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Thursday, December 09, 2010

Arsenic-based DNA in bacteria? NOT!

Just as I predicted, the Darwinists make a big and misleading announcement and then the fizzle-out comes...

From the Creationist-unfriendly ScienceBlogs

Mono Lake, Earth

[guest post: Alex Bradley, PhD] Arsenate-based DNA: a big idea with big holes


Category: Microbial Ecology
Posted on: December 5, 2010 2:58 PM, by Heather Olins
In the wake of the NASA excitement over the new arsenic study, and my promise to give a detailed review of the paper itself, I have recruited a colleague with strong opinons about the work, a solid chemistry and microbiology background, and "Dr." in front of his name to share his analysis. I will be posting have posted my personal and less-technical take on the whole thing soon, so stay tuned as well.

Dr. Alex Bradley uses modern geochemistry and microbiology tools to study the evolution of life and Earth. He has the following to say about the paper.
ResearchBlogging.org

There's been a lot of hype around the news of GFAJ-1, the microbe claimed to substitute arsenate for phosphate in its DNA. In the midst of all the excitement, one thing has been overlooked:

The claim is almost certainly wrong.

The study published in Science has a number of flaws. In particular, one subtle but critical piece of evidence has been overlooked, and it demonstrates that the DNA in question actually has a phosphate - not an arsenate -backbone.

Mono Lake

To understand why, we need to back up a bit. One thing that everyone agrees on is that all things being equal, DNA with an arsenate backbone will hydrolyze quickly in water, while DNA with a phosphate backbone will not. Steve Benner has pointed out that the half-life of the hydrolysis reaction is about 10 minutes.

Wolfe-Simon et al. recognize this, but claim that the bacterium GFAJ-1 must have some unknown biological mechanism to compensate, and this prevents the DNA from falling apart in the cells. Let's assume for now that they are correct. It might be plausible - biology has all kinds of strange tricks and this idea can't be quickly dismissed, even if it seems radical.

But chemistry is much more predictable. Once DNA is out of the cell, pure chemical processes take over, and experiments have demonstrated that hydrolysis of arsenate links is fast. So you could do a simple experiment to test whether DNA had a phosphate or arsenate backbone: just remove DNA from the cell and put it in water for a few minutes. Then examine whether it hydrolyzes or not.

In an accidental way, Wolfe-Simon et al. performed precisely this experiment. The result indicates that the DNA of GFAJ-1 has a phosphate backbone.

The details are these: to isolate DNA, Wolfe-Simon et al. performed a phenol-chloroform extraction. In this technique, after cellular disruption, DNA and other cellular material were dissolved in water, and then the non-DNA material (such as lipids and proteins) were cleaned out of the mixture using phenol and chloroform. This is a pretty common laboratory procedure, and typically would take an hour or two. But here is the key point:

During this whole procedure, the DNA was in water.

Remember, proteins were removed from this mixture. Any cellular machinery that stabilized arsenate-DNA was removed. In the absence of biochemistry, pure chemistry takes over: any arsenate-DNA would have been quickly hydrolyzed in the water, breaking down into fragments of small size. Alternatively, phosphate-DNA would not hydrolyze quickly, and large-sized fragments might be recoverable.

So what size are the fragments of DNA extracted from GFAJ-1? They are large. Figure 1 shows a single strong band. This pattern is a bit unusual for a genomic DNA extract, but the important thing is that the fragments in this band have around 10,000 nucleotides between breaks in the DNA. These long chains of nucleotides did not hydrolyze in water. Yet it is precisely this DNA band that is claimed to have an arsenate backbone.

How can this be?

The answer is: it can't be. If this DNA did not hydrolyze in water during the long extraction process, then it doesn't have an arsenate backbone. It has a phosphate backbone. It is normal DNA.

So what accounts for the claim of arsenic in this DNA? Wolfe-Simon et al. used a technique called nanoSIMS to analyze elemental concentrations of the agarose gel at the location of the DNA band. They determined that the part of the gel containing DNA also contained both arsenic and phosphorus. But what did they really analyze?

The answer is that the nanoSIMS determined the concentration of arsenic in the gel - not specifically in the DNA. Arsenic was present in the gel at the location of the DNA band. But these data do not require that arsenic is part of the DNA, only that it is somehow associated with the DNA. So here is a more plausible explanation: arsenate sticks to stuff. When you grow bacteria in media containing lots of arsenate, cellular material gets covered in arsenate. If you analyze this material chemically, you see a high arsenic background. The arsenic background will remain even after you separate the cellular material into its constituent parts - DNA, lipids, and proteins - because the chemical separation is imperfect. You could imagine a parallel experiment: if you grew bacteria in seawater, a band of DNA extracted from these bacteria might show a high background of sodium and chloride. This would not be very surprising - and it certainly wouldn't imply that the DNA had a chloride backbone.

Wolfe-Simon and her colleagues might quibble with this, and claim that arsenate is not that 'sticky'. This should have been resolved by running a negative control. Grow some bacteria with phosphate-backboned DNA in media containing high concentrations of arsenate. Then extract the DNA, run a gel, and just demonstrate that the gel does not have a high arsenic concentration associated with the DNA band. That would be evidence that my explanation is wrong. But this simple control was not performed in study published in Science.

One objection to my claim might be: if the GFAJ-1 DNA contains phosphate, where did the phosphate come from? The researchers claim that there wasn't much phosphate in their growth media. In fact, they did a very good job of quantifying the background phosphate concentration: it was about 3 micromolar, which was certainly much lower than the arsenate concentrations (by a factor of about 10,000).

But here's the relevant question: Is 3 micromolar phosphate a lot? Or a little? One point of comparison is the Sargasso Sea, where plenty of microbes survive and make normal DNA. Here, the phosphate concentrations are less than 10 nanomolar - or 300 times less phosphate than the "phosphate-free" media in the GFAJ-1 experiment. At such low phosphate concentrations, some bacteria compensate by removing phosphorus from their lipids - but not from their DNA.

 Sargasso Sea

So the Sargasso Sea tells us that some bacteria are capable of making DNA at very low phosphate concentrations. The most plausible explanation is that the bacterium GFAJ-1 can make normal DNA at micromolar phosphate concentrations, and that it also has the ability to tolerate very high arsenate concentrations.

There are numerous other aspects of this study that don't make sense. Why would bacteria from Mono Lake need the ability to substitute arsenate for phosphate in their DNA? Yes, arsenic concentrations are high in Mono Lake. But so are phosphate concentrations, which approach 1 millimolar - or 100,000 times higher than in the Sargasso Sea. Mono Lake has more phosphate available than nearly any other environment on Earth. There is no selective pressure for the evolution of what would surely be a massively complex switch in nucleic acid chemistry from phosphate to arsenate. I can only begin to imagine the structural problems that would be imposed on DNA by this switch, which would change bond lengths between nucleotides, and cause secondary problems with transcription, etc. Then there is the radical suggestion that nucleotide chemistry is stable because might occur in a 'non-aqueous' environment. It's not clear how that could work.

Finally, there's a simple experiment that could resolve this debate: analyze the nucleotides directly. Show a mass spectrum of DNA sequences demonstrating that nucleotides contain arsenate instead of phosphate. This is a very simple experiment, and would be quite convincing - but it has not been performed.
This study lacks any real evidence for arsenate-based DNA; unfortunately these exciting claims are very very shaky.

Update (12/6/2010): Dr. Rosie Redfield has a quantitative discussion of why there's plenty of phosphorus here.

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, & Oremland RS (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.) PMID: 21127214

~~~~~~

Rosie's update:

Arsenic-associated bacteria (NASA's claims)

ResearchBlogging.org

Wolfe-Simon F, Blum JS, Kulp TR, Gordon GW, Hoeft SE, Pett-Ridge J, Stolz JF, Webb SM, Weber PK, Davies PC, Anbar AD, & Oremland RS (2010). A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus. Science (New York, N.Y.) PMID: 21127214

Note to new readers:  I wrote this post on Saturday Dec. 4, mainly to clarify my own thinking.  I didn't expect anyone other than a few researchers to ever read it.  Since then I've made a few minor corrections and clarifications (typos, decimal places, cells not cfu), but I haven't changed anything significant.  Please read the comments - they contain a lot of good scientific thinking by other researchers.

Here's a detailed review of the new paper from NASA claiming to have isolated a bacterium that substitutes arsenic for phosphorus on its macromolecules and metabolites.  (Wolfe-Simon et al. 2010, A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus.)  NASA's shameful analysis of the alleged bacteria in the Mars meteorite made me very suspicious of their microbiology, an attitude that's only strengthened by my reading of this paper.  Basically, it doesn't present ANY convincing evidence that arsenic has been incorporated into DNA (or any other biological molecule).

What did the authors actually do?  They took sediment from Mono Lake in California, a very salty and alkaline lake containing 88 mg of phosphate and 17 mg of arsenic per liter.  They put the sediment into a similarly alkaline and hypersaline defined medium containing 10 mM glucose as a carbon source, 0.8 mM NH4SO4 as a nitrogen and sulfur source, and a full assortment of the vitamins and trace minerals that might be needed for bacterial growth.  Although this basic medium had no added phosphate or arsenate, contamination of the ingredients caused it to contain about 3 µM phosphate (PO4) and about 0.3 µM arsenate (AsO4) as.  For bacterial growth it was supplemented with arsenate or phosphate at various concentrations.

The interesting results came from sediment originally diluted into medium supplemented with the highest arsenate concentration they initially tried (5 mM) but no phosphate.  Over the course of several months they did seven tenfold dilutions; in the sixth one they saw a gradual turbidity increase suggesting that bacteria were growing at a rate of about 0.1 per day.  I think this means that the bacteria were doubling about every 10 days (no, every 7 days - corrected by an anonymous commenter).

After one more tenfold dilution they put some of the culture onto an agar plate made with the same medium; at least one colony grew, which they then inoculated into the same defined medium with 5 mM arsenate.  They gradually increased the arsenate to 40 mM (Mono Lake water contains 200 µM arsenate).  Descendants of these cells eventually grew in 40 mM arsenate, with about one doubling every two days.  They grew faster if the arsenate was replaced by1.5 mM phosphate but grew only about threefold if neither supplement was provided (Fig. 1 A and B, below).  The authors misleadingly claim that the cells didn't grow at all with no supplements.

In Fig. 1 (below), the correspondence between OD600 (Fig. 1 A) and cells (Fig. 1 B) is not good.  Although the lines in the two graphs have similar proportions, OD600 is plotted on a linear scale and cells/ml on a log scale (is this a shabby trick to increase their superficial similarity?).  OD600 in arsenate medium was almost as high as that in phosphate medium, but the number of cells was at least tenfold lower.  And the OD in arsenate continued to increase for many days after the cells has leveled off.  I suspect most of the continuing growth was just compensating for cell death.  It would be interesting to test whether the cells were scavenging phosphate from their dead siblings.



The authors never calculated whether the amount of growth they saw in the arsenate-only medium (2-3 x 10^7 cfu/ml) could be supported by the phosphate in this medium (or maybe they did but they didn't like the result).  For simplicity I'll start by assume that a phosphorus-starved cell uses half of its phosphorus for DNA and the rest for RNA and other molecule, and that the genome is 5x10^6 bp.  Each cell then needs 1x10^7 atoms of phosphorus for DNA, and 2x10^7 for everything.  The medium is 3.1 µM phosphate, which is 3.1x10^-6 moles per liter.  Mutiply by Avogadro's number (6.02x10^23 atoms per mole) and we have 1.9x10^18 atoms of phosphorus per liter, or 1.9x10^15 per ml.  Divide by the phosphorus requirement of each cell (2x10^7) and we get 9.5 x 10^7 cells per ml.  This value is just comfortably larger than the observed final density, suggesting that, although these bacteria grow poorly in the absence of arsenate, in its presence their growth is limited by phosphate. (Note:  This calculation originally dropped a decimal point.  I've changed it a bit and corrected the error.)

Under the microscope the bacteria grown with arsenate and no added phosphate (Fig. 1 C) look like plump little corn kernels, about 1 µm across and 2 µm long.  They contain many structures (Fig. 1 E) which the authors think may be granules of the wax-like carbon/energy storage material polyhydroxybutyrate (PHB).  Bacterial cells produce this when their carbon/energy supply is good but other nutrients needed for growth are in short supply.  Cells grown with phospate and no added arsenate are thinner and lack the granules (Fig. 1 D).  The authors used 16S rRNA sequencing to identify this bacterium as belonging to the genus Halomonas, a member of the gammaproteobacterial order Oceanospirillales.  Members of this group are diverse but not known to have any uniquely dramatic features.

According to an interview with the first author, this research was motivated by a desire to show that organisms could use arsenic in place of phosphorus.  The two atoms have very similar chemical properties, but bonds with arsenic are known to be much less stable than those with phosphate, so most researchers think that biological molecules containing arsenic rather than phosphorus would be too unstable to support life.  Thus the authors wanted to show that the bacteria had incorporated the arsenic in places where phosphorus would normally be found.  They used several methods, each involving a low-tech preparation of cell material and a high-tech identification of the atoms present in the material.
 
First they collected the bacteria by centrifugation, washed them well, and precisely measured the fraction of arsenic and phosphorus (as ppb dry weight, Tables 1 and S1).  Cells given only the arsenate supplement contained about 10-fold more arsenic than phosphorus (0.2% arsenic and 0.02% phosphorus) and cells given only the phosphate supplement had 0.5% phosphorus and only 0.001%  arsenic.

The authors argue that the arsenate-grown cells don't contain enough phosphorus to support life.  They say that typical heterotrophic bacteria require 1-3% P to support life, but this isn't true.  These numbers are just the amounts found in E. coli cells grown in medium with abundant phosphate.   They are very unlikely to apply to bacteria growing very slowly under phosphate limitation, and aren't even true of their own phosphate-grown bacteria (0.5% P).  The large amount of PHB in the arsenate-grown cells would have skewed this comparison - PHB granules are mainly carbon with no water, and in other species can be as much as 90% of the dry weight of the cells.  Thus their presence only in arsenate-grown cells could depress these cells' apparent phosphate concentration by as much as 10-fold.

The authors then grew some cells with radioactive arsenate (73-As) and no phosphate, washed and dissolved them, and used extraction with phenol and phenol:chloroform to separate the major macromolecules.  The protein fraction at the interface between the organic and aqueous phases had about 10% of the arsenic label but, because the interface material is typically contaminated with liquid from the aqueous phase, this is not good evidence that the cells' protein contained covalently-bound arsenate in place of phosphorus.  About 75% of the arsenic label was in the  aqueous (upper) fraction.  The authors describe this fraction as DNA/RNA, but it also contains most of the small water-soluble molecules of the cell, so its high arsenic content is not evidence that the DNA and RNA contain arsenic in place of phosphorus.  The authors use very indirect evidence to argue that the distribution of arsenic mirrors that expected for phosphate, but this argument depends on so many assumptions that it should be ignored.

(They also measured the absolute amounts of arsenic and phosphorus in the supernatant fraction - surprisingly, no arsenic (<20 ppb) was detected in the fraction from arsenate-supplemented cells, although the fraction from phosphate-grown cells had 118 ppb!  See Table S1.)

They especially wanted to show that the cells' DNA contained arsenic in place of phosphorus, so they gel-purified chromosomal DNA from cells grown with arsenate (lane 2) or with phosphate (lane 3), and measured the ratio of arsenic to carbon by mass spectrometry.  The numbers at the bottom give these ratios (the legend says 'multiplied by 10^-6 but they surely mean 'multiplied by 10^6'). 



As expected, this ratio was very low for the phosphate-grown cells (6.9x10^-6), but it was only twofold higher for the arsenate-grown cells (13.4x10^-6).  Normal DNA has one phosphorus atom for each ten carbons (P:C = 10^-1), so the arsenate-grown ratio is only about one arsenic atom per 10,000 phosphorus atoms (i.e. one per 5 kb of double-stranded DNA).  A 2x10^6 bp genome would contain 4x10^6 atoms of phosphorus, so if all this arsenate was really covalently in the DNA, each genome would only contain about 400 atoms of arsenic.  And a phosphate-grown genome would contain 200!

Could 400 atoms of arsenate per genome be due to carryover of the arsenate in the phenol-chloroform supernatant rather than to covalent incorporation of As in DNA?   The Methods describes a standard ethanol precipitation with no washing (and no column purification which would have included washing), so I think some arsenate could easily have been carried over with the DNA, especially if it is not very soluble in 70% ethanol.  Would this arsenate have left the DNA during the gel purification?  Maybe not - the methods don't say that the DNA was purified away from the agarose gel matrix before being analyzed.  This step is certainly standard, but if it was omitted then any contaminating arsenic might have been carried over into the elemental analysis.

Failure to purify the DNA away from the agarose would also compromise their elemental analysis in other ways, since much of the carbon in the purified 'DNA' would have been from the agarose.  The authors did do the same elemental analysis on a gel slice with no DNA in it, a control that only makes sense if they didn't purify the DNA.  Not purifying away the gel might affect the arsenate-grown DNA more because the band contains less DNA; this would explain why this excised DNA has 3.5-fold lower ratio of phosphorus to carbon than the phosphate-grown DNA, a difference that is certainly not explained by its very low arsenic content.)

(Might they have not presented assays using properly purified (washed) DNA because these turned out to not have any arsenic?  Am I just paranoid?)

Finally, the authors examined the chemical environment (neighbouring atoms and bonds) of the arsenic in the cells using synchrotron X-ray studies.  This is over my head, but they seem to be trying to interpret the signal as indicating that the environment of the arsenic is similar to that of phosphorus in normal DNA.  But the cellular arsenic being in DNA can't be the explanation, because their DNA analysis indicated that very little of the cellular arsenic purifies with the DNA.  The cells contained 0.19% arsenic (1.9x10^6 ppb), but the DNA only contained 27 ppb arsenic.

Bottom line:  Lots of flim-flam, but very little reliable information.  The mass spec measurements may be very well done (I lack expertise here), but their value is severely compromised by the poor quality of the inputs.  If this data was presented by a PhD student at their committee meeting, I'd send them back to the bench to do more cleanup and controls.

There's a difference between controls done to genuinely test your hypothesis and those done when you just want to show that your hypothesis is true.  The authors have done some of the latter, but not the former.  They should have mixed pregrown E. coli or other cells with the arsenate supplemented medium and then done the same purifications.  They should have thoroughly washed their DNA preps (a column cleanup is ridiculously easy), and maybe incubated it with phosphate buffer to displace any associated arsenate before doing the elemental analysis.  They should have mixed E. coli DNA with arsenate and then gel-purified it.  They should have tested whether their arsenic-containing DNA could be used as a template by normal DNA polymerases.  They should have noticed all the discrepancies in their data and done experiments to find the causes.

I don't know whether the authors are just bad scientists or whether they're unscrupulously pushing NASA's 'There's life in outer space!' agenda.  I hesitate to blame the reviewers, as their objections are likely to have been overruled by Science's editors in their eagerness to score such a high-impact publication.


37 comments:

Chaos Engineer said...

Notorious atheist P. Z. Myers agrees with you that the study is flawed. He wrote a blog entry linking to the same paper back on December 7th.

I'm wondering why you've decided to side with Dr. Myers. How do you know that the NASA researchers aren't being persecuted by the same people who persecute Creationists and Global-Warming Deniers?

Also, can you explain why you think that this is blow to "Darwinism"? There's nothing in the Theory of Evolution that says that arsenic-based lifeforms have to exist, and there's nothing in the Bible that says that arsenic-based lifeforms can't exist. This is just a boring debate among scientists with no theological implications; the only reason we know about it is because some hyperactive journalists heard the phrase "Life in Outer Space" and built a headline around it.

Here's the relevant XKCD strip

radar said...

Chaos,

Just for the cartoon alone this was your best comment ever! I would have said that Dr. Myers was siding, like me, with good science. Good science is a rarity amongst Darwinists and my series on the "thinking" is going to clarify why I say that. Taking it in stages.

Really, the point is that DNA is obviously designed and ADP ATP engines are obviously designed and biogenesis is a law and ONLY a person who is a sold-out atheist cannot see the implications thereof.

When you walk out in the woods and see trees and rocks and birds, hey, they are part of the natural environment. If you come to a barb-wire fence, you don't try to make up stories about how fences evolved from holly bushes or such tommyrot. You clearly understand that somebody built the fence!

Same with DNA and bacterial motors and photosynthesis and etc. Somebody built it! Duh.

Empiricism doesn't rule out the supernatural, it merely first looks for natural causes and, should they prove inadequate, then one goes to the supernatural. Francis Bacon understood this. Newton knew this. Myers doesn't. Me? I side with Newton.

radar said...

XKCD

X is for rated
K is for kind of weird
C is for way cool far out man
D is for don't go there or you might wind up spending twenty minutes hitting the "random" box

Anonymous said...

"Empiricism doesn't rule out the supernatural, it merely first looks for natural causes and, should they prove inadequate, then one goes to the supernatural."

At that point you're faced with an untestable hypothesis.

Then what do you do?

radar said...

What some call an untestable hypothesis, others will call an answer. If God created life, then instead of using, say, ten percent of the resources of the science world trying to prove the unprovable, they work on improving things with a foundation based on a designed ecosystem.

Understanding that all life, like the Universe, was created and is devolving helps us understand that learning to repair the genome and clearly learning to "read" DNA code can help us cure cancer and other diseases.

When one realizes that all living things were designed with a purpose but because of the fall of man and the ravages of time there are mutations and extinctions, then science can peruse each organism to see what benefit it might have to us. We already know that many medicines are also poisons, depending on the amount taken.

Discovering quorum sensing in bacteria is a major breakthrough and I wish science was focusing on this chemical bacterial language as a means of eliminating the threat of "bad" bacteria within people. Eh, I am going to be posting on this later so enough for now.

Anonymous said...

"What some call an untestable hypothesis, others will call an answer."

You do understand that this would then no longer fall under empiricism, right?

Anonymous said...

"If God created life, then instead of using, say, ten percent of the resources of the science world trying to prove the unprovable, they work on improving things with a foundation based on a designed ecosystem."

Please tell me you don't really think there's any significant percentage of the science world working on abiogenesis.

Anonymous said...

"When one realizes that all living things were designed with a purpose but because of the fall of man and the ravages of time there are mutations and extinctions, then science can peruse each organism to see what benefit it might have to us. We already know that many medicines are also poisons, depending on the amount taken. "

What you call a "realization" is actually an assumption, but for the sake of argument, if there was such a "realization", exactly how would it change the process of science from the way it's being conducted today?

What would/should scientists be doing differently in your view, and how would that be an improvement?

Anonymous said...

No answer, Radar?

radar said...

I do not read every comment and I make a lot of posts, but I noticed this question:

"When one realizes that all living things were designed with a purpose but because of the fall of man and the ravages of time there are mutations and extinctions, then science can peruse each organism to see what benefit it might have to us. We already know that many medicines are also poisons, depending on the amount taken. "

What you call a "realization" is actually an assumption, but for the sake of argument, if there was such a "realization", exactly how would it change the process of science from the way it's being conducted today?

What would/should scientists be doing differently in your view, and how would that be an improvement?


1- Resources. There are so many scientists and academics whose main goal seems to be to push the religion of Darwinism and try to stamp out ID/creationism. Lots of time and money trying to protect a religious belief that could be used in research.

2- Operational science grants and peer review. No longer would there be a Darwin filter that requires grants and papers to somehow include a Darwinist tagline on the research. Research would be about what is happening and what the researcher intends to measure, study, etc, to understand better.

3- Medical field. If everyone trying to make life from non-life was working on a cure for cancer, cancer might be defeated already. One important point here is that, if we know that DNA was designed and the processes of reproduction are designed, we look for ways to return organisms to the original design and thereby produce healthier organisms in some cases. Since cancer is simply unregulated cellular production, accepting that these processes are designed will provide a baseline for understanding what causes cancer to start and how we can manipulate the DNA of the cells to turn off the explosive growth of cancerous cells.

radar said...

I notice that you Darwinists did not come back and admit how terribly wrong you were and how the NASA astrobiology department was sloppy to the point of deliberate equivocation in this situation. In fact there is no reason for NASA to have an astrobiology department at all and, if this is typical of their work, they should all be given pink slips.

radar said...

"Empiricism doesn't rule out the supernatural, it merely first looks for natural causes and, should they prove inadequate, then one goes to the supernatural."

At that point you're faced with an untestable hypothesis.

Then what do you do?


This is another intelligent comment worth noting. Since Darwinism is untestable, or perhaps better so say it has been falsified, why do scientists still adhere to it?

Anyway, if the supernatural is the answer you have nothing to test concerning the origin and instead you test function and design and intentionality and practical applications. There are myriad things to do with the world if you start with the working hypothesis that it all was originally designed and designed well at the time of design.

BTW, the same sigmoidal curve used to analyze human population has appeared in the analysis of transposons in the human genome. Interesting correlation...

radar said...

Empiricism is a process designed to find answers to questions. If you find that God created life, then you have come to the end of the road for that question. I am saying this in more than one way so the point is understood. Science doesn't pack up and go home when we realize God made everything, instead it opens up new lines of investigation with design as the working hypothesis rather than blind chance.

Jon Woolf said...

"Since cancer is simply unregulated cellular production..."

There's rather more to cancer than that.

"accepting that these processes are designed will provide a baseline for understanding what causes cancer to start and how we can manipulate the DNA of the cells to turn off the explosive growth of cancerous cells."

Oncologists are making enormous strides toward doing exactly that, without resorting to any form of creationist pseudoscience.

It should be noted that the exact same genetic research which is finding and deciphering oncogenes and their effects is also providing new evidence for common descent among terrestrial life-forms, as it uncovers genetic oddity after genetic oddity that makes no sense in a creationist worldview, but makes perfect sense under evolutionary theory.

Anonymous said...

"Empiricism is a process designed to find answers to questions."

To scientific questions, to be specific.

"If you find that God created life, then you have come to the end of the road for that question."

In empiricism, you haven't come to the end of the road or "found" anything until it has been tested. If you haven't done that, you have an untested hypothesis - and in this case even an untestable hypothesis. That doesn't mean it's wrong, but empirically speaking it is not the final answer.

"I am saying this in more than one way so the point is understood. Science doesn't pack up and go home when we realize God made everything, instead it opens up new lines of investigation with design as the working hypothesis rather than blind chance."

That's all well and good, but you're still at this point departing from science, since all you've done at this point is come up with an untestable hypothesis. This is indeed where science packs up and goes home (or rather, focuses on testable hypotheses). Scientifically, it is not a "realization", but an "assumption". Big difference.

You may personally choose this answer because it fits your worldview, but don't pretend it's superior science or even that it's scientific. This assumption is religious in nature, pure and simple.

Anonymous said...

About your three answers as to how including creationism would benefit science:

Answers 1 and 3 seem to focus just on resources. Roughly what percentage of scientists do you think are actually working on abiogenesis, for example? I would think it's an extremely small percentage, perhaps even smaller than that of YECs trying to prove the global flood hypothesis. Purely from anecdotal evidence, I'm aware of one scientist working in each of those fields respectively.

Answer 2: can you name a single testable falsifiable claim that was tested and that confirmed creationism that was submitted to a peer-reviewed scientific publication and rejected? A single one would do.

Anonymous said...

Because there is an alternative explanation for the lack of creationist papers making it into peer-reviewed scientific publications, and that is that it is simply poor science. Non-creationists who produce poor science get their papers rejected as well - why should creationists get a pass?

I may be wrong of course, and perhaps creationists are treated unfairly. If that is the case, then you should be able to name name a testable falsifiable claim that was tested and that confirmed creationism that was submitted to a peer-reviewed scientific publication and rejected.

If you can't, then the alternative explanation seems more likely - that creationists haven't come up with that all-important scientific evidence yet.

Anonymous said...

And regarding abiogenesis research, regardless of your religious point of view, who's to say that any insights derived from that research might not be a tremendous boon for mankind in future?

You're arguing against the acquisition of scientific knowledge on the basis of resources, but why give a pass to the people currently trying to prove that the Bible is a science textbook? Might they not be spending their time more efficiently if they tried to cure cancer?

Anonymous said...

"This is another intelligent comment worth noting. Since Darwinism is untestable, or perhaps better so say it has been falsified, why do scientists still adhere to it?"

You may note that there is no "theory of Darwinism". "Darwinism" is a vague term tossed around mostly by creationists, and generally stands for some mishmash of the theory of evolution, atheism, abiogenesis, big bang theory etc. etc. Such an ill-defined mishmash is indeed untestable unless you are a little more careful with your definitions.

The theory of evolution itself has been tested and confirmed in numerous ways. It really doesn't take a whole lot of open-minded research to figure that out. Organisms evolving over time and the mechanisms that can bring this about have been tested and confirmed ad nauseam. I don't recall if you've ever posted any falsifications of it. You've posted numerous misconceptions and strawman arguments and arguments from incredulity etc., but your two faves of late - the law of biogenesis and the 2nd LOT - aren't related to the theory of evolution and do not pose problems for it.

Abiogenesis has likewise not been falsified, nor has it yet been confirmed, though research is making interesting progress on this. It is not falsified by the law of biogenesis (which never tested and confirmed the impossibility of abiogenesis) nor by the 2nd LOT or any of the LOTs for that matter.

Atheism? Also not falsified.

Anything else?

Anonymous said...

"Anyway, if the supernatural is the answer you have nothing to test concerning the origin"

Exactly. That's where such ruminations depart from the realm of science.

"and instead you test function and design and intentionality and practical applications."

Function and practical applications are simply about functionality. Functionality is just as easily explained by evolution: the application of trial and error, with more beneficial functionalities selected over millions of generations. We know that such a process can generate very efficient solutions that a designer might not necessarily have thought of, as modeled so efficiently in genetic algorithms.

We know that nature features interesting functionalities. This is something we can even verify empirically, through observation, regardless of our worldview or religion. It doesn't matter whether we think that is because of evolution or because God created it or whatever other reason.

Anonymous said...

Design and intentionality... you realize that we know nothing about the intentionality of the designer, or even that the object in question was designed in the first place, right? What do we know about, say, the intentionality of the design behind the bumblebee, and how does that help science in an area where it is currently hindered, relatively speaking?

"There are myriad things to do with the world if you start with the working hypothesis that it all was originally designed and designed well at the time of design."

Name one.

radar said...

Name ONE???

I can name entire disciplines - Nano-engineering, Biomimetics and Biomimicy are just three. There are all sorts of people doing research on the assumption that organisms are designed better than anything man had done and we are trying to copy or come close to copying them for our purposes.

radar said...

The theory of evolution itself has been tested and confirmed in numerous ways.

those ways would be the null set

It really doesn't take a whole lot of open-minded research to figure that out. Organisms evolving over time and the mechanisms that can bring this about have been tested and confirmed ad nauseam.

Actually, every time a Darwinist claims he has an example of evolution in process, it turns out to be mere speciation, which is part of the design of the organism and we prove that by pointing out all the various choices and switches built in to the DNA

I don't recall if you've ever posted any falsifications of it. You've posted numerous misconceptions and strawman arguments and arguments from incredulity etc., but your two faves of late - the law of biogenesis and the 2nd LOT - aren't related to the theory of evolution and do not pose problems for it.

Darwinism is in direct opposition to the 2LOT and as we study the genome we are finding that organisms are devolving, not evolving. Darwinism is never observed. Also, the Law of Biogenesis actually did falsify abiogenesis. We used to call it spontaneous generation. No one has ever falsifed the LOB

Abiogenesis has likewise not been falsified, nor has it yet been confirmed, though research is making interesting progress on this. It is not falsified by the law of biogenesis (which never tested and confirmed the impossibility of abiogenesis) nor by the 2nd LOT or any of the LOTs for that matter.

abiogenesis cannot be tested per se because it cannot even begin to be tested. The basic laws of chemistry and molecular behavior prohibit life forming by chance. You cannot even begin to form life because of the formaldehyde problems, the oxygen problems and the chirality problems, just to name three. Two little kids with rocks and sticks are more likely to build a Saturn Five than scientists are going to produce life from non-life. Might as well just admit it

radar said...

Because there is an alternative explanation for the lack of creationist papers making it into peer-reviewed scientific publications, and that is that it is simply poor science. Non-creationists who produce poor science get their papers rejected as well - why should creationists get a pass?

I may be wrong of course, and perhaps creationists are treated unfairly. If that is the case, then you should be able to name name a testable falsifiable claim that was tested and that confirmed creationism that was submitted to a peer-reviewed scientific publication and rejected.

If you can't, then the alternative explanation seems more likely - that creationists haven't come up with that all-important scientific evidence yet.


I guess you were afraid to go see the movie, EXPELLED, No Intelligence Allowed. Great scientists such as Sarfati have largely given up on the secular scientific community and helped build peer groups and scientific institutions apart from the Darwinist Paradigm because censorship is the default setting.
Even Behe and Ross and Gonzalez have given up on them.

Recently over a thousand highly-qualified scientists "spanked" the ruling paradigm for supporting the now-ludicrous AGW thesis as fact. But it will take years to deprogram the public and years to undo the damage to economies around the world. One day the movement to end Dawinism will pick up momentum. It must.

radar said...

Nonsense! The more we learn about DNA, the more we see that macroevolution did not happen because Darwinist morphology is falsified by the varying places on the DNA string that code for structures and systems and that we see degradation rather than progress within the DNA code. Mutations and copying errors have devolved organisms and helped cause many extinctions.

Furthermore, complex structures such as the eye are found in widely varying organisms with very different styles, so that the odds against eyes evolving just adds more impossibility to the already enormous impossibility of random generation of life and information.

We just keep finding more complexity and more design. Sorry, Darwinists, science is for grownups. The Evolution Fairy is for kids.

radar said...

It occurs to me that P.Z. Myers and I would very rarely agree on anything!

Notice how when something like this arsenic bacteria thing is unleashed, it is broadcast widely and then, when it inevitably turns out to be either a mistake or a hoax, almost no press coverage at all?

Actually, Chaos, there are religious implications involved in origins science and that is why we have Darwinism. No way such a hypothesis would have survived the end of uniformitarianism and the discovery of DNA and the falsification of the geological table and the exposure of hoaxes like the Haeckel Embryos and the Peppered Moths otherwise. Anyone with sense takes anything Darwinists proclaim with a grain of salt now, because today's whale is tomorrow's quadruped and today's missing link is tomorrow's old lemur fossil dragged out of the basement. This Arsenic Bacteria was just another farce.

Anonymous said...

"I guess you were afraid to go see the movie, EXPELLED, No Intelligence Allowed."

Why, did it feature an example of a testable falsifiable claim that was tested and that confirmed creationism that was submitted to a peer-reviewed scientific publication and rejected?

Anonymous said...

"We just keep finding more complexity"

Certainly not a problem for the theory of evolution.

"and more design."

Unproven and untested conjecture.

"Sorry, Darwinists, science is for grownups."

My, what a grown-up thing for you to say.

"The Evolution Fairy is for kids."

What about the Design Fairy?

Anonymous said...

"The basic laws of chemistry and molecular behavior prohibit life forming by chance."

Do these laws prohibit the spontaneous formation of self-replicating structures?

If so, how?

Anonymous said...

"Actually, every time a Darwinist claims he has an example of evolution in process, it turns out to be mere speciation"

Speciation = evolution at species level, in other words, the origin of species. If you don't think that's evolution, you should read up on the theory of evolution sometime. Seriously.

Anonymous said...

"Darwinism is in direct opposition to the 2LOT"

The theory of evolution certainly is not, if that's what you're saying.

Anonymous said...

"Nano-engineering, Biomimetics and Biomimicy are just three. There are all sorts of people doing research on the assumption that organisms are designed better than anything man had done and we are trying to copy or come close to copying them for our purposes."

They can (and do) do the same work on the assumption that nature has evolved useful functionality through countless trial and error with natural selection resulting in improved functionality.

Are you suggesting that nano-engineering and biomimicry/biomimetics research is only carried out by creationists?

Of course it isn't.

So your example falls flat - a belief in divine design wouldn't change a thing in these examples.

Got anything else?

Anonymous said...

"Nano-engineering, Biomimetics and Biomimicy are just three. There are all sorts of people doing research on the assumption that organisms are designed better than anything man had done and we are trying to copy or come close to copying them for our purposes."

They can (and do) do the same work on the assumption that nature has evolved useful functionality through countless trial and error with natural selection resulting in improved functionality.

Are you suggesting that nano-engineering and biomimicry/biomimetics research is only carried out by creationists?

Of course it isn't.

So your example falls flat - a belief in divine design wouldn't change a thing in these examples.

Got anything else?

Anonymous said...

Sorry about the double post.

Anonymous said...

i can't believe that idiots like yourself even know how to write. let alone own a computer. go bush! i could tell by your pictures that your part of that top 1% money earners republicans love so much....

radar said...

"i can't believe that idiots like yourself even know how to write. let alone own a computer. go bush! i could tell by your pictures that your part of that top 1% money earners republicans love so much...."

No, if I was both rich and an idiot I would have to be a Democrat and a politician and I am neither. Or I could have inherited my money from someone who did something worthwhile.

I am a struggling small businessman and your comment has NOTHING to do with science at all. Again, methodological investigation is the scientific method and naturalism is metaphysical and therefore needs to remain in the realm of religion.

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