiment exemplifies are still true and valuable, especially as a teaching example. See http://www.talkorigins.org/indexcc/CB/CB601.html for an excellent overview and references to the specific research.. Second, while Haekle indeed used doctored photographs over-emphasizing embryonic similarities across species, his research has been repeated using correct images. These accurate images show that both the similarities and differences among embryos are consistent with – and make a stronger case for – evolutionary theory. See http://www.talkorigins.org/indexcc/CB/CB701.html for more information.

(Note, I reference Talk.Origins a lot, since they’ve done such a fantastic job organizing the relevant material, and putting it into a context useful for addressing creationists’ claims. I recommend anyone – especially a fundamentalist with an open mind – to spend some time there)

Sheppard/Riddle then spends a significant amount of time attacking Miller’s 1953 experiment in which Miller passed an electric spark through a mixture of water, methane, hydrogen and ammonia (to simulate lightning strikes in a theorized “primordial soup” of the earth’s early atmosphere) and got biological precursor chemicals such as amino acids and small organics. Riddle objects to the resulting mixture of right and left “handedness” of the resulting molecules (real life tends to prefer only “left handed” molecules), claiming it debunks Miller’s research (see Talk.Origin’s comments on this). He also claims that Miller “purposely chose which gases to include” which somehow invalidates the experiments.

A few points about this. Most importantly, origin-of-life explanations are not required for evolutionary theory to be valid. Riddle claims that “since any biological evolution is first dependent upon life first starting, evolution has no foundation or starting point for their model”. But in fact, even if God DID create the first forms of life, evolutionary fact and theory would be just as valid as they are today. Evolutionary theory is about how biological entities change and mutate and evolve, not about where the first entities came from. That said, evolutionary theory both informs – and is informed by – origin-of-life research. Advances in the biochemistry of evolution point to possible origin-of-life scenarios, and early “life” and its precursors would have been impacted by evolutionary processes. For an excellent article on this topic, see Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks.

Back to Miller: first, all valid experiments add to scientific knowledge, and this was a first in a long chain of important research. Miller didn’t attempt to “explain” the origin of life, but rather to test a hypothesis about early conditions. In that he succeeded famously, but no respectable scientist thinks he proved anything about abiogenisis. Second, all science is a long history of building on the work done before. Early science is – by definition – “early”. The Model T is a historical precursor to the fighter jet, yet the fact that the Model T didn’t fly does not make flight impossible. In fact there has been some very exciting research and speculation done on abiogenisis since Miller’s time, some of it including new information about the earth’s early atmosphere (see the above article for examples).

Riddle then floats a few more of the standard creationism pseudo-arguments. There’s the problem with ‘life being too complicated to have evolved “even a small protein”’ argument. But this implies a lot of assumptions about such a “small protein,” even that it formed randomly. It’s possible, even likely, early proteins were themselves the result of evolutionary forces. See http://www.talkorigins.org/indexcc/CB/CB010.html for further information.

Then there’s the information theory canard, claiming that “life evolved from lifeless chemicals into a complex cell consisting of vast amounts of information…”. Not only does this approach demonstrate ignorance of basic Information Theory, but the argument fails anyway, since “complex” systems are found in nature even when “life” is not involved. No deity is required to form a snowflake, or shape a spiral galaxy. More specifically, one can claim a deity is involved, but not that the science demonstrates the existence of that deity.

When Riddle says that “Both science and the Bible agree that only God could create life”, he continues one of the fundamental lies of creationism: Science does not and can not demonstrate the existence of a supernatural origin to life. Science looks only at the natural, material world. All the evidence and all the results are based in the natural world. The amazing success of science over the centuries demonstrate the effectiveness of that approach. Even if God personally did direct the origin of life and its subsequent evolution, that does not contradict the conclusions of science. To twist the conclusions of science, to lie about the results and crowbar them into one specific interpretation of a religious doctrine, insults both the science and insults the religion.

Science and Kids

This is the text of a comment I made over at The Panda’s Thumb, in response to a posting titled How would *you* strengthen science in the U.S.?, Summit Lists Ways—but Not Means—to Strengthen Science, by Tara Smith. The gist being there are a lot of great ideas but no committment to fund them. The phrase I quote is from that article, where Tara is referring to comments she sees on Panda’s Thumb and on other science blogs.

——————————————————-

teachers “never made science this interesting when I was in school.”

My daughter, who is six years old, thinks science is boring! When I try to figure out what she means by this, I don’t get any clear explanation, and I suspect it’s a kind of kiddie group-think.

At home, from time to time, I show her something fun that has scientific principles involved. Recently we played with a large magnifying lens, seeing what materials catch on fire easily. And earlier I gave her a 6v battery, a light bulb and some wires with clips on the ends. We had a great time finding out what materials allow the bulb to light (barbies are not good conductors). She likes these activities but doesn’t know (from me) that they are “science”.

It’s in school she’s learning to “hate science”, and I worry that she is predisposing herself to hate it even when she’s older. I’ve seen this in other activities too, and suspect it’s part of the ‘boy vs girl’ games they play. When she was four she said once that “boys are doctors and girls are nurses” (!) She probably doesn’t even know the difference between them, but a result I now ask for the “lady doctor” in my daughter’s pediatric group.

I love science, wish I had pursued a scientific career, and hope my daughter will at least appreciate how exciting it can be.

But it seems counter-effective to first “teach” young people – especially girls – that “science is boring” and then later try to entice them back in.

I think the solution is to have “cool science” a regular part of the classroom. There should be regular and FUN demonstrations of scientific principles using, say, lots of liquid nitrogen and big flames. Or a wing that lifts the kids a foot or two off the ground. Or teach them to make catapults that actually break things. Keep all but the absolutely necessary “scientific explanations” out of the activities.

Of course, this won’t happen soon. Naturally schools must deal with funding, educational priorities, teacher knowledge, etc. But I think these are just symptoms of a bigger problem: science is made “boring” by society at large. Science is not “done” (vs “taught”) by anyone but “ivory tower” types, and only in institutions of “higher learning”. How many kids these days have an uncle or aunt who has a science lab/workshop in their house?? My dad – a chemist – did some of his research at home, and had to lock the door to keep me out of his hair.

Improving scientific learning and access to science is great. But if kids don’t grow up with it, don’t see it around them or hear adults talking about it, it’ll just end up an obscure field that only certain nerdy types do, not something that “normal people” do, and certainly not done for pleasure.

Interesting overview of origin-of-life research – scientific process in action

The recent article at Panda’s Thumb references a list of interesting articles in the November issue of Public Library of Science (PLoS) Biology. Among them is a very nice overview of the current state of abiogenesis, or origin-of-life research, “Jump-Starting a Cellular World: Investigating the Origin of Life, from Soup to Networks” (it’s a .pdf so expect a long download over a slow connection).

I’ve always been drawn to origin-of-life research, ever since I first read about Oparin and (the independent researcher) Haldane’s theories of a “primordial soup”. To me there is something – dare I say it – miraculous about quasi-random processes, fueled by various forms of energy, self-organizing themselves into self-replicating biological system.

(As an aside, I first learned about these ideas in a Human Biology 101 at San Francisco State in the 80’s. The teacher of that class – in a bizarre retroactive twist – was Dr. Dean Kenyon, a co-author of “Of Pandas and People,” that nefarious tomb of pseudo-scientific creationist propaganda-babble. I would like to take this moment to thank Dr. Kenyon for inspiring me later to become an enthusiastic “evolutionist”. This in spite of – or perhaps because of – his attempts to teach the “alternative explanation” in class.)

Returning to the point of this post, this accessible article explores various theories of abiogenesis, from the early “primordial soup” theory through a proto-RNA replication replication, and how those theories interact with other research on early geological evolution (for example, the amount of hydrogen in an early atmosphere impacts how likely a particular theory is valid. Discoveries of ocean vents has played a big part as well). While the information itself is fascinating, I noticed one aspect inherent in the article that was probably not purposely included: It gives a wonderful perspective on the scientific process itself.

Creationists like to dismiss evolutionary theory by pointing out “problems”. Yet this scientific article very candidly discusses various “problems” with some of the theories of abiogenesis, and the context is of the progress of understanding, NOT debunking an idea because a “problem” was found, or “your side lost my side won, neener neener neener!” The so-called “problems” in the mentioned in the article don’t “disprove” a particular theory, but challenge scientists to defend or modify their theories and – most importantly – gather additional facts (facts are completely lacking in ID “research”). In real science, “problems” (I keep putting it in quotes because it can be such a loaded word in this context) move the body of understanding forward. In creation science (CS) – or ID as they like to call it now – it’s the opposite; a “problem,” no matter how obscure, is “proof” that the original theory is deeply flawed and their theory is right. This is rather ironic, since ID/CS has absolutely no facts and no theory; scientists can’t point to “problems” with ID because, well, with no facts there ain’t no problems!

New Mexico lands space business!

This is incredible! This story from BBC News reports that Virgin Galactic has selected the state of New Mexico to build their spaceport!

I have some reservations about the overall practicality of human space flight (NASA, at least, should be emphasizing robotic missions at least until more of the space-bugs are ironed out and the technology for interplanetary space travel has advanced). But I have no reservations about the sense of pure wonder, awe and excitement it brings. I am absolutely thrilled about this project. I want to move there and help them out!

Diebold voting machines are easily hackable!

I’m shocked, simply shocked. Those Diebold voting machines? You know, the ones that handed G.W. Bush the presidency last year? Well it turns out that – surprise, surprise – they can be hacked without leaving a trace to change the votes any way desired. And this is on the memory card that Diebold swore was not hackable. The test was done for Leon County (FL), and a post of the test is on the site BlackBoxVoting.org. As a result of this test Leon County is dumping their Diebold voting machines, and I’m adding these folks to my Links sidebar!

I’ve heard a lot of complaints about these boxes. Not only are they hackable, but the people who set them up did some very stupid things (not intentional of course) like telling the poll workers the password – which could be used to alter the results any way desired on all the machines. There are lots of stories – verifiable ones I should add (unlike the tall tales the Republicans were telling about supposed voter fraud) – about voting machine victories: Areas that had them had a disproportionate number of votes for Bush, compared to districts that didn’t have them – a statistical impossibility. Or traditionally black, Democratic districts “voting” for Bush when other similar districts nearby did not. I heard this all most recently on the radio some weeks ago, but don’t have a source (didn’t have a ‘blog then). Sorry about that if I find info I’ll update this page.

This issue stirs a lot of outrage for me. Aside from who won the election – and that’s not something to be complacent about either – it is VITAL that we trust the election process. Compared to all the sneaky, dishonest, dirty tricks played by the Right, fiddling with the voting machines cuts the deepest into our political rights and freedoms. I don’t care how god-awful the elections get, if we want to preserve our democracy we have to be able to trust the process!

Political Blogging Addiction, and Firefox

Blogs on the Left and the Right

I started following political blogs around the time Special Prosecutor Fitzgerald was doing his magic, and discovered a number of great mostly left-leaning blogs to follow, some of which I will list here. I also tried out a couple of the right-wing blogs, but got too angry reading them – too full of outrageous lies and spin in the face of the most solid facts, the advocacy of punditry over journalism. Of course that’s what they say about the blogs on the left, but any objective reader can tell in a flash which side respects the truth and which side is soaked with contrived outrage. Right?

Of course, there are “bad apples” in every bushel. There are some sane voices on the Right (generally they are the real conservatives, as opposed to the wack-job neo-cons), and there are some real wackos on the Left. But I know that I’m not a wacko because…because… well just because!

Firefox and Sage

Here’s what made reading political blogs into an addiction: I started using the Firefox browser, then added the Sage extension. For those of you who live on deserted islands and only read this in Morse Code, Firefox is a new, upstart open-source browser that’s dramatically more useful, small and faster, and more extendible than Internet Explorer. Sage “is a lightweight RSS and Atom feed aggregator.” In English that means that most blogs (those that support RSS – it’s easy to tell) can be listed in a column to one side. You know immediately if there are updates – usually new and recent entries – and they are listed below. You can check your favorite blogs without having to browse to the web page. Only if you want to read the article in full, or interact with the content in some way, do you need to browse the web page by jumping to the specific entry. It saves a huge amount of time which some people – like me – waste by adding additional blogs.

Different Blogs

There seem to be a few styles of political blogs. There are those that mostly just reference a story or comment made by a “real” news outlet or by another blogger. This is very handy since they have done all the work reading commentary and watching TV, and just supply a link and a few comments. Of these I use AMERICAblog, Think Progress, Daily Kos and Atrios. My current favorite is AMERICAblog – the comments are concise yet they are very passionate, updating several times an hour (which is Good Stuff to the blogging addict). Atrios, though it has great links, is a little terse for my taste. Think Progress goes both ways – sometimes no commentary and sometimes a bit of reporting. In their current (as I write this) entry, Think Progress has a great bit on O’Reilly’s “War on Christmas” stupidity. Daily Kos has great commentary too.

Then there are the blogs that write coherent articles on various topics. I put foreign policy expert Steven Clemens’ The Washington Note into this category, along with NO QUARTER, run by Larry Johnson, a former Intelligence professional who applies his extensive expertise and contacts to great stories.

Commentary

Most if not all of these provide a venue for comments. I find this a mixed bag as they allow pretty open commentary – only the most inappropriate comments are filtered out – and hundreds of comments can accumulate. Right-wing blogs, by the way, tend to be closed to commentary (this makes sense – if you’re going to lie on a regular basis it would be inconvenient to have a hundred different commentators reminding everyone what the facts are). Also, some blogs have resident “trolls” – these are regular commentators on a mission to disrupt the discussion. Usually with absurd or inflammatory comments. While this makes participation less engaging then it should be, it does not distract from the article or entry itself.

Addiction

I started this entry as a way to put the links to some of my favorite blogs (and these are just a few of the political ones) in an article. As with most of my writing it got quite long and I’ll be really impressed if anyone bothered to read all the way through! But if anyone wants to share this addiction, all you have to do is get Firefox, get Sage, and start adding blogs like crazy. Pretty soon you, too, will be staying up until 4AM clicking on articles, searching the web for more blogs, and tweaking your list by organizing blogs into folders. Have fun!

Why is the White House Pushing so Hard to Allow Torture?

The White House — especially Dick Cheney — is pushing pretty hard to allow the US to torture captives under certain circumstances (news is all over, but here’s a recent link via AMERICAblog). This has got to be a public relations nightmare both at home and at broad. Why are they pushing so hard when it clearly is costing them so much?

I have a theory about this: I think they are trying to cover their asses when the news gets out that THEY HAVE ALREADY BEEN TORTURING PEOPLE. I don’t mean all these insinuations and implications and tip-of-the-iceberg news stories we’ve been hearing a lot lately. I mean when the story impinges on the reality of the mainstream media and fully enters the consciousness of the American people and – more importantly – Bush’s political base (it’ll be morbidly funny to watch the Religious Right try to defend torture). At that point Bush & Co are going to be in a LOT of legal trouble, and having this exemption already in place would help protect them.

Of course, such an exemption would not protect them from past crimes, but it would give them some pretty effective talking points to distribute to Fox “News” and similar White House stenographic organizations: ‘the law now supports this kind of treatment – that it wasn’t yet legal at the time is only a “technicality”

Answers NOT in Genesis #1: “Christian” Environmentalism

Every once in a while, for yucks, I browse the Christian fundamentalist site Answers in Genesis. I have a morbid curiosity to see how generally smart people tie themselves into knots trying to crowbar a biblical interpretation into the Real World – trying to reconcile scientific facts with biblical contradictions and their political goals (the latter seems to dominate). Take, for one mild example, this article on environmentalism, “‘Earth Day’ — a Christian perspective.”

Here’s a snippet:

While it is laudable to see humans exercising their God-ordained responsibility to care for the creation (Genesis 1:26–28), the above quotes show the prevailing view on environmental issues is skewed, as a proper Biblical foundation is lacking.

First, the fate of the planet is, ultimately, not in the hands of mankind. While humans are responsible for caring for the Earth (as per the ‘Dominion mandate’ in Genesis 1:26–28), we are not in control of the Earth. Rather it belongs to the Creator Himself (Psalm 24:1), who has made us His earthly stewards.

OK, we don’t own the Earth or are in control of it, but are God’s “earthly stewards”. I’m not convinced by the ‘not really our responsibility’ rhetoric (it’s amazing what you can get away with when you preface a statement with “ultimately”), but so far so good. Then begins a whole series of convoluted efforts to be anti-environmentalist without directly saying so. Notice that these folks have NO trouble injecting their interpretations and views into everything and everyone – individual, business, science, home, school district, courtroom – around them, but here, where environmentalism follows very nicely from religious values, suddenly it’s none of our business:

… the fate of the living planet is not the most important issue facing mankind. Ultimately, this decaying system will be replaced with a New Heavens and Earth anyway (Romans 8:20–22, 2 Peter 3:13, Revelation 21:1, Hebrews 1:10–12). Rather, the most important issue facing mankind is: will the individual choose to acknowledge his Creator and be reconciled to Him? Romans 1:20

So here’s God. He makes a wonderful planet. He also makes some people and puts those people in charge of the planet (not as owners but as stewards) and of the resident plants and animals. A lot of time goes by, and those people believe they’re going to have to move out pretty soon, into nicer digs. So what do they do? According to this Christian site, it’s fine to burn up the forests, pollute the oceans, trash the land and poison the air. Not because the bible says to but because a feeble case can be argued that the bible doesn’t say not to do it. If I were landlord and my tenants treated my property like this before moving out, I would NOT be a happy camper. Neither would the tenants, after I was done with them.

I prefer pragmatic interpretations over legalistic ones. If the most important document ever, written by the person who created me and everything around me, says that my job here is to be a steward, then I would think it’s reasonable to give that creator the benefit of a doubt and consider acting like a steward. Just in case.