Stepwise formation of the bacterial flagellar system

#evolution
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Every so often, some creationist will come out with the claim that flagellum of the bacteria is an irreducibly complex system.  This points to a dead-Jew on a stick designing it- I mean, an unspecified intelligent creator (wink, wink)- designing it. 

The only problem is that we know that the flagellum is not irreducibly complex. It can be shown to form in a stepwise fashion as per the article attached.

Of course, it does seem that it would be easier to find another way to leave a biological clue for design than the flagellum of a bacterium.  That creator is such a tease…

I am not an evolutionist

#evolution #atheist #atheism -

Until I got on to the web and started interacting with creationists again, I’d never heard this term before.  Lets be clear- I reject it, utterly and totally. 

I am a biologist, not an evolutionist.  That means I’ve spent years at University getting an advanced education.  That means a lot of practical work in the field and in the lab.  It means that I know the difference between a monkey and an ape. I have traveled to, and worked on 4 different continents with a variety of wildlife.  In the course of this work, I have discovered and published things.  I have been exposed to various hazards along the way. I have lost colleagues to fatal diseases and accidents.

At no point in time, have I taken a course in evolutionism.  There are no journals on evolutionism.  There are no academic or government positions that have evolutionist as the title.  The term only exists as a pejorative attempt by creationists to create the fiction that an entire scientific discipline is a mere dogma.

If your claims are built entirely on what you have read on creationist websites and sources, then your beliefs are dogmatic.  There is no symmetry between creationism and biology. Until you get off your arses, stop trying to appropriate other people’s research, and start doing your own, not one iota of credit can be given to the creationist view.

No, Intelligent Design isn’t science

#evolution #atheist #atheism

ID [Intelligent Design] is not science and cannot be adjudged a
valid, accepted scientific theory, as it has failed to publish in
peer-reviewed journals, engage in research and testing, and
gain acceptance in the scientific community. ID, as noted, is
grounded in theology, not science.… Moreover, ID’s backers
have sought to avoid the scientific scrutiny which we have now
determined that it cannot withstand by advocating that the
controversy, but not ID itself, should be taught in science class.
This tactic is at best disingenuous, and at worst a canard. The
goal of the IDM [Intelligent Design Movement] is not to
encourage critical thought, but to foment a revolution which
would supplant evolutionary theory with ID.”

From the Dover Trial in 2005. This excerpt is from the District Court decision.

Intelligent design originated in the attempt to deceive the public that this was anything other than a rebrand of creationism. It has not survived scientific scrutiny. And of course, it has not survived any legal test of its scientific credentials.

One should note that this is also the trial where the creationists were chastised for lying under oath.

What’s rocks got to do with it?

#evolution #atheist
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In a bizarre and absurd twist, a number of creationists have jumped on the ‘life from rocks' meme. This is an attempt to ridicule the theory of evolution.  It is based on the false belief that the theory of evolution claims that life- including people- originated from rocks.

This at the outset illustrates that the principal prerequisites to being a creationist is ignorance of basic science and an utter lack of intellectual honesty.  Instead of addressing the theory of evolution, they make up an entirely false claim that has nothing to do with the Theory of Evolution.

Evolution is the change in gene frequency over time, and as such, is an observable natural phenomenon.  The Theory of Evolution is the way scientists explain how evolution occurs (via mechanisms like natural selection or genetic drift). It is not- as the definition plainly sets out- an explanation of the origin of life.

The creationist strategy depends on conflating abiogenesis with evolution. Even then, they can’t get abiogenesis correct. The natural model of abiogenesis does not depend on rocks. The Miller-Urrey experiments of the 1950s did not use rocks but a blend of liquids and gases. Abiogenesis is based on the presence of 6 macro elements. These are:

  • Hydrogen- which we should point is a gas and not very rock-like.
  • Oxygen- hmm, again, another gas
  • Nitrogen- nope, not a rock
  • Phosphorous
  • Carbon
  • Sulphur

There is no credible way to class this set of macro-elements as rocks. The model of abiogenesis that is being developed is largely based on a liquid environment.

So not only does this attempt at ridicule miss the target completely, it’s also utterly inane. The creationist alternative is that human life originated from dust. That’s hardly less ridiculous than the completely fallacious assertion that life came from rocks.

Abiogenesis: a creationist trend on twitter

#atheist #atheism #evolution
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The entertaining thing about creationists is how they parrot the latest propaganda on twitter. They think they have the latest killer argument against atheism, or evolution. In the end, it’s just the usual contemptuous combination of ignorance and logical fallacies. Still, it’s good for a laugh right.

One line that seems to be trending at the moment seems to be this:

  1. Life can only originate by natural means or by a divine cause (say, a dead Jew-on-a-stick)
  2. Pasteur proved that spontaneous generation was impossible in the 1800s
  3. Ergo life can’t originate from non-life
  4. Ergo, atheism is false

Assuming you have stopped laughing by now:

One- this is a standard false-dichotomy fallacy. Aliens could have started life here. A giant cosmic-chicken could have laid an egg here. You can’t propose your divine agent as a credible alternative until there’s actually evidence he exists.  And the book with the talking snake, really is unconvincing.

Two- well this is true, but irrelevant. Spontaneous generation is utterly and entirely different to abiogenesis.

  • Spontaneous generation is the sudden appearance of complex organisms in a closed thermodynamic system.
  • Abiogenesis is the gradual, stepwise appearance of simple organisms in an open thermodynamic system

See, this makes all the difference. In order to form complex molecules, energy has to be supplied so that local entropy is reduced.  So what’s impossible in a closed system, is very possible in an open.

If you’re going to tell me that spontaneous generation is the same as abiogenesis, expect that I’m going to laugh at you a lot. In fact, a lot of people are going to be laughing at your ignorance.

Three- well, as point two of this creationist argument hasn’t been proved, three doesn’t follow.  In fact, we have a lot of research now that says life is pretty much the inevitable result of biochemistry interacting with the physics of self-organising molecules. And please, we’ve discovered a lot more since the Miller-Urry experiments of the 1950s.

Four- sorry, atheism has nothing to do with the origin of life. Atheism only means that the theist claim that gods are real, remains unproven. An atheist has no onus to prove there is a viable alternative to a god. If you’re claiming that your magic sky-daddy was responsible for life on earth, it’s up to you to prove it. And Louis Pasteur isn’t going to help you one iota on that claim.

Why creationists keep losing

#atheist #atheism #evolution

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There are many reasons why creationists have been unable to succeed (in the West). Evolution is still taught as a science; creationism in all its variants has been confirmed as a religious doctrine in a string of court-cases stretching over decades.

My recent epiphany on why biologists are winning is based on passion. Biologists are passionate about nature. There’s nothing easy about being a biologist. I’ve been shot at, nearly bombed by local insurrectionists, & caught some nasty tropical diseases. I’ve lost colleagues to malaria and to air-crashes.

In the process, we discover things. We find new species, we develop cures for diseases, we publish papers in peer-reviewed journals. The database Biological Abstracts records about 26,000 papers validating evolution in 2010 alone.

Creationists can’t match that. They can’t because they’re not passionate about nature. They’re not committed to understanding the natural world. They’re committed to a bronze-age fairy tale. And that’s not leading to new discoveries.There’s nothing in Biological Abstracts that supports creationism or intelligent-design being a credible alternative.

This is why biologists win. We win because we care more. We win because we have the facts and the research. We win because we don’t think sitting on our fat-arses in church is a viable scientific methodology. We win, because we are actually prepared to do the work that demonstrates evolution is true.

Sigh, a house is not a universe

#atheist #atheism

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Sometimes I get this argument popping up. It’s an argument from analogy. Kind of, because we know houses were designed and built, and a house is like the universe, it must be that the universe was designed and built by a creator.

Like most arguments from analogy, it is a weak argument*. It is not an appeal to evidence. It is an appeal to all sorts of hidden assumptions and presumptions that get attached to it. It fails simply because those assumptions aren’t shared by others.

We can test the claim that houses are designed objects. This is based on the following traits:

  • Observations: we actually see houses getting built by human agents. So far, nobody has observed a universe being built by an external agent.
  • Objective: a house has a specific objective. It provides shelter etc for the occupants. It is this use to which it is purposely built that tells us its designed. Nobody has proved that the universe has a like-objective. The universe appears entirely indifferent to our existence. It was around about 14bn years before we turned up, and will continue long after our solar-system dies.
  • Efficiency: this relatives to objective. Objects that are designed try to meet their objectives in efficient ways- needless redundancy, wastage of materials, inflated risks- all invalidate the idea of design. A vast universe that hurtles deadly space rocks at us, and bathes us in deadly UV radiation, could do with some tweaks.
  • Economy: designed artifacts are constrained by the resources available for their use. The decision to use one input over another, is driven by a conscious and deliberate observable decision. We don’t observe these substitutions occurring in the universe.

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* Indeed, if you have to make an argument based on an analogy that cannot be supported by evidence, chances are it’s fatally flawed. Please stop.

#atheist #atheism #evolution
- The curious mind of the creationist-

Creationists have their own peculiar logic to dealing with scientific evidence. For biologists, mutations are observed to lead to new genes being generated and new functions. This is illustrated by the case of Brown et al. (1998) and the quadruplication of the HXT6/7 genes alluded to above.

For a creationist committed to the dogmatic view that mutations can’t generate new information, ‘special’ steps needed to be added into the process to lead to the exact opposite conclusion.

Sadly bluff and making shit up, doesn’t make a very convincing case.

3 decades of molecular biology Vs

Creationism- #evolution #atheist #atheism -

One of the fascinating aspects of creationism is how it backtracks and retreats from previous positions under the weight of scientific advances. In the last thirty years, molecular biology has advanced in leaps and bounds, producing a flood of papers that substantiate evolution.

In the early 1980s, creationists deployed the argument that no-one had ever seen shifts in actual genes, therefore evolution wasn’t true. Okay, aside from the dubious nature of the argument, it was rapidly refuted by advances in DNA-mapping. Suddenly we could show that for a wide range of model organisms, selection pressure induced exactly these shifts in gene frequency.

So, either creationists could concede that evolution is true (uh huh, intellectual honesty, can’t have that) or form a new defensive line.And that’s where most creationists went. It is an even more tenuous and absurd two-part claim:

  • Evolution on small scales is now (usually) conceded. They have been forced to accept that shifts in gene frequency occur by the mechanisms of inheritance and selection.
  • Evolution on large scales is denied. Genetic shifts in two different populations can diverge and accumulate, but it is asserted that this won’t generate speciation events. It won’t matter how much difference accumulates (and this can include shifts in chromosome number) - it’s not possible for this to yield speciation.

This is the classic, micro-evolution versus macro-evolution divide. For biologists, the same forces of selection, inheritance and drift operate on all scales. Creationists are trapped in a mire of their own making. If you concede that evolution operates on small scales, you can’t deny that it will operate on large scales unless you have a mechanism that kicks in to prevent it. No such mechanism has ever been provided, so there’s no basis for this claim.

Abiogenesis is supported by evidence

#atheist #evolution

One of the big scientific questions is how life began on earth. Many scientists are now agreed that life is almost certain to have originated out of simpler, chemical compounds. Further, that this is practically inevitable given the early conditions on earth.  This isn’t about faith, but the evidence that has been accumulated.

Since the Miller experiments of the 1950s, the application of the principles of chemistry and physics to this problem has shown that nearly all the components of a simple-cell can and do form naturally.

The evidence can be summarised as:

  • Environmental - There are several conditions that must apply to make chemical evolution possible. First, there has to be an external energy source*. Prebiotic earth has lots of these- lightning, volcanoes, radiation. Second, we can’t have a lot of oxygen. Lots of oxygen will make any formed complex molecules short-lived. Again, prebiotic earth had little atmospheric oxygen. Third, there has to be the chemicals available for life around to work with. That means 6 indispensable macro-elements- C, H, O, N, P and S have to be around. Again, these are known to be present.
  • Why not Panspermia? Every cell of every organism is remarkably the same at an elemental level. It doesn’t matter if we are looking at fungi or fish or humans. The percentages of the macro-elements above are very similar. This is exactly what we’d see if life started by using the available chemicals on earth. In fact, the proportions of elements in every organism aligns most closely to river water. This supports abiogenesis occurring here on earth, and is a smoking gun for a natural origin of life.
  • Forming complex molecules- the environmental conditions above are necessary for abiogenesis but not sufficient to show its feasibility. Since the Miller-Urey experiments of the 1950s, we have shown that the building blocks of a cell will occur naturally. We have shown that amino-acids, sugars, RNA/DNA bases, hydrocarbons, phosphate esters, peptides etc will all be formed under the right abiotic conditions. The 8 amino-acids that dominate these abiotic conditions are also those most common in proteins. This is another ‘smoking gun’ that life began from abiotic conditions on earth.
  • The Proto-cell - A cell is basically a package of organic & inorganic molecules surrounded by a double-lipid membrane. We have shown small double-lipid membranes will form in small vesicles that surround organic molecules (since the experiments of Fox in the 1970s).  In fact, it is remarkably easy to generate these.
  • Replicating molecules. Life also needs molecules to be able to replicate. This is also a natural chemical phenomenon. In 1996 the jounal Nature reported the discovery of a self-replicating alpha-helical peptide. This had a 32-amino-acid sequence, and interestingly, had several dipeptides found in the membrane proteins of ancient archaebacteria.

The scientific evidence is consistent with and supports an origin of life on earth out of abiotic conditions. There has been no chemical, biological or physical law that has been discovered in this research that would prevent life emerging. We have discovered so much about the processes of this chemical evolution that recreating life in the test-tube now looks feasible.

Of course, we should for completeness consider the evidence for a divine creator or intelligent designer. I’ve made a list, but it’s blank. 

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* The external energy sources for abiogenesis is why Pasteur’s experiments on spontaneous generation don’t apply. Pasteur looked at a closed thermodynamic system. Abiogenesis is about open thermodynamic systems. In order for complex molecules to be formed, local entropy has to be reduced and this is only possible in open-energy systems.