Good Bad Adaptations

Here are some quirks in the design of the human body/mind which may turn out to be adaptations:

Abstract of "Morning Sickness: Adaptive Cause or Nonadaptive Consequence of Embryo Viability?" Samuel M. Flaxman1,* and Paul W. Sherman2,†

“Morning sickness” is the common term for nausea and vomiting in early human pregnancy (NVP). Recent interest in why NVP occurs-that is, in the evolutionary costs and benefits of NVP-has spurred the development of two alternative hypotheses. The “prophylaxis,” or “maternal and embryonic protection,” hypothesis suggests that NVP serves a beneficial function by expelling foods that may contain harmful toxins and microorganisms and triggering aversions to such foods throughout pregnancy. The alternative “by-product” hypothesis suggests that NVP is a nonfunctional by-product of conflict-over resource allocation-between the pregnant woman and the embryo. The critical predictions of the prophylaxis hypothesis have been developed and tested, whereas the by-product hypothesis has not been subjected to similar scrutiny. To address this gap, we developed a graphical model and used it to derive predictions from the by-product hypothesis under two different assumptions, namely, that NVP is either (i) a by-product of current conflict between a pregnant woman and an embryo or (ii) a by-product of honest signals of viability produced by the embryo. Neither version of the by-product hypothesis is fully consistent with available data. By contrast, the timing of NVP, its variation among societies, and associated patterns of food cravings and aversions are consistent with the prophylaxis hypothesis.

On Depression:

I recently wrote a paper for my Psychology class about Depression, allow me to quote it:

Why does depression exist? Is it simply a genetic disorder, or is it possible that it is so common because it helps individuals survive in some way? Charles Darwin said, “…Pain or suffering of any kind, if long continued, causes depression and lessens the power of action; yet is well adapted to make a creature guard itself against any great or sudden evil.” [1] Today Psychologists are following suggestions like his in order to find out why so many people suffer from depression. Some believe that after a series of defeats it would be useful to an organism’s survival to adopt a pessimistic attitude and act conservatively[2].

References
[1] p.89, “The Life and Letters of Charles Darwin” by Charles and Francis Darwin. Accessed at: http://darwin-online.org.uk
[2] Nesse RM, et. al “Is Depression an Adaptation?” Arch Gen Psychiatry 2000; 57:14-20
Accessed at:
http://www-personal.umich.edu/~nesse/Articles/IsDepAdapt-ArchGenPsychiat-2000.pdf

AiG's News to Note: Ventastega

It has been a while since I have posted something specifically debunking Answers in Genesis. Anyway, the creationists are up in a tizzy about the latest fossil find, and for good reason. Here is what they have to say:

"[C]ase closed on fish evolving into land animals. Or is it? It is interesting that the authors would suggest that Ventastega is a “midpoint” between the fish Tiktaalik and land animals, since this is not entirely accurate—even using their own framework. In fact, according to the BBC News report, “Ventastega is a later species [than Tiktaalik] but is a more primitive animal.” Setting aside the arbitrary application of “primitive,” it is interesting that something hailed as transitional would be, by the author’s own estimation, a step backwards of sorts. After all, Ventastega was a dead-end that went extinct."

Will anyone teach these idiots about cladistics? The history of life is a branching bush. Think of every transition in life, like the one from water to land, as an explosion of many different species, one of which was the ancestor of modern life forms. We must therefore not be surprised if most fossils appear not as direct ancestors of today's life, but rather as forms related to the ancestors of today's life. And Ventastega is not a "step backwards" but rather should be interpreted as a sort of "cousin species" of our ancestor.

Will Creationists Ever Learn?

I went in a bookstore yesterday and guess what I found: Michael Behe's book, The Edge of Evolution, now in paperback. I even flipped through it and found the passage in which he said HIV hadn't evolved anything biochemically new. When will he learn? I thought ERV handed him his tail on this issue months ago.

Vantastega: Another Transitional

Pharyngula has done a great write up on the newly published fossil, Ventastega. Devonian Times also has a nice page on it, plus lots of other pages on the transition from fish to amphibian.

Baloney Detection, Episode 1

I am starting a new series of posts here at AiG Busted, called "Baloney Detection" (name subject to change). This series is going to be all about detecting pseudoscience. Of course, creationism will be referred to, but this series should give you a good idea of how to detect any type of pseudoscience. The first installment will be a repost of the late Carl Sagan's baloney detection kit, to be found on his website. Here goes:

Warning signs that suggest deception. Based on the book by Carl Sagan, The Demon Haunted World. The following are suggested as tools for testing arguments and detecting fallacious or fraudulent arguments:

Wherever possible there must be independent confirmation of the facts.

Encourage substantive debate on the evidence by knowledgeable proponents of all points of view.

Arguments from authority carry little weight (in science there are no "authorities").

Spin more than one hypothesis - don't simply run with the first idea that caught your fancy.

Try not to get overly attached to a hypothesis just because it's yours.

Quantify, wherever possible.

If there is a chain of argument every link in the chain must work.

Occam's razor - if there are two hypotheses that explain the data equally well choose the simpler.

Ask whether the hypothesis can, at least in principle, be falsified (shown to be false by some unambiguous test). In other words, it is testable? Can others duplicate the experiment and get the same result?

Additional issues are:

Conduct control experiments - especially "double blind" experiments where the person taking measurements is not aware of the test and control subjects.

Check for confounding factors - separate the variables.

Common fallacies of logic and rhetoric

Ad hominem - attacking the arguer and not the argument.

Argument from "authority".

Argument from adverse consequences (putting pressure on the decision maker by pointing out dire consequences of an "unfavorable" decision).

Appeal to ignorance (absence of evidence is not evidence of absence).

Special pleading (typically referring to god's will).

Begging the question (assuming an answer in the way the question is phrased).

Observational selection (counting the hits and forgetting the misses).

Statistics of small numbers (such as drawing conclusions from inadequate sample sizes).

Misunderstanding the nature of statistics (President Eisenhower expressing astonishment and alarm on discovering that fully half of all Americans have below average intelligence!)

Inconsistency (e.g. military expenditures based on worst case scenarios but scientific projections on environmental dangers thriftily ignored because they are not "proved").

Non sequitur - "it does not follow" - the logic falls down.

Post hoc, ergo propter hoc - "it happened after so it was caused by" - confusion of cause and effect.

Meaningless question ("what happens when an irresistible force meets an immovable object?).

Excluded middle - considering only the two extremes in a range of possibilities (making the "other side" look worse than it really is).

Short-term v. long-term - a subset of excluded middle ("why pursue fundamental science when we have so huge a budget deficit?").

Slippery slope - a subset of excluded middle - unwarranted extrapolation of the effects (give an inch and they will take a mile).

Confusion of correlation and causation.

Caricaturing (or stereotyping) a position to make it easier to attack.

Suppressed evidence or half-truths.

Weasel words - for example, use of euphemisms for war such as "police action" to get around limitations on Presidential powers. "An important art of politicians is to find new names for institutions which under old names have become odious to the public"

Opening Up a Dialogue...

I want to open up the dialogue on theistic evolution. I know very little about it, all though I have read some of the literature.

Now, my biggest problem with theistic evolution used to be the age of the earth. The bible had genealogies in it that added up to only a few thousand years time, yet we know that the earth is billions of years old. However, I discussed this with blogger "Created and Rational" and he responded:

"Well it has to do with whether or not the geneologies are complete. For example in Matthew 1:8 it says that Joram begot Uzziah, however this is actually skipping several generations as Joram was Uzziah's great-great grandfather.This could be the case in the Geneologies leading from Adam to Abraham."

Indeed, it does appear the genealogies were abbrieviated. It is plausible that the earth is old and Christianity/Judaism true. But what about the evolution of man and the soul? Do theistic evolutionists think that a Homo Erectus was infused with a soul one day, or did the soul come in a little at a time? And was there a religion in the first tens of thousands of years before Moses 5,000 years ago?

More on the Origin of New Genes

Panda's Thumb has once again posted an article on the origin of new genes. For some reason, I find gene origination interesting, not least because it defeats the claims of creationists.

Lenski schools Conservapedia

Some of you may have heard of this, but if not, let me explain: Richard Lenski has been growing bacteria for a record breaking length of time (Over 40,000 generations!). Recently it was reported that one of his strains had evolved the ability to utilize Citrate. Of course, this poses a problem for creationists, as they repeatedly claim that "Random Mutation cannot increase the information in the genome". Andy Schlafly, the head wackaloon at conservapedia, wrote to Lenski demanding "data" about this evolution. It's not clear what "data" Schlafly would want, or why he would want it. After all, he is not a scientist. He also seems to think that because Lenski's work is tax-funded, he as a taxpayer should be able to obtain whatever "data" he desires. Lenski sent him a link to the peer reviewed paper, but apparently that wasn't all the "data" Schlafly wanted. He complained, and Lenski fired back at him, completely schooling him in the process. Click here to read the conversation the two have been having. It is entertaining.

Questions for Atheists

I thought I'd do something fun for this post and answer a set of questions that's been circling the atheist blogroll.

1. How would you define “atheism”?

Lack of belief in a personal creator.

2. Was your upbringing religious? If so, what tradition?

Yes. Church of Christ.

3. How would you describe “Intelligent Design”, using only one word?

Hoax.

4. What scientific endeavour really excites you?

Origin of Life Research.

5. If you could change one thing about the “atheist community”, what would it be and why?

I would make them a little more mature and kinder to theists.

6. If your child came up to you and said “I’m joining the clergy”, what would be your first response?

I accept your decision, but please explain this to me!

7. What’s your favorite theistic argument, and how do you usually refute it?

Consciousness. I don't actually hear it much, but it is an intelligent argument and (at first) seems to defy material explanation. I have an explanation for it here.

8. What’s your most “controversial” (as far as general attitudes amongst other atheists goes) viewpoint?

Probably that the universe sprang from a complete vacuum. More on that here. My second "controversial" viewpoint is that Jesus was a real person.

9. Of the “Four Horsemen” (Dawkins, Dennett, Hitchens and Harris) who is your favourite, and why?

Richard Dawkins because of his science writings. My second pick would be Dennett because of his fascinating writings on the Origin of Religion and Cosciousness.

10. If you could convince just one theistic person to abandon their beliefs, who would it be?

Perhaps if I planned to marry a girl who was Christian it would be her. Otherwise, Ken Ham would be a good candidate for deconversion. Imagine the attention that would bring!

How Life Began (History Channel Special)

Ok, so I watched the History Channel Special How Life Began. I wasn't too impressed with it. If you have nothing to do, feel free to watch it as it is entertaining. But there isn't anything fundamentally new in the program, and it feels at times as though they move off-topic. Instead of spending two hours watching this television program, why not spend fifteen minutes reading this article about one of Stanley Miller's final-and perhaps most important- experiment. Or spend five minutes reading about the recent creation of self replicating protocells by Jack Szostak. The program does touch Szostak's work briefly, but I actually think the article is far more interesting and informative.

The program isn't horrible, but perhaps I stay so up to date with science and have read so much about the origin of life that it simply does not appeal to me. And by the way, I may as well introduce some good books about the subject for those who want to read further:

The Fifth Miracle by Paul Davies - An excellent, excellent book. Very engaging, easy to understand, and at the same time marvelously educational. A must read.

Seven Clues to the Origin of Life - A very entertaining introduction to the clay theory of the origin of life. Though the theory is probably wrong, and of course some of the obstacles of the RNA World Theory have been overcome (see above article, nucleotides and other complex molecules are relatively easy to make), the logic used in trying to understand how the complexity of life arose is impeccable and will change the way you think.

Gen•e•sis - Have not read this one, but P.Z. Myers gave it a good review, so check it out.

That's all, folks!

Of Fish and Phenotypes

Apparently this is old news, reported back in January, but I missed it and you may have too: It's a transitional fossil of a fish's eye! Via ScienceDaily:

Dr Gavin Young from the Department of Earth and Marine Sciences at ANU has analysed fossilised remains of 400-million-year-old Devonian placoderms – jawed ancestors of modern fish whose bodies were protected by thick bony armour.

“The ancient limestone reefs exposed around Lake Burrinjuck in New South Wales have produced exceptionally well preserved placoderm specimens with the braincase intact,” Dr Young said.

The palaeobiologist discovered that unlike all living vertebrate animals – which includes everything from the jawless lamprey fish to humans – placoderms had a different arrangement of muscles and nerves supporting the eyeball – evidence of an “intermediate stage” between the evolution of jawless and jawed vertebrates.

“The vertebrate eye is the best example of structural perfection – as used by proponents of intelligent design to claim that something so complex couldn’t possibly have evolved,” Dr Young said.

“Part of the trouble in tracing the evolution of the eye is that soft tissues don’t tend to fossilise. But the eye cavities in the braincase of these 400 million-year-old fossil fish were lined with a delicate layer of very thin bone. All the details of the nerve canals and muscle insertions inside the eye socket are preserved – the first definite fossil evidence demonstrating an intermediate stage in the evolution of our most complex sensory organ.

“These extinct placoderms had the eyeball still connected to the braincase by cartilage, as in modern sharks, and a primitive eye muscle arrangement as in living jawless fish.” Dr Young said that this anatomical arrangement is different from all modern vertebrates, in which there is a consistent pattern of tiny muscles for rotating each eyeball.

The placoderm fossils were analysed using computer X-ray tomography at ANU, a scanning technique that creates a three-dimensional image of complex organic structures. “What this research shows is that 400 million years ago there was already a complex eye, and one that was an intermediate form between jawless and jawed vertebrates,” Dr Young says. “This means that we’re able to add one more piece to the puzzle of how the human eye came to be.”
(END QUOTE)

Here's something totally unrelated, except that it still has to do with fish and evolution: The Primate Diaries' blogger has written up a nice post on blind cavefish and the creationist distortions thereof. A very good read, check it out!

Random Updates

I just had a couple of things I wanted to post. First of all, Youtube User KingHeathen has posted a great video about the Georgia Aquarium that shows a lot of colorful sea creatures and such. You may remember my blog post about it a few weeks ago. One of the really cool things to notice is how the Beluga Whales and Otters swim by moving their bodies up and down, in contrast to fish which move their bodies from side to side. Could that be because whales are descended from land mammals?

; )

The History Channel is airing a program about How Life Began (click here for showtimes). I haven't watched it yet, but according to PZ Meyers the second hour is when all the good stuff begins. I will be sure and write something about it after I watch it.

Only a Theory

Kenneth Miller has written a new book, "Only a Theory: Evolution and the Battle for America's Soul". The amazon link includes an excerpt, and I think it will be a good book. In the next month or two I will probably read it and publish a review here. In the meantime, check out the hilarious interview he did on The Colbert Report.

De Novo Gene Origination

Good article:
http://pandasthumb.org/archives/2008/06/de-novo-origina.html#more

Really just drives another stake into the hearts of those who say "Evolution-Can't-Produce-New-Information-Nurny-Nurny-Nur-Nur"!

Challenge? ...

It has been over a week since I posted my "challenge for creationists" and no creationist has responded. I am beginning to wonder if that is revealing. We did have a guy saying that evolution is not falsifiable, but that just isn't true. Don Lindsay tells us that:

In "The Origin Of Species" (1859), Darwin said:
"If it could be proved that any part of the structure of any one species had been formed for the exclusive good of another species, it would annihilate my theory, for such could not have been produced through natural selection." Chapter VI, Difficulties Of The Theory

This challenge has not been met. In the ensuing 140 years, no such thing has been found. Plants give away nectar and fruit, but they get something in return. Taking care of other members of one's own species (kin selection) doesn't count, so ants and bees (and mammalian milk) don't count.

I don't know how many times I have stated things that would falsify evolutionary theory.

Michael Behe: Evolution-and-Information-Part-Gazillion-And-One

To recap yesterday's post: E. Coli were observed in the lab to evolve a 3-mutation-requiring ability to utilize Citrate for food. The researchers see this as being due mainly to genetic drift: Two of these mutations were random changes that did not effect the fitness of the E. Coli, and they became somewhat prominent in the population. Sort of like having many different color butterflies in a population when no color effects the butterfly's survival.

Michael Behe has given his two cents about this over at his amazon blog. In short, he sees this as being an example of how rare it is for multiple mutations to come together and produce something new. He feels that he has established that multiple mutations must be required to produce much of the complex machinery in the cell. (By the way, PZ Myer's rebuttal to this is also well worth checking out). He also feels that much of the evolution we observe today is destructive rather than constructive.

Let's think about this for a moment: Life began perhaps about 4 billion years ago, single cellular organisms are known from about 3.8 billion years ago, and multicellular organisms are known from about 1.7 billion years ago. Michael Behe stated in his book that the earth hosts about 10^20 bacteria. This is astronomically more bacteria than are observed in the experiment. Two billion years were devoted solely to evolution at the cellular level. We also know that the claim that evolution tends to be destructive is not quite true. Via Mad Mike's blog:

"Research by Dan Andersson and colleagues has demonstrated that following mutations that confer resistance, and that lower growth rates in the absence of antibiotics (the supposed "loss of functional system"), compensatory mutations evolve.

What's a compensatory mutation? A compensatory mutation reduces or eliminates the fitness cost of a mutation (often lower growth rate)--in this case, the original mutation that confers (antibiotic) resistance. For instance, compensatory mutations in the rpsL gene reduced or eliminate the costs of streptomycin resistance in Salmonella typhimurium. More recent work has demonstrated this in other bacteria, and in mouse models."

I recall that Behe mentions in his book something called "C. Harlem". This is a variant of hemoglobin which confers resistance to Malaria but does not have the nasty side effects that Sickle-Cell hemoglobin does. This may be a fairly rare form, but if it was present in the Malaria plagued parts of Africa (Unfortunately it was discovered in Harlem, hence the name), it would most likely spread through the population and replace the sickle cell hemoglobin gene in the gene pool. So sometimes mutations are selected for that provide an advantage (with a hefty cost, mind you) but there are better mutations and compensatory mutations.

And Behe's claim about evolution being unable to account for the complexity of the cell is very, very shaky. The main thesis of "The Edge of Evolution" is that two protein-protein binding sites simply must evolve at the same time in order to produce things like the bacterial flagellum or Cilium. Ian Musgrave has written about some research that shows this claim to be false.

Not to mention the fact that we know the bacterial flagellum is not "unevolvable".

Evolution and Information, Part Gazillion

Remember that old creationist arument that "Evolution cannot produce new information" ? Another nail has been put in the coffin. Excerpted from New Scientist:

"Twenty years ago, evolutionary biologist Richard Lenski of Michigan State University in East Lansing, US, took a single Escherichia coli bacterium and used its descendants to found 12 laboratory populations.

The 12 have been growing ever since, gradually accumulating mutations and evolving for more than 44,000 generations, while Lenski watches what happens.
Profound change

Mostly, the patterns Lenski saw were similar in each separate population. All 12 evolved larger cells, for example, as well as faster growth rates on the glucose they were fed, and lower peak population densities.

But sometime around the 31,500th generation, something dramatic happened in just one of the populations – the bacteria suddenly acquired the ability to metabolise citrate, a second nutrient in their culture medium that E. coli normally cannot use.

Indeed, the inability to use citrate is one of the traits by which bacteriologists distinguish E. coli from other species. The citrate-using mutants increased in population size and diversity.

"It's the most profound change we have seen during the experiment. This was clearly something quite different for them, and it's outside what was normally considered the bounds of E. coli as a species, which makes it especially interesting," says Lenski.

By this time, Lenski calculated, enough bacterial cells had lived and died that all simple mutations must already have occurred several times over.

That meant the "citrate-plus" trait must have been something special – either it was a single mutation of an unusually improbable sort, a rare chromosome inversion, say, or else gaining the ability to use citrate required the accumulation of several mutations in sequence.

To find out which, Lenski turned to his freezer, where he had saved samples of each population every 500 generations. These allowed him to replay history from any starting point he chose, by reviving the bacteria and letting evolution "replay" again.
Would the same population evolve Cit+ again, he wondered, or would any of the 12 be equally likely to hit the jackpot?

The replays showed that even when he looked at trillions of cells, only the original population re-evolved Cit+ – and only when he started the replay from generation 20,000 or greater. Something, he concluded, must have happened around generation 20,000 that laid the groundwork for Cit+ to later evolve. Lenski and his colleagues are now working to identify just what that earlier change was, and how it made the Cit+ mutation possible more than 10,000 generations later.

In the meantime, the experiment stands as proof that evolution does not always lead to the best possible outcome. Instead, a chance event can sometimes open evolutionary doors for one population that remain forever closed to other populations with different histories."

Challenge for Creationists

Dear readers:

I know I have been slow to update, but Summer courses have been really tough at my college, so I have not had much time to write. I saw an interesting post over at Internet Infidels Debate Forum, I am going to repost it and allow creationists to respond:

"I would like to see what evidence the Creationists have to support their view of the origin of life, the variety of life and also an explanation of how "micro-evolution" is prevented from going any further when it gets close to being "macro-evolution".I ask that posters cite their sources and use clear and concise language and not arbitrary terms like "Kind".Also for those of you who believe in "The Flood" I would like to know how land animals got back to places like Australia, which are separated from the Eurasian landmass (where the Ark supposedly was) by seas/oceans. I'd like to see your evidence and not just wild guesses.The reason for this challenge is that I see lots of attacks on Evolution etc, but no evidence to back up Creationist claims. I thought it would be fun to turn the tables for once.Anyone up for the challenge?"

Update...

Dear readers,



I just wanted to let you know that I have not forgotten about the blog even though I have not updated it in a few days. I have been really busy with school, but I plan to write an article on science and religion sometime soon. In the mean time: Remember when I launched my 'Aig Busted' site? Most of the content I put on it was simply revised blog posts that I had made here. But several pages are brand new and were made just for the site. These include:



Radiometric Dating: An Accurate Tool



Marsupial 'Kinds'



Transitional Fossils (A lot of neat pics here, please have a look!)

Jerry Coyne talks about ID

Rockefeller University has posted a series of videos about the origin of life and evolution. The most relevant one (to this blog at least) was Jerry Coyne's talk on ID and creationism. I highly recommend it.