Tag Archives: Evolution

Polemics

The origin of life, part 1 of 2: the building blocks of life

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The origin of life

There are two problems related to the origin of the first living cell, on atheism:

  1. The problem of getting the building blocks needed to create life – i.e. the amino acids
  2. The problem of creating the functional sequences of amino acids and proteins that can support the minimal operations of a simple living cell

Normally, I concede the first problem and grant the atheist all the building blocks he needs. This is because step 2 is impossible. There is no way, on atheism, to form the sequences of amino acids that will fold up into proteins, and then to form the sequences of proteins that can be used to form everything else in the cell, including the DNA itself. But that’s tomorrow’s topic.

Today, let’s take a look at the problems with step 1.

The problem of getting the building blocks of life

Now you may have heard that some scientists managed to spark some gasses to generate most of the 20 amino acids found in living systems. These experiments are called the “Miller-Urey” experiments.

The IDEA center has a nice summary of origin-of-life research that explains a few of the main problems with step 1.

Miler and Urey used the wrong gasses:

Miller’s experiment requires a reducing methane and ammonia atmosphere,11, 12 however geochemical evidence says the atmosphere was hydrogen, water, and carbon dioxide (non-reducing).15, 16 The only amino acid produced in a such an atmosphere is glycine (and only when the hydrogen content is unreasonably high), and could not form the necessary building blocks of life.11

Miller and Urey didn’t account for UV of molecular instability:

Not only would UV radiation destroy any molecules that were made, but their own short lifespans would also greatly limit their numbers. For example, at 100ºC (boiling point of water), the half lives of the nucleic acids Adenine and Guanine are 1 year, uracil is 12 years, and cytozine is 19 days20 (nucleic acids and other important proteins such as chlorophyll and hemoglobin have never been synthesized in origin-of-life type experiments19).

Miller and Urey didn’t account for molecular oxygen:

We all have know ozone in the upper atmosphere protects life from harmful UV radiation. However, ozone is composed of oxygen which is the very gas that Stanley Miller-type experiments avoided, for it prevents the synthesis of organic molecules like the ones obtained from the experiments! Pre-biotic synthesis is in a “damned if you do, damned if you don’t” scenario. The chemistry does not work if there is oxygen because the atmosphere would be non-reducing, but if there is no UV-light-blocking oxygen (i.e. ozone – O3) in the atmosphere, the amino acids would be quickly destroyed by extremely high amounts of UV light (which would have been 100 times stronger than today on the early earth).20, 21, 22 This radiation could destroy methane within a few tens of years,23 and atmospheric ammonia within 30,000 years.15

And there were three other problems too:

At best the processes would likely create a dilute “thin soup,”24 destroyed by meteorite impacts every 10 million years.20, 25 This severely limits the time available to create pre-biotic chemicals and allow for the OOL.

Chemically speaking, life uses only “left-handed” (“L”) amino acids and “right-handed” (“R)” genetic molecules. This is called “chirality,” and any account of the origin of life must somehow explain the origin of chirality. Nearly all chemical reactions produce “racemic” mixtures–mixtures with products that are 50% L and 50% R.

Two more problems are not mentioned in the article. A non-peptide bond anywhere in the chain will ruin the chain. You need around 200 amino acids to make a protein. If any of the bonds is not a peptide bond, the chain will not work in a living system. Additionally, the article does not mention the need for the experimenter to intervene in order to prevent interfering cross-reactions that would prevent the amino acids from forming.

The progress of science

As science has progressed, the discoveries have proved out the need for a Creator and Designer in every area – the big bang, cosmic, galactic and stellar fine-tuning, the Cambrian explosion, etc…. and even the origin of life.

“More than 30 years of experimentation on the origin of life in the fields of chemical and molecular evolution have led to a better perception of the immensity of the problem of the origin of life on Earth rather than to its solution. At present all discussions on principal theories and experiments in the field either end in stalemate or in a confession of ignorance. New lines of thinking and experimentation must be tried.”

(Dose, Klaus, “The Origin of Life: More Questions Than Answers,” Interdisciplinary Science Reviews, Vol. 13, No. 4, 1988, p.348.)

Meanwhile, atheists are left to have blind faith that the progress scientists have made during decades of research will be miraculously overturned by new evidence that their beloved unobservable Flying Spaghetti Monster, (peas be upon him), did it. Hey! Don’t blaspheme against the non-supernatural powers of his noodly appendage! (Two Ph.Ds in biology will not save you from the wrath of the Darwoid cultists!)

To see how bad this gets for atheists, watch this video where Dawkins says that unobservable aliens evolved somewhere else and then seeded the Earth with life. He has no evidence that these aliens did evolve (no fossil record), and even worse, he does not know whether they even exist. Nevertheless, that is the state of atheism today – an unobservable Flying Spaghetti Monster evolved somewhere else and seeded the Earth with life.

What else could have happened?

Further study

One of my favorite resources on the origin of life is this interview from the University of California with former atheist and origin of life researcher Dean Kenyon. Kenyon, a professor of Biology at San Francisco State University, wrote the textbook on “chemical evolution”, which is the view that chemicals can arrange themselves in order to create the first living cell, without intervention.

This interview from the University of California with another origin of life researcher, Charles Thaxton, is also one of my favorites.

You’ll need Quicktime to see the videos, or buy the videos from ARN. (Kenyon, Thaxton) I have both of them – they rock!

Commentary

Scientific American assesses naturalistic explanations for the origin of life

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From Scientific American. (H/T Letitia via Mary)

Excerpt:

As recently as the middle of the 20th century, many scientists thought that the first organisms were made of self-replicating proteins. After Francis Crick and James Watson showed that DNA is the basis for genetic transmission in the 1950s, many researchers began to favor nucleic acids over proteins as the ur-molecules. But there was a major hitch in this scenario. DNA can make neither proteins nor copies of itself without the help of catalytic proteins called enzymes. This fact turned the origin of life into a classic chicken-or-egg puzzle: Which came first, proteins or DNA?

RNA, DNA’s helpmate, remains the most popular answer to this conundrum, just as it was when I wrote “In the Beginning…” Certain forms of RNA can act as their own enzymes, snipping themselves in two and splicing themselves back together again. If RNA could act as an enzyme, then it might be able to replicate itself without help from proteins. RNA could serve as gene and catalyst, egg and chicken.

But the “RNA-world” hypothesis remains problematic. RNA and its components are difficult to synthesize under the best of circumstances, in a laboratory, let alone under plausible prebiotic conditions. Once RNA is synthesized, it can make new copies of itself only with a great deal of chemical coaxing from the scientist. Overbye notes that “even if RNA did appear naturally, the odds that it would happen in the right sequence to drive Darwinian evolution seem small.”

The RNA world is so dissatisfying that some frustrated scientists are resorting to much more far out—literally—speculation. The most startling revelation in Overbye’s article is that scientists have resuscitated a proposal once floated by Crick. Dissatisfied with conventional theories of life’s beginning, Crick conjectured that aliens came to Earth in a spaceship and planted the seeds of life here billions of years ago. This notion is called directed panspermia. In less dramatic versions of panspermia, microbes arrived on our planet via asteroids, comets or meteorites, or drifted down like confetti.

John Horgan is not a Christian, nor even a theist. This is the state of the art if you are a naturalist.

Basically, you have at most a couple hundred million years from the time the Earth cools to the appearance of first life. You are unlikely to get one measly protein without an intelligence arranging the amino acids. This is assuming we spot you a favorable environment for creating amino acids without intervention. And then there would still be the problem of sequencing the proteins.

Atheists oppose science and evidence

Theists support science and evidence

News

Should ID researchers be “marked down” for defending intelligent design?

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Here’s an interesting post from Evolution News about a teacher in New Zealand who grades her students down if they try to discuss intelligent design in class.

Excerpt:

Biology lecturer Alison Campbell at the University of Waikato in Hillcrest, New Zealand, exemplifies a mindset that is tragically common in academia. She openly boasts that if a student were to use standard ID arguments such as the irreducible complexity of the bacterial flagellum, that student would be “marked down”:

If, for example, a student were to use examples such as the bacterial flagellum to advance an ID view then they should expect to be marked down; that particular creationist trophe has been well & truly discredited.

And in fact in reading over that post by Alison Campbell and the comments, it’s not clear that she has read anything by an ID theorist. She quotes from a an anti-ID philosopher and a anti-ID judge to argue against intelligent design. She doesn’t interact with any intelligent design books, by quoting pro-ID  arguments and citing page numbers. She doesn’t mention a single research paper written by an ID theorist. It’s just something that an English teacher could have written. She has to keep everything very vague in that post. “There is lots of evidence against ID, so let me quote a philosopher”. “There is lots of evidence against ID, so let me quote a judge”. Neither of those authorities has any training in biology. Does Alison Campbell? Let’s see.

Here are some of her recent publications:

Campbell, A. 2009 You let them talk in lectures? Student discussion as formative assessment . In: Meyer, Luanna H., Davidson, Susan, Anderson, Helen, Fletcher, Richard, Johnston, Patricia M., Rees, Malcolm(eds) Tertiary assessment & higher education studnet outcomes: policy, practice & research. Wellington : Ako Aotearoa pp91-96.

Campbell, A., Künnemeyer, R. and Prinsep, M. R. 2008. Staff perceptions of higher education science and engineering learning communities. Research in Science & Technological Education, Vol 26, No 3, pp279-294.

Campbell A. 2008. The creep of creationism – is it relevant to teaching earth sciences? Geological Society of New Zealand (Inc) 146, pp 23-26.

Campbell, A. 2007. Is intelligent design a scientific alternative to the theory of evolution? New Zealand Science Teacher 116 pp11-12.

Campbell, Alison. (2005). Intelligent Design? Radio New Zealand ‘Our Changing World’ interview 6th October.

Otrel-Cass, Kathrin, Earl, Kerry, Campbell, Alison, Cooke, Penelope. (2005). Evolution for Teaching Website evaluation report. NZ Science Teacher, Number 109, pp 27-29.

Buntting, Cathy, Coll, Richard Kevin and Campbell, Alison. 2005. Student views of concept mapping use in introductory tertiary biology classes. International Journal of Science and Mathematics Education. ISSN: 1573-1774 (Online).

Zepke Nick, Leach Linda, Prebble Tom, Campbell Alison, Coltman David, Dewart Bonnie, Gibson Maree, Henderson Judy, Leadbeater Jenny, Purnell Sue, Rowan Linda, Solomon Nika and Wilson Stewart. 2005. Improving tertiary student outcomes in the first year of study. Teaching & Learning Research Initiative.

Campbell, Alison. (2004). Book review: The flight of the huia. New Zealand Journal of Zoology, Vol.31, pp 379-380.

Campbell A, Cooke P, Earl K and Otrell-Cass K. (2004). A New Zealand “Evolution for Teaching” Online Resource. Teaching EARTH SCIENCES Vol 29, Number 3/4, pp 31-32.

Campbell, A.M., P. Cooke, K. Cass & K. Earl (2004) “Evolution for Teaching”.

I don’t see a single publication in experimental science in there. She doesn’t do research. She has no research publications. But if a genuine experimental biologist came into her classroom, that person would be marked down for disagreeing with her religion – the religion of materialism. The assumption of naturalism. Both of which are easily demonstrated as false simply by looking at the experimental evidence supporting the Big Bang theory, e.g. – redshift, cosmic microwave background radiation, light element abudnances, etc. But some people don’t let the science inform their worldview. They just write about teaching and then mark down actual experimental biologists who question their faith commitments to materialism and naturalism.

Here are some papers from Biologic Institute researchers:

D’Andrea-Winslow L, Novitski AK (2008) Active bleb formation is abated in Lytechinus variegatus red spherule coelomocytes after disruption of acto-myosin contractility. Integrative Zoology 3: 106-113. doi:10.1111/j.1749-4877.2008.00086.x

Axe DD, Dixon BW, Lu P (2008) Stylus: A system for evolutionary experimentation based on a protein/proteome model with non-arbitrary functional constraints. PLoS ONE 3: e2246. doi:10.1371/journal.pone.0002246

Sternberg RV (2008) DNA codes and information: Formal structures and relational causes. Acta Biotheoretica doi:10.1007/s10441-008-9049-6. PMID: 18465197

Gonzalez G (2008) Parent stars of extrasolar planets – IX. Lithium abundances. Monthly Notices of the Royal Astronomical Society, Online Early Articles doi:10.1111/j.1365-2966.2008.13067.x

Duren RW, Marks II RJ, Reynolds PD, Trumbo ML (2007) Real-time neural network inversion on the SRC-6e reconfigurable computer. IEEE Transactions on Neural Networks 18: 889-901. PMID: 17526353

Gonzalez G, Laws C (2007) Parent stars of extrasolar planets VIII. Chemical abundances for 18 elements in 31 stars. Monthly Notices of the Royal Astronomical Society 378: 1141-1152. doi:10.1111/j.1365-2966.2007.11867.x

Gravagne IA, Marks II RJ (2007) Emergent behaviors of protector, refugee and aggressor swarms. IEEE Transactions on Systems, Man and Cybernetics, Part B: Cybernetics 37: 471- 476. PMID: 17416173

Weinschenk JJ, Combs WE, Marks II RJ (2007) On the avoidance of rule explosion in fuzzy inference engines. International Journal of Information Technology and Intelligent Computing 1, #4.

Gonzalez G (2006) Condensation temperatures trends among stars with planets. Monthly Notices of the Royal Astronomical Society: Letters 367: L37-L41. doi:10.1111/j.1745-3933.2005.00136.x

Gonzalez G (2006) The sun’s interior metallicity constrained by neutrinos. Monthly Notices of the Royal Astronomical Society: Letters 370 : L90–L93.
doi:10.1111/j.1745-3933.2006.00197.x

Gonzalez G (2006) The chemical compositions of stars with planets: A review.
Publications of the Astronomical Society of the Pacific 118: 1494-1505 (invited review paper). doi:10.1086/509792

Gonzalez G (2005) Habitable zones in the universe. Origins of Life and Evolution of Biospheres 35: 555-606. doi:10.1007/s11084-005-5010-8

Keller D, Brozik JA (2005) Framework model for DNA polymerases. Biochemistry 44: 6877-6888. PMID: 15865433

Shapiro JA, von Sternberg R (2005) Why repetitive DNA is essential to genome function. Biological Reviews 80: 227-250. Review. PMID: 15921050

von Sternberg R, Shapiro JA (2005) How repeated retroelements format genome function. Cytogenetic and Genome Research 110: 108-116. PMID: 16093662

Axe DD (2004) Estimating the prevalence of protein sequences adopting functional enzyme folds. Journal of Molecular Biology 341: 1295-1315. PMID: 15321723

Lu H, Macosko J, Habel-Rodriguez D, Keller RW, Brozik JA, Keller D (2004) Closing of the fingers domain generates motor forces in the HIV reverse transcriptase. Journal of Biological Chemistry 279: 54529-54532. PMID: 15385563

Keller D, Swigon D, Bustamante C (2003) Relating single-molecule measurements to thermodynamics. Biophysical Journal 84: 733-738. PMID: 12547757

von Sternberg R, Cumberlidge N (2003) Autapomorphies of the endophragmal system in trichodactylid freshwater crabs (Crustacea: Decapoda: Eubrachyura). Journal of Morphology 256: 23-28. PMID: 12616572

Bustamante C, Keller D, Oster G (2001) The physics of molecular motors. Accounts of Chemical Research 34: 412-420. PMID: 11412078

D’Andrea-Winslow L, Strohmeier G, Rossi B, and Hofman P (2001) Identification of a Na/K/2Cl cotransporter (NKCC) in sea urchin coelomocytes: microfilament dependent surface expression mediated by hypotonic shock and cAMP. Journal of Experimental Biology 204: 147-156. PMID: 11104718

Gonzalez G, Brownlee D, Ward P (2001) The Galactic Habitable Zone: Galactic chemical evolution. Icarus 152: 185-200. doi:10.1006/icar.2001.6617

Axe DD (2000) Extreme functional sensitivity to conservative amino acid changes on enzyme exteriors. Journal of Molecular Biology 301: 585-595. PMID: 10966772

von Sternberg R (2000) Genomes and form. The case for teleomorphic recursivity.
Annals of the New York Academy of Sciences 901: 224-236. PMID: 10818573

Wuite GJ, Smith SB, Young M, Keller D, Bustamante C (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404: 103-106. PMID: 10716452

Axe DD, Foster NW, Fersht AR (1998) A search for single substitutions that eliminate enzymatic function in a bacterial ribonuclease. Biochemistry 37: 7157-7166. PMID: 9585527

Axe DD, Foster NW, Fersht AR (1996) Active barnase variants with completely random hydrophobic cores. Proceedings of the National Academy of Sciences USA. 93: 5590-5594. PMID: 8643620

Gauger AK, Goldstein LS (1993) The Drosophila kinesin light chain. Primary structure and interaction with kinesin heavy chain. Journal of Biological Chemistry 268: 13657-13666. PMID: 8514798

Notice any differences between Alison’s papers and these papers? That’s right! These papers are science. Alison’s papers are not science. They are secular-left education policy. But all of these real scientists from Biologic would be “marked down” in her classroom – because philosophers and judges say that they must be marked down. Why assess the complicated science when you can just impose your religion by force on dissenters? It worked for the Catholic Church against Galileo. Maybe Alison doesn’t understand experimental science? Maybe ID papers are just too complicated for her to understand?

Since Alison mentions the bacterial flagellum by name, I thought that it might be useful for us to see a popular-level article on the bacterial flagellum written by an anonymous graduate student of biology. He has to be anonymous because of religious people like Alison who will mark him down for doing actual science that contradicts her faith. (I know who he is)

Excerpt:

As I mentioned in my previous essay, the synthesis of the bacterial flagellum is orchestrated by genes which are organised into a tightly ordered cascade in which expression of one gene at a given level requires the prior transcription of another gene at a higher level.

In Salmonella, the flagellar system has three classes of promoters — Class I, Class II, and Class III. This sequential transcription is coupled to the process of flagellar assembly. Class I contains only two genes in one operon, namely FlhD and FlhC. Class II consists of 35 genes across eight operons. These genes include those involved in the biosynthesis of the hook-basal-body and other components of the flagellum and export apparatus, as well as the regulatory genes FliA and FlgM. Those genes which are involved in the synthesis of the filament are controlled by virtue of the Class III promoters.

The Class I promoter is required to drive the expression of the enteric master regulator, FldH4C2. The Class II promoters are subsequently turned on by this master regulator in association with the sigma factor, σ70. The Class II promoters are responsible for the gene expression of the hook-basal-body subunits and its regulators, including σ28 (encoded by a gene called FliA) and its anti-sigma factor, FlgM. The sigma factor σ28 is, in turn, required in order to activate the class III promoters. Before the construction of the Hook-Basal-Body has been completed, one obviously does not want the flagellin monomers to be prematurely expressed. Thus, in order to inhibit the σ28, its anti-sigma factor FlgM keeps it away from the RNA polymerase holoenzyme complex. When, finally, the Hook Basal Body has been completed, the anti-sigma factor FlgM is secreted, remarkably, through the flagellar substructures which are produced by the expression of the Class II hook-basal-body genes. The Class III promoters are then finally turned on by the sigma factor σ28, and the flagellum is completed. These Class III promoters are responsible for the expression of flagellin monomers, the chemotaxis system and the motorforce generators. In all, more than 50 genes are necessary for flagellar self-assembly to take place.

The flagellar apparatus can basically be divided into two key components: the secretion system and the axial structure. As discussed in my previous piece, the key components of the axial structure are FlgG for the rod, FlgE for the hook, and FliC for the filament. Each of those has its own respective cap protein, by virtue of which it assembles. The cap protein for FlgG is FlgJ; for FlgE, it is FlgD; and for FliC, it is FliD.

The cap protein FliD remains at the tip of the filament in the finished product. Some other components of the axial structure — FlgB, FlgC and FlgF — connect the rod and MS ring complex. The hook and filament are connected by FlgK and FlgL.

The structural foundation of the flagellar apparatus is the MS ring complex. When the C ring and C rod attach to the cytoplasmic surface of the M ring, the complex begins to secrete flagellar proteins.

One particularly remarkable feature of the flagellar assembly is the construction of the rod structure (which is built through the peptidoglycan layer with the assistance of cap protein FlgJ). The outer membrane represents a road block such that it cannot continue to grow. Incredibly, the outer ring complex actually cuts a hole in the membrane to allow the hook to continue to grow beneath the FlgD scaffold until it reaches a specified critical length, upon which the substrates which are being secreted switch from the rod-hook mode to flagellin mode. FlgD is then replaced by hook associated proteins (or HAPs) and the filament continues to grow. This, of course, only works correctly in the presence of the cap protein FliD; otherwise the flagellin monomers are lost.

Alison thinks that that is creationism. Notice how often the Bible was cited? That’s right. It wasn’t. This guy is not even a young-earther, and he leans towards common descent, too. (UPDATE: He just post a pack of research against common descent last week and now he is leaning away from it)

Don’t read that Alison – it’s nasty science, and it would offend your beliefs! Just stick to writing the stuff you’re good at. And for Darwin’s sake, don’t try to debate the science with anyone who disagrees with you. Don’t read any books that disagree with you. And don’t read any research papers and cite them in your writings. Just mark the ID scientists down – that’s the safest way to silence them. Ram your religion down their throats. Who cares about evidence? Not you. Otherwise you would be reading theirs, and writing some of your own.

UPDATE: Lenny has a good post about biases at Come Reason.