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Questions college students should ask science professors

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Students who ask science professors certain questions will be the ones who’ll appreciate the weaknesses in various anti-ID or anti-creation theories. Preferably they’ll ask after they’ve gotten an “A” in the class, maybe even after they’ve gotten their diploma. The ideal IDist or creationist student can hopefully score in the 99th percentile on evolutionary tests, but still understand the difficulties with anti-ID theories like Darwinian evolution.

Jonathan Wells had his list of questions that high school students should ask their biology teachers, and there have been some good responses, thus I didn’t think Wells’ list provided pointed enough questions.

So I’m developing a list for college students interested in ID or creation science. Here are some questions off the top of my head which were occasionally inspired even by anti-IDists or anti-creationists:

1. How can functional proteins form without ribosomes or ribosome-like machines?

2. How can natural selection or neutral evolution evolve poly constrained DNA or any poly constrained systems in general?

3. How did the first organism regulate protein expression and cellular development without regulatory elements or developmental mechanisms?

4. How did any vital organ or protein form given the absence of the organ would be fatal? Absence of insulin is fatal in organisms requiring insulin. How did insulin become a vital part of living organisms? If you say it wasn’t essential when it first evolved, then how can you say selection had any role in evolving insulin without just guessing?

5. How did DNA evolve in a proteins-first or RNA first scenario?

6. How did amino acid homochirality evolve since the amino acids in biotic soup experiments are racemic, plus homochiral amino acids spontaneously racemize outside of living systems? How about DNAs and sugars? If the expectation value is 50% left, how do 100% left or right forms emerge in pre-biotic soups, and more importantly how is homochirality maintained long enough for chemical evolution to work?

7. Don’t dead dogs stay dead dogs and doesn’t Humpty Dumpty stay broken?

8. Describe how a partially functioning ribosomes or any partial implementation of the DNA code could operate in a working cell, and how a such cell can operate without such vital parts.

9. Are most laboratory and field observations of evolution reductive rather than constructive of new coordinated functions? For the sake of argument, let extinction can count as reductive evolution. When bacteria evolve antibiotic resistance, what proportion of cases involved evolution of a new complex protein?

10. Cite an experiment or field observation where a substantially new protein was evolved in real time or is expected to evolve in real time over the next few generations. Nylonase is the most cited example, but that wasn’t a substantially new protein. But even granting that, how many complex proteins are evolving in the biosphere versus those getting lost forever.

11. What new trait in human populations do you expect to become genetically fixed in all 7 Billion or so people, and how fast do you expect that trait to overtake the population in how many generation? If you can’t identify convincingly one or a few traits, how then can you argue for evolution of so many traits in the past?

12. If a species has a population of 10,000, how can selection act in a particulate manner on 4 giga bases of DNA individually? Wouldn’t such a large genome relative to small population size result in lots of selection interference, hence wouldn’t most molecular evolution be neutral of necessity as Kimura asserted?

13. Do geological layers involving permineralized fossils or other kinds of well-preserved fossils require rapid burial? If the burial process is rapid, does it really take millions of years then to make that particular layer that has fossils? If you find C14 in Cambrian fossils not the result of contamination or lab error, does that mean the fossil had a more recent time of death than 500,000,000 years? Given the half lives of DNA and amino acids or other decay processes of biological organisms, how can we account for preservation of these biotic materials for far longer than indicated by their chemical half-lives?

14. Can geological strata form rapidly? What about the university experiments and field observations that show strata can form rapidly? If they can form rapidly, and if fossil presence demands they form rapidly, doesn’t that suggest they formed rapidly?

15. If redshifts in the Big Bang model are discovered to be possibly caused by other mechanisms than relative motion, wouldn’t that put the Big Bang in doubt? Wouldn’t that also raise questions about stellar distances?

16. What is the farthest astronomical distance that can be determined by parallax or very long base line interferometry, and what fraction is that detection distance relative to the claimed size of the visible universe relative to the Big Bang? How do you account for Super Nova by stars not inside galaxies? If so, doesn’t that mean there is a higher probability of Super Nova in a star outside a galaxy by a factor of hundreds of billions if not more? If so, why should this be?

Feel free to list your ideas or improve the list above.

Remember, the goal is the question will be so powerful, that when the student asks the scientist or other authority figure, and when the scientist is forced to admit the truth, the student will realize the weakness in mainstream claims. I didn’t list vague or ambiguous soft ball questions. The strength of the biology questions is in complex design details, not some 19th century Darwinian view of the simplicity of life. I added a few YEC-friendly questions just for fun. A good scientist ought to welcome and value skepticism and hard questions.

I once gambled a little bit on a weaker question that a creationist biology student should ask her anatomy and physiology professor regarding the evolution of hearts. I basically suggested she ask about how the intermediate plumbing can work if it is not all wired-correctly in the first place. Here for example are the some various reptilian hearts:

how does it evolve from a fish heart?

When that biology junior posed that question, she came back the next week at our ID/Creation meeting beaming. She said, “you’re right, there are no transitionals!” I realized then whatever I said might not be as powerful as what professors are unable to say when asked the right questions!

Feel free to add your questions in the comment section or CEU Questions students should ask professors. I’ll be collecting them at a website for future reference which I can direct students to. Thanks in advance.

Photo credits: Encyclopedia Britannica, Quia.com.

Comments
Sal quoted:
From transcription of DNA
Yes, a little detail you missed in your original response, DNA had to be there too!
But Sal has only quoted a fraction of my text. It continues thus:
From transcription of DNA (or RNA if proteins preceded DNA rather than vice versa) by a ribozyme rather than an enzyme.
That's naughty, Sal. Add to the above sleight of hand that you chopped up and reordered my response without indicating such, and the fact that my response was about the necessity of ribosomes for protein formation from mRNA (so the presence/absence of DNA was no more missed in my answer than a description of mitochondria or even the Taj Mahal) and we're left with yet another example of creationist 'debating' tactics. Roy Roy
Sal, use your design inference. It’s obvious CandiceC is a bot.
Here we go again arguing about the identity of the designer. My bet is it's some Ukranian guy actually visiting websites that were targeted by a spider. So lets run an experiment and see if the designer shows up. Oh CandiceC, oh CandiceC can you show up and prove the designer exists? scordova
Sal, use your design inference. It's obvious CandiceC is a bot. JoeCoder
Not to put you on the spot, but how much of this evidence had you heard about when you scoffed at the claim that the Big Bang was supported by a “mountain of evidence” and accused astronomers of having “mountains of circular reasoning” instead?
All that you cited above including the fact the supposed time dilation in SN could be due to Malmquist bias and other factors. I studied physics and cosmology at the school that a scientist was awarded the Nobel Prize for the discovery of Dark Energy.
As for the Big Bang itself, the mere existence of the CMB is a huge phenomenon, it has a perfect “black body” spectrum proving that the universe was once filled with a hot opaque medium, i.e. it was utterly different from its present state.
How do you know it's everywhere, it could be a local bubble that surrounds us for all we know. The question of insufficient intergalactic shadows suggests MBR ubiquity is in doubt. The arguments over this are still going back and forth. The MBR is embarrassingly smooth, and In general, you look hard enough, you're going to find an anisotropy somewhere! Further the fixes of dark matter and dark energy are dubious to this day and the Galaxies looking mature at high redshifts are suggestive we have no idea of what's what.
Massive surveys have been done of the distribution of galaxies in the universe, galaxies are clustered in filaments and sheets leaving huge galaxy free voids hundreds of millions of light years in diameter. This observed distribution of galaxies (called “baryon acoustic oscillations”) fits the pattern predicted by the Big Bang.
Yes, filaments with dark matter fortuitously sprinkled in the right spots. Plus the voids are nicely positioned to say the fingers of God are pointing at us! That's OK if one is not swearing by the Copernican principle. scordova
@64 You ask: "What mountain of evidence?" You claim there is a serious problem with the Big Bang because there is some evidence that time does not slow down (time dilation) for fast moving (high redshift) quasars which, if true, would imply that quasars are not receding from us and therefore the universe is not expanding. The evidence is that those quasars which are at higher z (redshift) do not seem to vary in brightness more slowly than those at lower redshift. Unfortunately, no one knows precisely why quasars vary, quasars are thought be immense black holes which are engulfing large amounts of matter. The infalling matter radiates prodigiously. The problem is that high redshift quasars are billions of years older than low redshift ones and the factors which make quasars fluctuate are unlikely to remain unchanged over billions of years. In particular, the universe was much denser at high redshift which should affect the infall rate. So it is not clear whether or not the effects of time dilation would be counteracted by changes in the rate at which quasars vary. So there is only one line of evidence against the Big Bang and it has problems, while there are multiple solid arguments for the Big Bang. There are 3 independent arguments for time dilation 1) Type Ia supernovae should and do show time dilation (high redshift Type Ia's fade more slowly) see a)The Astrophysical Journal, 626:L11–L14, 2005 June 10 and b) The Astrophysical Journal, 682:724-736, 2008 August 1 Ref [a] is cited in the paper on quasars which you mention (but you didn't give the reference, bad habit that!) The reference is: Monthly Notices Royal Astron. Soc. 405, 1940–1946 (2010). Since the fading time of Type Ia's should be the same regardless of the age of the universe (same natural laws) they are a more definitive test of time dilation due to the expansion of the universe than quasar fluctuations. 2) Another test of the expansion of the universe is the surface brightness test which can be applied to 1) to the cosmic microwave background (CMB) radiation itself or 2) elliptical galaxies. See THE ASTRONOMICAL JOURNAL, 122:1084-1103, 2001 September. From their abstract: "We have also used the high-redshift HST data to test the 'tired light' speculation for a nonexpansion model for the redshift. The HST data rule out the tired light model at a significance level of better than 10 sigma". 3) And then there are the tests of the prediction that the CMB was hotter at higher z, (i.e. the universe cooled as it expanded, so at higher redshift it was less expanded and therefore hotter.) See Astronomy and Astrophysics. Vol 482, L39-42 (2008). Astronomy and Astrophysics. Feb. 2011 Vol 526, L7. Astronomy and Astrophysics. Mar. 2013 A109 Those are the 3 tests of time dilation as cross check on whether the universe is really expanding. As for the Big Bang itself, the mere existence of the CMB is a huge phenomenon, it has a perfect "black body" spectrum proving that the universe was once filled with a hot opaque medium, i.e. it was utterly different from its present state. And then there are the fine details of the CMB such as the predicted ripples (acoustic peaks), the Plank and WMAP satellites have found 5 of them now. Besides acoustic peaks there are the predicted (and observed) complex patterns in the polarization of the CMB (E modes and B modes). Massive surveys have been done of the distribution of galaxies in the universe, galaxies are clustered in filaments and sheets leaving huge galaxy free voids hundreds of millions of light years in diameter. This observed distribution of galaxies (called "baryon acoustic oscillations") fits the pattern predicted by the Big Bang. In summary, astronomers are testing the Big Bang model in every way it can be tested and have gone to great efforts in advancing in observational technology in order to do so. That is exactly what they should be doing. You complain that Hawkins' quasar evidence is being "ignored." Science is about doing things, so the real problem is that no one knows what to do to follow up Hawkin's results. There is no point in redoing Hawkins' analysis unless you think he got it wrong. Lacking some understanding of how to reconcile Hawkins' results with the evidence for the Big Bang, the best approach is to keep on testing the Big Bang every way it can be tested. And astronomers are doing that. Not to put you on the spot, but how much of this evidence had you heard about when you scoffed at the claim that the Big Bang was supported by a "mountain of evidence" and accused astronomers of having "mountains of circular reasoning" instead? tlawry
CandiceC, I hope you're not offended if I ask, but are you some sort of AdBot or guy tasked to post on forums and blogs to advertise essay services? I got this Honey Pot report on your IP:
This IP addresses has been seen by at least one Honey Pot. However, none of its visits have resulted in any bad events yet. It's possible that this IP is just a harmless web spider or Internet user. If you know something about this IP, please leave a comment. Lookup IP In: Domain Tools | SpamHaus | Spamcop | SenderBase | Google Groups | Google Geographic Location Ukraine Spider First Seen approximately 2 months, 1 week ago Spider Last Seen within 2 months, 1 week Spider Sightings 1 visit(s) User-Agents seen with 1 user-agent(s)
Your posts at UD seemed to be well written ads. Here is a list of what you wrote before:
CandiceC amanakova4@gmail.com 217.77.215.214 Submitted on 2014/04/11 at 4:30 am I in general think that students should not be afraid to ask any questions they want to. It is just I have seen so many students being afraid to ask something as they were afraid to look silly in their professor’s eyes, so they were ending up at Essay Online Store or some other helpful website where they could use some help with home assignments. Students should never be afraid to ask questions. Questions college students should ask science professors 71 View Post CandiceC Submitted on 2014/03/17 at 3:40 am The very first thing that is so wrong about higher education is that it is so unaffordable for many young people. I am sure we are missing to educated potentially great economists (Economics College Level Papers for Students), educators, scientist who could find the cure for cancer and so on as for. And the only reason is children monetary incapable for the university or the college. It is so not fair. So the entire system needs to be broken in order to fix higher education. It is my personal opinion. What’s wrong with higher ed?: “Science has precisely nothing to tell us about values” 1 View Post CandiceC Submitted on 2014/02/28 at 3:02 am I am sure that so many people (possibly all of us) has at least once asked exact same question. But do we know the answer? I guess I can call it a tradition. But this is a tradition with too many responsibilities and consequences. I would not want education to be the same as it is today. Education should not be so closely related to a debt. It has to be related to great achievements, admission essays (order college papers from Essay Online Store), and students’ research projects and so on and so far. So why are you going into debt for higher education? 6 View Post CandiceC Submitted on 2014/02/20 at 12:42 am Planning is very important for education. If many people think that it is ok to simply come to college and study. No, they are wrong; they need to plan their personal education system. This way it would be easier for students to succeed, not to miss deadlines on their academic assignments such as students’ research papers in Economics, for example. So yeas, planning is vital here. Thank you for the short post New at The Best Schools I 1 View Post CandiceC Submitted on 2014/01/24 at 2:43 am Yes, you are absolutely right that we do not really care as much as we should. But I do not understand why? And, by the way, by “we” I mostly mean the government which shutting lots of funding, well, in some cases, reduces it. The whole system is pretty messed up and yet still we do nothing about it, we just and watch and let bad things continue to happen in the education segment. I mean is that really what we should be doing? Why not finally speak up of the existing problems: low test results scores around the country in writing (look for safe website to purchase paper from), reading, math, science, etc.! New at The Best Schools I 1 View Post CandiceC Submitted on 2013/12/23 at 3:15 am Looks like STEM jobs have been very popular lately, but it is not like I can actually understand why. I understand that everyone wants to become certified engineers but we also should remember about other professions. Like, we always lack qualified writers (find professional writers to compose academic level essays), certified teachers and many others. All I am trying to say is that the government should create conditions where students would want to study different subjects as the compensation and the growth possibility is present everywhere, but it is a long path for us to take. New at The Best Schools II 1 View Post CandiceC Submitted on 2013/11/24 at 12:36 pm You know, I used to think that writing is not that complicated and there are no special skills are required to actually write a decent essay for example. But I was wrong. This is something that is difficult to do, especially when you have a deadline and you are completely unfamiliar with the topic. So the only solution for me was to use this helpful service. I have found it so much easier to trust professionals with writing my essays all the time from now on! New at The Best Schools I 1 View Post CandiceC Submitted on 2013/11/12 at 3:25 am There are so many questions are being raised in such a small post. And unfortunately, there are no positive answers to them. No matter what angle you are looking on education from, there are problems which require to be fixed. I like that you’ve noticed a problem with editing and yet still everyone thinks that we have no problems with good writing at all, but isn’t that the reason why students and other people apply to different writing services to get a qualified writing help in a first place? Still, everybody keep on talking about math, reading and science as if these are the three most important subjects ever. New at The Best Schools I 1 View Post CandiceC Submitted on 2013/10/16 at 3:16 am Everybody has a right to believe in whatever he thinks is right for him. But when it comes to schools, well I do not think that this is right. Maybe I am saying this because I am not an atheist just like the majority people are. But think further, what will children write in their essays when they will be sending their applications to colleges? How will such information be accepted by the board of education? But from another side again everyone has a right to think that way as we live in a democratic country! Candice from dissertation writing service at MyEssayService Online An example of why atheist creation stories should not be taught in tax-funded schools 9 View Post CandiceC Submitted on 2013/10/07 at 1:37 am Here is the trick: no one wants to go with the lowest price education. We all know that the lower does not necessarily the better. But unfortunately not many have an option to choose. Unless of course they choose to study online, which I think is great. It is cheaper (but I do not know how much cheaper though), you are basically in charge of your classes and home assignments. Besides, it is very convenient to do home work online as you can easily get academic help at MyEssayService as they can write professional essays, term-papers, dissertations and so on. So yes, it is smarter to study online these days. New at The Best Schools 4 View Post CandiceC Submitted on 2013/09/10 at 1:31 am America used to be a country where everyone could easily say what he was thinking about without being punished for that. And the main force were students who were not afraid to show their most outrageous opinion in essays, research papers and sometimes even dissertations (please check MyEssayService for more information). Yes, this time has gone already. It is time to face the truth: it is very difficult to get heard unless there is a big crowd of people who have same opinion and yet still no one can guarantee success. Same thing with students: they are simply being afraid of consequences and I can understand them!
scordova
I in general think that students should not be afraid to ask any questions they want to. It is just I have seen so many students being afraid to ask something as they were afraid to look silly in their professor’s eyes, so they were ending up at Essay Online Store or some other helpful website where they could use some help with home assignments. Students should never be afraid to ask questions. CandiceC
For the geology questions I would also recommend adding how a deluge could have rapidly deposited the layers we observe. The cosmology questions are also very good! Had not seen those before. Evidences of the falsity of general relativity, how no death took place before the Fall, and things like the Shroud of Turin are also proofs I have used to question arrogant Darwinists and to show how many answers they are lacking! TruthCrusader
Couldn’t you start with a smooth surface, followed by a bump on each side? And then another pair of bumps, and so on?
Then maybe I should put on a list of things worth looking into, I'll remove it from the list of "vetted" IC questions. Maybe what to do is write a thread for each of the separate IC systems and see if ID proponents think it is good enough. The evolution of hearts was one I considered shaky, but I tried it anyway. I think there is no harm in actually getting students to investigate and find out what arguments are good and bad if they are the sort that is fairly convinced ID is true, but just want to fish for the best arguments. They might find some gems. I surely can't pull the project off on my own! scordova
mechanical gear evolution
Like in the insect? This seems like a particularly weak point. Couldn't you start with a smooth surface, followed by a bump on each side? And then another pair of bumps, and so on? I'm sure it's much more complex than that at the molecular level, but that can't be articulated in a quick argument, nor do I expect anyone has even studied it. JoeCoder
From Neil Degras Cosmos Tyson himself:
“question everything, especially those things that everyone else took for granted.”
scordova
In light of the very good feedback and criticisms, I've tentatively decided to make at least 5 lists: 1. core list of basic questions that should be above reproach, that are educational, and actually questions that are stated in professional literature, and which scientists do not have good answer for. For example, geneticist George Church himself suggested IDists raise the issue of the ribosome, so I did not have to make that one up. Questions of that variety will make the core list. 2. a list of raw quotations from where the core list came from. It will at least show the references that helped make the core list. The reason I separate this out is that it won't be quite so streamlined, but it shows evidence of where the questions came from professional literature. 3. list of IC and specific questions that are credible but aren't supported by the mainstream. Examples: A. mechanical gear evolution B. Trochlea evolution C. heart evolution They are legitimate questions, but I haven't necessarily seen something like a paper in biocomplexity that raises the issue. Maybe this highlights a need to find a way to vet such ideas. For example there are some kinds of mimicry that are powereful, but I'm not totally convinced it can't arise from selection. I could list the IC examples from Darwin's Black Box. That's a good list, and it has had lots of public peer review. I think these sorts of questions would be especially beneficial to biology students in their particular disciplines. A student of physiology and anatomy might appreciate a different variety of questions than a student of cellular or molecular biology. I want to see what sort of questions will be particularly helpful in seeing the failure of certain mainstream claims. One reason I particularly liked the heart evolution question is it takes precedence over things like Tiktaalik. It makes the student think hard about soft tissue evolution even in principle, and why just finding fossils that like Tiktaalik might not even in principle prove gradual evolution of important systems. 4. Theoretical and empirical problems with Darwinian evolution 5. The FRINGE topics lists. I wouldn't say these are questions that students will necessarily ask. They explore fringe topics for those interested. They are good topics, the student will learn by even understanding the question, but it doesn't have quite the mainstream support of the core questions. It will take time to develop quality lists and they will probably undergo revision. For myself, I was one good enough terms with some professors I was able to ask non-threatening fringe questions. I once asked Dr. Trefil about variable speed of light, and he said he studied the topic himself and the idea had fallen out of favor. I was very grateful for that because I became properly more skeptical of the whole thing. I also asked two professors (of classical mechanics) about Eric Laithwaite's (a respected engineer who pioneered magnetic levitation for trains) claims about gyroscopy. I learned something and have since rejected Laithwaite's claims. Finally, over time I hope the students themselves will provide feedback as to which questions were good and bad and help the list get periodically amended. scordova
Dr JDD @ 26, @ 39, @ 55 Interesting comments. Thank you. Dionisio
Sal@61, If Cepheids are a thorn in your side, how do you deal them?
Study them, and be willing to admit I'm wrong. Hence, I might revise the above list and withdraw a particular question. That's why I posted this thread to solicit feedback. I don't want to pass on questions that are too far out on the fringe. I'm thinking the Cepheid evidence is pretty good at this stage. Even in the remote chance we're misinterpreting the Cepheids, there isn't enough evidence to overturn the mainstream view. By way of contrast, I don't think that is the case for Quasars. The absence of time-dilation to redshift in quasars discovered by Mike Hawkins at the Royal Observatory should have given huge pause to the Big Bang paradigm. So far it has been ignored.
Quasars, the massive, enigmatic and energetic centers of distant galaxies, have long fascinated us with their bizarre behaviors. Why do they pump out so much energy? Why do they produce the radiation that they do? How did they affect the early universe? A recent publication, however, finds the a lack of bizarre activity of quasars that is, well, bizarre. Mike Hawkins from the Royal Observatory in Edinburgh searched for, and did not find evidence for, so-called time dilation in distant quasars. Time dilation is a counter-intuitive, yet actual, feature of Einstein's special relativity in which time slows down for an object that is in motion relative to another. Since the universe is expanding — and the distant quasars are racing away from us — a clock placed in one of these distant galaxies should be running more slowly than a clock we have on Earth. Therefore, the effects of time dilation for distant objects can be measured if we can observe the ticking clock in the distant galaxy. HowStuffWorks: Does time change speed? Time dilation explained. Hawkins took advantage of the fact that quasars blink. This blinking, or variability, can be viewed as the "ticking clock." He used data from quasar monitoring programs stored on photographic plates to measure the timescale of the blinking. Looking at the timescales for two groups of quasars, one distant and the other even farther away, there was no measurable difference. That meant no time dilation: meaning that for both groups of quasars, the clocks were the same. This could mean several things. could be a sign that the universe is not expanding., it could indicate that quasars are not really what we think they are. However, for either of these scenarios to be true, you'd have to explain away or disprove mountains of evidence in favor of these models.
What mountains of evidence? Mountains of circular reasoning that seems to concoct ad hoc explanations for every inconvenient observation. To quote Larry Moran, maybe, "I don't know" is a good answer at this stage. scordova
Question: 1a. Does life appear to be a product of design? (DNA coding, cellular machinery, origin, etc.) 1b. If life appears to be designed, on what scientific basis do we I. exclude the possibility of design, and ii. exclude research into detecting whether or not the seemingly designed features are actually designed features via forensic or other method? johnp
Sal@61, If Cepheids are a thorn in your side, how do you deal them? Henry Crun
tlawry, Great response and criticism! Yes, cepheids are a thorn in my side. :-) Welcome to UD. Sal scordova
AFAIK the farthest object with a purely trigonometric parallax is a star forming cluster near the center of the Milky Way galaxy at 7.9 kpc (25,800 ly) (see The Astrophysical Journal, Volume 705, Issue 2, pp. 1548-1553 (2009). If you relax slightly the requirement of purely trigonometric parallax you can get a geometric parallax by doing VLBI on water maser clouds orbiting black holes in the centers of galaxies. The shifts in the maser frequencies give the orbital speeds, comparing speeds to the change in position on the sky gives the distance. Galaxy NGC4268 is at 7.2 +- 0.3 Mpc (23.5 million ly, NATURE |VOL 400 | 5 AUGUST 1999 p. 539), Galaxy UGC 3789 is at 49.9 +- 7 Mpc (162.7 million ly see http://arxiv.org/abs/1207.7292v2), and Galaxy NGC 6264 is at 144 +- 19 Mpc (470 million ly http://arxiv.org/abs/1207.7273v2) So you can get direct geometric distance measurements out to half a billion ly. These distances can be cross checked against the standard distance measurements such as Cepheid variables. The HST found 281 Cepheid variables in NGC4268 giving yet another calibration of the Cepheid distance scale. (The Astrophysical Journal, 652:1133Y1149, 2006 December 1) Another massive calibration of standard techniques will come from the Gaia satellite which was launched last year and will measure the distances of a billion stars in our galaxy to high accuracy. tlawry
scordova @ 57
In fact Dr. Hunter’s article is the first google hit I got regarding “histone evolution” Lol!
That's ironically funny! :) Does that mean that the Darwinian propaganda machine is losing momentum? Or is it that undeniable facts and evidences are gradually popping up everywhere, as more data keeps coming out of research? Dionisio
scordova @ 46 That's a good idea. Thank you. Yes, agree, graphical tools usually work better than many words, specially to explain complex concepts like these, which include heavy duty engineering design that exceeds any system created by humans so far. Dionisio
Read specifically about the modifications of histone and the “histone code” and how incredibly complex it is (mono-, di- and tri-methylation of lysine exquisitely distinguished by regulatory proteins). It is truly astounding. It is also odd that archaea have histones but bacteria do not, but all eukaryotes do (and strongly conserved).
Ok, suggested question:
How did histones and histone codes evolve? Also how did hitstone evolve in archaea and eukaryotes but not in bacteria?
Cornelius Hunter has a really interesting take. He argues selection on histones is actually weak, which to implies (to me anyway) selection can't play much of a role in histone conservation. How evolutionists stole histones In fact Dr. Hunter's article is the first google hit I got regarding "histone evolution" Lol! scordova
Sal you turned my evidence of design into another criticism of evolution! Which is what I thought we were trying to avoid since we already had too many :P A few points: 1. This argument (or at least my familiarity with it) is not ready for prime time. I need to track down and verify primary sources and quantify each point. 2. I would stress that redundant genes are not paralogs but operate in different ways. Otherwise it can just be claimed they all arose through duplication, which seems reasonable enough. 3. Will most professors be familiar with what "scale-free" means? JoeCoder
JoeCoder, It's a tough one because the theory of evolution can accommodate any finding therefore it is not something that can be challenged or analysed. Therefore you have to resort to showing the impossibilities or rather extreme unlikelihood of it explaining life as we know it. What do I mean by the theroy of evolution can accommodate any finding? Example (10yrs ago): All this extra non-coding DNA that does not encode for genes has no function - it is the by product of evolution, left over, and strong evidence that we are the product of mere evolution from a common ancestor. (After findings of "junk" DNA having function): Evolution is incredibly efficient process and has selected the DNA it needs for life to function optimally over many millions of years. Example #2 (Vestigal organs/structures): These are left-over structures that were only useful in a previous ancestoral form, and are useless structures/organs now, a by-product of evolution providing proof that no designer would be so poor as to have these functionless parts present. (On finding function for vestigal organs/structures): Evolution has allowed for the introduction of organs that are highly useful for optimal growth, survival and reproduction. It is a remarkably efficient process that is not wasteful and very directional. This rationale is the approach to any and all findings that show more complexity than once thought, or give explanation for something that was previously attributed to left-over or a by-product of evolution. Therefore how can you actually provide someone of this mindset with any real evidence for design, when they will take everything with the premise that it occurred from evolution (as evolution is in fact, an axiom). You have little option but to highlight the illogical nature of the arguments, and how following it through to its ultimate completion makes little sense in terms of natural laws we know, observations we make, and probabilities of likelihood. Not long ago, I read an article about duons. The finding recently that there may be a second layer to the DNA triplet codons, in gene regulation. The article was pitched "the code has evolved to also include this additional information..." Scroll down to the comments and of course you get a post straight away from someone saying, "see, more proof of evolution against those dumb creationists. They know nothing!" Ironically, I fail to see how a "duon code" is in anyway supportive of the evolutionary theory. If anything, it is the opposite. It increases the complexity of DNA, thus decreasing the probability of arisal from chance on a simplistic view, but then it also raises questions about what "redundant" mutations are truly redundant? When people see a change in the codon that still encodes for the same amino acid, it is apparently redundant. But if the duon code is true, that could imply that this change has an effect on the regulation of the gene, therefore it is not redundant! So how in any intellectual sense is that a proof or evidence of evolution?! Its not, but evolution is tagged on to any novel finding about life as it is viewed as a fundamental cornerstone of understanding every bit of biology around us. Therefore, if you have your cornerstone of evolution on which Biological sciences are considered to be built, anything that tries to chip away or remove that cornerstone in their mind is threatening the whole of science - it will all come tumbling down. So of course they will personally attack, of course they will be dismissive and largely not engage, of course they won't see it from your view, and of course they will portray you falsely and also portray it as "non-science". Add into this mix the fact that most naturalist evolutionists do not recognise or understand that most IDers accept a significant level of evolution (natural selection without macro-evolution, which is purely an extrapolation of natural selection and nothing more) Your hope with the ID movement cannot be to sway those with a firm belief in naturalistic evolution to acceptance of ID, as it is easier to persuade a life-long Buddhist towards atheism, or a life-long Muslim to Judaism. Your battle is informing those who are undecided, who are unaware, who sit on the fence, who get the media side pushed by the Dawkins and the like of the world with their incredible bias and dismissive belittling nature, and inform them that actually, this is not a given fact. It should not be an axiom; that there are equally viable (we could argue more viable) alternatives and ID is not pseudoscience or religious superlative. The more you can spread the questions, highlight the problems, encourage questioning, reasoning and frankly REAL science, the more understanding of the problem there will be and we might start to see a shift towards the middle ground. The public's perception needs to be changed to accurately reflect both sides of the argument, not one side, and you will not do this by trying to only engage with dismissive and belittling attitudes. But what does this mean for us? It is the classic "lead by example." There is nothing wrong with accepting good evolutionary arguments, with saying "I see your point and it supports your theory." I think people who are not in the religion of naturalistic evolution and open to discussion/engagement or unaware of the problems with evolution will be more engaging, more willing to accept and listen to your arguments if you are someone who can try to not show extreme bias by instantly rejecting anything the other side says. That is how staunch naturalistic evolutionists react. Instant rejection. Cannot possibly agree with any argument an IDer makes. IDers cannot be like that - they have to show vigour in seeking a true scientific approach of examining the evidence and making conclusions on this - even if the evidence does not always seem to favour them. JD Dr JDD
JoeCoder, Thanks! In light of what you said, suggested question:
How can genetic redundancy evolve and be maintained since in principle it will be mostly invisible to selection? The random walks of neutral evolution cannot serve as explanation either since random walks are not expected to make functional genes. Selection doesn't plausibly act on individual nodes of a scale-free, redundant genetic system. From an evolutionary standpoint, genes with overlapping functions implies minimal, if any, selective pressures acting on these genes. One therefore expects that the genes participating in such buffering of mutations will be subject to severe mutational drift diverging their functions and/or expression patterns with considerably high rates. For paralogous genes this has been demonstrated.
scordova
Sal, you should really read Peter Borger's paper on Genetic Redundancy in the Journal of Creation if you haven't already. Borger notes that just like in our own most critical designs, genetic systems are highly redundant with fallbacks and failsafes ready for when primary systems fails. These systems are never used unless the primary systems fail and therefore can't be maintained by selection and should deteriorate through genetic drift. Moreso they don't show similarity to the primary systems so they couldn't have been created through duplications. Of course what evolution can't maintain it certainly can't create. Dennis Noble had similar points in his talk that got passed around several months ago. At 16:27:
Simply by knocking genes out we don't necessarily reveal function, because the network may buffer what is happening. So you may need to do two knockouts or even three before you finally get through to the phenotype. ... If one network doesn't succeed in producing a component necessary to the functioning of the cell and the organism, then another network is used instead. So most knockouts and mutations are buffered by the network.
And at 19:40:
Is this an unusual result, ... or is it general? This study went through all 6000 genes in the organism yeast. knocking them out one by one. 80% of the knockouts were silent. So this physiological process of buffering against gene change is general. It's usual in fact. Now that doesn't mean to say that these proteins that are made as a consequence of gene templates for them don't have a function. Of course they do. If you stress the organism you can reveal the function. .. If the organism can't make product X by mechanism A, it makes it by mechanism B.
The well known (within my industry at least) mechanical engineer turned programmer Walter Bright talks about how critical it is to have redundant but non-homologous components in reliable systems:
All I know in detail is the 757 system, which uses triply-redundant hydraulic systems. Any computer control of the flight control systems (such as the autopilot) can be quickly locked out by the pilot who then reverts to manual control. The computer control systems were dual, meaning two independent computer boards. The boards were designed independently, had different CPU architectures on board, were programmed in different languages, were developed by different teams, the algorithms used were different, and a third group would check that there was no inadvertent similarity. An electronic comparator compared the results of the boards, and if they differed, automatically locked out both and alerted the pilot. And oh yea, there were dual comparators, and either one could lock them out. This was pretty much standard practice at the time. Note the complete lack of "we can write software that won't fail!" nonsense. This attitude permeates everything in airframe design, which is why air travel is so incredibly safe despite its inherent danger.
So I think this is a pattern that both has eerie similarty to our own designs, while also being the opposite of what Darwinian evolution should produce. However, it's something I hope to study more before presenting it as an argument. JoeCoder
Here is Moran's response to the Humpty Dumpty question: http://sandwalk.blogspot.com/2014/04/jonathan-wells-proves-that-life-must.html
This YouTube video is described as "The most ignorant 82 seconds you'll ever see." I don't know about that. I been around IDiots for quite a long time. It may not be the "most ignorant" but it's surely in the top ten. Remember, this is the best they've got. Really. Trust me on this.
What did Wells say that brought about Dr. Moran's response?
“Even if Miller’s experiment were valid, you’re still light years away from making life. It comes down to this: no matter how many molecules you can produce with early Earth conditions, plausible conditions, you’re still nowhere near producing a living cell. And here’s how I know: if I take a sterile test tube and I put in a little bit of fluid, with just the right salts, just the right balance of acidity and alkalinity, just the right temperature, the perfect solution for a living cell, and I put in it one living cell. This cell is alive. It has everything it needs for life. Now I take a sterile needle and I poke that cell, and all its stuff leaks out into this test tube. You have in this nice little test tube all the molecules you need for a living cell. Not just the pieces of the molecules but the molecules themselves, and (still) you cannot make a living cell out of them. You can’t put Humpty Dumpy back together again. So what makes you think that a few amino acids in the ocean are going to give you a living cell? It’s totally unrealistic.”
I'm happy to pass Dr. Moran's response to students who asked the Humpty Dumpty question. scordova
Sam, If you have links to videos you would prefer that students watch instead of POL or Unlokcing to learn the workings of the cell, feel free to post links. I'll be glad to pass them on. When I saw a crash course in biology about the translation process, the video wasn't materially different than POL or Unlocking. Feel free to post links to videos you prefer for teaching cellular process like: 1. translation 2. signaling 3. garbage disposal etc. scordova
JoeCoder, It's tough doing this because I have to swallow my pride constantly and be willing to say an idea I put forward is a bad one. If some of the questions are bad, I have to be willing to revise them or withdraw them. I can't in good conscience give junk to students just to save face in an internet debate. Art had some good criticisms, for example. I'm glad science professors like Larry and Art are participating. We'll get to see how they would answer these questions for such hypothetical students. Some of the questions I obviously made up on my own, others I got from literature of professional scientists asking exactly those same questions and having no answers.
I think one improvement we could make is to focus more on patterns in biology that match what’s expected under design, but are the opposite of what evolutionary theory predicts or could do.
This is why I posted this thread. I need other ideas for other people. That Trochlea example was pretty good! That reminded me of the mechanical gear. Few are as openly honest about origins problems as AG Cairns-Smith, but a lot of this follows his own writing on the subject. I hope the science professors on the net find errors in what I wrote as that will help me clean up my question list. I thank them in advance for helping deliver good science to college students. The questions posed are questions, not assertions. Students will learn by pondering the questions. I don't see why, fundamentally speaking, these list of questions should be viewed as bad science. I would hope professional scientists would welcome skepticism and good questions which force them to say, "I don't know." :-) scordova
Larry Moran blogged about this post. I read his blog regularly because unlike our other detractors, he often has some kernels of truth once you filter out all the ad hominems. I think he's right about this point:
The reality is that 99.9% of everything they say is an attack on science and evolution. They don't have any answers themselves and they desperately want to show their flock that scientists don't have any answers either.
I think one improvement we could make is to focus more on patterns in biology that match what's expected under design, but are the opposite of what evolutionary theory predicts or could do. JoeCoder
Re: #46 Is it your position that this video presents a technically accurate representation of the goings-on inside a cell? SamHManning
Interesting questions, Scordova, but I think I might be more impressed, and better informed, if you spent your time producing substantive, supportive science instead of engaging in what seems to amount to little more than attempted 'victory by annoyance'. SamHManning
Dionisio, If you can show a video, that will really help, especially the Illustra Media video "Unlocking the Mystery of Life". The Programming of Life is a bit technical, but I use that too. The impact of the visual experience is more powerful imho than anything we can say. If you are presenting to a Christian audience, you might try following the structure of the argument here, but it is still getting reworked to make it easier to understand: http://www.creationevolutionuniversity.com/idcs/?p=9 scordova
Art sorry for the delays in releasing your comments. FWIW, I set you up an account at CEU if you wish to record some of your comments there. Your objections and responses are especially welcome since you are a professor of biology. I'm sending your CEU user name and temporary password to the e-mail on file at UD. Thanks again for participating in this discussion. scordova
RE: comment # 40 As an exercise for learning, I'm preparing a presentation on this topic for a general (non-biologist) audience. There's much information on this topic out there, but it's hard for me to determine the most valid and accurate answers to those questions. Maybe you can help me with gathering serious reliable information on this subject? Thank you in advance. Dionisio
Sorry – I’m not good with HTC tags and not sure how to quote. The wiki bit is from “Unlike this simplified model…” to “readers, writers and erasers of the histone code are revealed by a growing body of evidence.”
Thanks for your reply. Try this: <blockquote> readers, writers and erasers of the histone code are revealed by a growing body of evidence. </blockquote> Also, there should be an automatic preview if you scroll down so you can see if you tags are working. scordova
Does anyone know the answers to the these simple questions?
What mechanisms determine the fate (functional type & final location) of every cell during different phases of human development from zygote to birth, but specially the first few weeks? How did such mechanism arise gradually? What mechanism determines the timing? Where did that mechanism get from? How did it arise? We know that ongoing research will shed more light on this, but we expect the resulting information from research will reveal wonderfully elaborate choreographies and orchestrations. How did those choreographies and orchestrations gradually arise? How did the intermediate and transitional choreographies and orchestrations look like?
Dionisio
I'm tentatively scheduled to make a presentation to college students in a couple weeks. I'll refer them to my CreationEvolutionControversy.com website that will have a set of questions and observations they can discuss with their fellow students and former professors or professors outside their university (because I don't want them getting into confrontations with current professors). I found the students are in a state of disbelief that the establishment can be so wrong. Their eyes can be opened when they actually ask science professionals to defend Darwinian or OOL or whatever claims. I think I'm going to post with the questions the mechanical gear photo: https://uncommondescent.com/biomimicry/mechanical-gear-found-in-living-organism/ and the Troclea challenge http://kgov.com/PZ-Myers-trochlea-challenge I probably will compile several lists. The list by OOL researchers themselves was pretty good! Unfortunately the link is dead, so here is a cut and paste from the topics of a conference of professional OOL researchers:
Proposed Open Questions in OQOL2014 The following is the 15 open questions for your vote. 01. How can we make ordered sequences of amino acids, or mononucleotides by prebiotic means? This question is in fact never asked in the modern research on the origin of life. Do you agree then that we do not know how to make macromolecular sequences in many identical copies under prebiotic conditions? Do we have to wait for this orderly sequence until the genetic code has been developed? 02. Why is the origin of life still a mystery? Premise: Why is the origin of life still a mystery? The turning point nonlife-life has never been put into one experimental set up-actually it has never be clarified from a conceptual point of view either. There are of course several hypotheses, and this plethora of ideas means already that WE DO NOT HAVE A CONVINCING ONE! The most popular is with the RNA-world prebiotic scenario, which has the advantage of providing on paper a theoretical series of IMAGINARY events, each however with an UNINAMIGINABLY SMALL PROBABILITY (be the prebiotic production of a self-replicating RNA, and its eventual transformation into a catalyst for DNA and independently for protein synthesis) Why should this happen, and what about the genetic code? Aside from the problem of experimental implementation, don’t you think we lack (until now) the capability of intellectually conceiving how the turning point really happened? 03. Is the molecular crowding critical for the beginning of life? Quite a dense concentration of macromolecules in cells: Is it an essential condition for origin of life? If so, how was the concentration acquired before the origin of life? Or, was it a result of the evolutionary process? 04. Can Artificial Life or Synthetic Biology contribute to the origin of life? Artificial life deals with life as it might have been. UP UNTIL NOW THESE EFFORTS HAVE NOT BEEN VERY SUCCESSFUL, and IT ALMOST APPEARS THAT THERE ARE NO FORMS OF LIFE SIMPLER THAN “OUR” LIFE. Do you have any data that imply alternative forms of life (still within the general category of metabolism + self-reproduction + evolvability) with molecules different from the biological ones? Or, do you think that synthetic biology research can provide a model or theory for the origin of life study? 05. Can catalysts come out from the free ticket of thermodynamics? 06. Can we construct real RNA world and RNA-based biological systems in a test tube? At the early stage of RNA world, RNA molecules should have no functional property. What physical or chemical process mediates the selection of specific RNA? Even when functional RNA enzymes are generated, it still remains a challenge to construct sustained self-replication and metabolic system in which multiple RNA molecules function cooperatively. Once we can construct the precursor of a replication system by a set of RNA molecules, is it possible to emulate another path of evolution in a test tube? 07. What is the origin of genetic code?: Investigating DESIGN PRINCIPLE of aa-tRNA and aa-RS? The genetic code is most essential part for the genetic systems. In the context of the origin of life, a major issue on the genetic code is to understand how the materials relevant to genetic code that can translate the sequence of four bases into a polypeptide. … Can we find or design simple aa-RS and aa-tRNA from the cocktail of molecules (e.g., amino acid, tRNA(-like) molecule, and ATP), which might be relevant to the origin of translation and genetic code? What features are required as a mechanism that ensures robust translation? 08. Prior to genetic code: Is the notion of prebiotic cells conceivable? The simplest cells on our Earth contain at least 500–600 genes, and more generally several thousand. This observation elicits the question, whether this high complexity is really necessary for the simplest form of cellular life, also in view of the fact that early cells in the origin of life and evolution could not have been as complex as modern cells…. Do you think it is possible to construct in the laboratory, models of early cells, displaying a kind of primitive cellular life (self-maintenance + self-reproduction + evolvability), based on a number of genes which is one order of magnitude smaller than the present day simplest cells. Say a living cell with 30–40 genes? [I’d like to know how they can come up with even one gene!] 09. What is the list of prebiotic molecules present in primodal cells? The “free ticket” of thermodynamic control is however not sufficient: if a chemist is given all these compounds in any amount he wishes, he would be unable to make life. For making life, one needs a series of additional reactions and products under kinetic control – enzymes and nucleic acids are not with us because they are the most stable chains. Thus, the origin of life can be traced back to the origin of kinetic control. Do you agree with this statement; and how would you envisage the prebiotic evolutionary bridge between thermodynamic and kinetic control? 10. On Contingency vs. Determinism The proteins (or nucleic acids) existing on our Earth correspond to an infinitesimal part of the theoretically possible sequences – the ratio between possible and existing structures corresponds more or less to the ratio between the space of the universe and the space occupied by one hydrogen atom. The above ratio can be interpreted as an indication that our “few” proteins have not been selected primarily because of distinctive properties (such as thermodynamic or thermal stability, solubility, particular kinetic processes of formation etc…) – but rather due to a most significant contribution of the vagaries of contingency. Do you agree with this statement, and with its corollary, that then life on our Earth, which is based on these “few” proteins, is not an obligatory pathway, but is largely based on contingency? 11. How to Make Prebiotically Long Hetero-Peptides or Hetero-Nucleotides? There are no or rather scanty reports in the literature on how to make under prebiotic conditions long – say 30 residues – specific sequences of co-oligopolypeptides (or polynucleotides) in many identical copies containing say five to six different amino acid residues or three to four bases (the Merrifield method cannot be considered a prebiotic method)… Do you agree then that we do not know – neither conceptually nor experimentally – how to make macromolecular sequences in many identical copies under prebiotic conditions? And if it so, would you not conclude that the bottom-up (sentence ends abruptly) 12. On the origin of catalytic cycles The question. How do you envisage the origin of sequentially catalytized reactions in a prebiotic scenario? And can you provide facts or scientific arguments, not simply beliefs, about this critical point? 13. Life as unity or confederacy 14. Universality – What properties of life are universal? 15. What is the physical mechanisms underlying the assembly of primitive cell-like structures?
scordova
Sorry - I'm not good with HTC tags and not sure how to quote. The wiki bit is from "Unlike this simplified model..." to "readers, writers and erasers of the histone code are revealed by a growing body of evidence." JD Dr JDD
Hi Scordova, I’ll admit, I have not given it a huge amount of thought – I am merely perplexed by the complexity of the most fundamental process of life (gene expression and regulation). However my question would be centred perhaps on the epigenetic nature of histones to such an exquisite degree. For example, how did the histone code develop from simple to complex? The histone code allows for complex repression of expression of genes through a series of various modifications. Such modifications include mono-, di- and tri-methylation of lysine (some enzymes can only recognise mono- and di- forms; others the tri- form as well), acetylation, ubiquitination, SUMOlation, citrullination, phosphorylation – the list goes on. Look at what is said about the possible combinations on Wiki: Unlike this simplified model [a modification = repression or activation], any real histone code has the potential to be massively complex; each of the four standard histones can be simultaneously modified at multiple different sites with multiple different modifications. To give an idea of this complexity, histone H3 contains nineteen lysines known to be methylated - each can be un-, mono-, di- or tri-methylated. If modifications are independent, this allows a potential 4e19 or 280 billion different lysine methylation patterns, far more than the maximum number of histones in a human genome (6.4 Gb / ~150 bp = ~44 million histones if they are very tightly packed). And this does not include lysine acetylation (known for H3 at nine residues), arginine methylation (known for H3 at three residues) or threonine/serine/tyrosine phosphorylation (known for H3 at eight residues), not to mention modifications of other histones. Every nucleosome in a cell can therefore have a different set of modifications, raising the question of whether common patterns of histone modifications exist. A recent study of about 40 histone modifications across human gene promoters found over 4000 differentcombinations used, over 3000 occurring at only a single promoter. However, patterns were discovered including a set of 17 histone modifications that are present together at over 3000 genes.[10] Therefore, patterns of histone modifications do occur but they are very intricate, and we currently have detailed biochemical understanding of the importance of a relatively small number of modifications. Structural determinants of histone recognition by readers, writers and erasers of the histone code are revealed by a growing body of experimental data. So how does this evolve? If there is an enzyme that evolves to methylate for example, how does it distinguish between the massive number of sites? You need readers, writers and erasers. Not one, not two – all three. If this suddenly appeared due to random evolutionary chance, you would get all sorts of genes being repressed or activated that were not meant to, resulting in chaotic gene expression patterns. If you do not also evolve the necessary demethylators (or negative regulators of the numerous other modifications) then you are stuck in a permanent state of that modification and what is to regulate the methylating/modifying enzyme? It would wreak havoc in that cell and the cell would die. You could argue that other methylating/modification enzymes present in the cell due to other processes did this job but it is a poor rebuttal due to the locality of this event and the exquisite specificity of it. Furthermore, it is becoming more apparent (and accepted) that very specific histones and their very specific modifications are required for differentiation into various cellular types in developing embryonic stem cells. Thus these modifications are crucial for cell fate, thus essential for complex multicellular organism’s survival to the point where they can reproduce. There are over 50 different histones described I believe, all with different roles most of which we do not understand. It is an incredible system, and just one small example of the stupendous complexity of the molecular machinery found within the cell. It would be naïve to say we have a good understanding of these modifications (even if they are cause or consequence) as we know so little. But their complexity and in many cases, requirement within a cell pose a problem (in my mind) for the arrival of functioning complex multicellular organisms with distinct, highly controlled development via gene regulation (including tightly controlled cell fate). JD Dr JDD
I was being facetious Sal. :) Upright BiPed
Well … okay. Apparently I must asked the wrong kind of question.
The best way to find out is to ask the students which ones they found the most beneficial to them. So far the weakest question, one that didn't make the list, had the most effect that I know of personally, the one referring to heart evolution. What question really did it for me years ago? The Humpty Dumpty question Dr. Wells posed to famed OOL researcher Robert Hazen in front of the GMU faculty and students. scordova
Ok, it is late and late in the discussion, so here is my knotty little question: "Professor, is your brain, especially in terms of its function, no more than a physical embodiment of a Universal Turing Machine? If not, how can a purely mechanistic description of life such as evolution hold sway? If so, well, why should I listen to you? A Hah haha ha!!!" Tim
What mechanisms determine the fate (functional type and final location) of every cell during different phases of human development from zygote to birth, but specially the first few weeks? How did such mechanism arise gradually? We know that ongoing research will shed more light on this, but we expect the resulting information from research will reveal wonderfully elaborate choreographies and orchestrations. How did those choreographies and orchestrations gradually arise? How did the intermediate and transitional choreographies and orchestrations look like? Dionisio
Well ... okay. Apparently I must asked the wrong kind of question. Upright BiPed
Sal, maybe you can tell us the gist of Cornelius' rebuttal of my essay. The only thing I can see is that he is of the opinion that complex proteins simply cannot arise by the mechanisms that we know gave rise to TURF13, therefore my claims must be wrong. He doesn't cite any data or research to support his incredulity, he just says "I cannot believe it, thus it cannot be" ( in so many words). Arthur Hunt
The questions that seem to pertain to the origins of life are hard to take seriously, as they ignore one undeniable fact - namely that the origin of life is all about the origin of ribosomal RNA. (Think about it - all life on earth is but one "created kind ", to use a vernacular that may be familiar to participants here. Everything is the rRNA "kind", everything else is window dressing.) Before one starts asking questions about this matter, I recommend looking up and reading research by Ada Yonath and Loren Williams. We know a whole lot more than can be related in an UD comment and it's all very, very cool. Arthur Hunt
Mk, Thanks for the Trochlea challenge. I should add that one! Sal scordova
On a side note, this is not necessarily proof against evolution but if you want to be fascinated by the complexity of DNA even more go to Wikipedia (fairly accurate on this subject) and look up “Histone”. Read specifically about the modifications of histone and the “histone code” and how incredibly complex it is (mono-, di- and tri-methylation of lysine exquisitely distinguished by regulatory proteins). It is truly astounding. It is also odd that archaea have histones but bacteria do not, but all eukaryotes do (and strongly conserved).
JD, what would be a good question to ask then about histone evolution? Thanks for responding. scordova
RNA-world hypothesis is that RNA can potentially fill all the roles in the ‘protein’ production process, since it can act as a template, a catalyst, and a product? That alone renders most of your questions moot.
Yes, exactly, you appeal to the discredited RNA world hypothesis. And you think your glib answers using discredited hypotheses somehow render the questions I posed moot?
Who said anything about there being no mRNA strand? I certainly didn’t.
I didn't either, but was pointing out to the reader the tRNA needed something like an mRNA strand to work with, and you yourself just pointed out this leads to more trouble:
From transcription of DNA
Yes, a little detail you missed in your original response, DNA had to be there too! Amazing what happens when your response is put under a little more scrutiny, it shows you were making generous assumptions like sufficiently specified DNA to provide sequencing information, not to mention DNA existing in the first place! How did those DNA strands with proper stop codons emerge, by random? And that is just the beginning of problems. If such a random strand specifies 1 viable protein in 10,000, the "organism" will be full of junk, not a tightly run ship, probably something that couldn't be alive. It's hard enough for life to run with most of the parts working much less having 99% of the parts junk. scordova
You were also assuming that the first organism included both proteins and differentiated cells, neither of which assumptions is justified.
I didn't assume differentiated cells, but a cell that could manage its own construction and replication. But you should be one to talk, because you responded to the question with a unjustified assertion yourself
3. They didn’t.
And then went you around acting like you actually provided credible answers by saying, "where are the HARD QUESTIONS", as if your glib and technically shallow responses somehow demonstrated the weakness of the question posed. A response I'd expect from a scientist would be, "we don't know", not "they didn't, why is this a hard question." In any case, I could modify the question to add, "if the first cell was made mostly of proteins", and that should fix it. Those editorial changes will be made, but the form of the original questions do not diminish the fact your responses were glib, shallow, and full of holes and bald assertions posing as fact, not exactly the circumspect answers we'd expect of a scientist. That's fine, your responses reassured me with a few tweaks most of the questions will be good ones to pass on. Thanks for your participation. scordova
Here's a question I actually asked my biochemistry professor in college. There was a question on the test that presented two sequences and asked how the second sequence came from the first or something like that. One of the answer options was that there was no relation between the two sequences. The "correct" option was a fusion event. One of my classmates, a grad student and not in the least sympathetic to ID, answered "no relation" and argued the point with the professor. I chipped in and asked about mutation rates, to which the professor quoted a large number at me. I responded with genome size or something, warming to a debate (this was an online forum for the class). Then the professor said that he thought the evolutionary process was basically over and that's why there wasn't a lot of observed evidence for his preferred answer. (!) I just stopped talking at that point and let that be the final word. :D tragic mishap
Ah the good old RNA hypothesis rendering DNA/protein points moot! Reminds me of my favourite publication on the subject, which is quite aptly entitled: The RNA world hypothesis: the worst theory of the early evolution of life (except for all the others)(a). It is equally as fun to read. Seriously, do read it. I am actually not sure if it is genuine or an actual joke. It even suggests that food science (compares the pre-biotic soup of being either like vinegarette or mayonnaise) could aid in determining the origin of life. If I submitted a paper anywhere like that about anything else speculative apart from OOL theories that supported naturalistic means, even with such a low impact factor I would be laughed at. This is why people find it hard to take any of this seriously - naturalistic evolutionists like to make out to IDists and creationists that the early world theories like the RNA world are well established, based on good science and generally have scientific concensus but all of this could not be further from the truth. The only reason many of these theories are entertained or given more credit than they are due (as they are based on virtually no evidence) is there is no naturalistic alternative and the worst possible concept is to give an IDer/creationist any reason to say their interpretation/theory on OOL has some validity. When everything relies on pure speculation it fails to become real science. On a side note, this is not necessarily proof against evolution but if you want to be fascinated by the complexity of DNA even more go to Wikipedia (fairly accurate on this subject) and look up "Histone". Read specifically about the modifications of histone and the "histone code" and how incredibly complex it is (mono-, di- and tri-methylation of lysine exquisitely distinguished by regulatory proteins). It is truly astounding. It is also odd that archaea have histones but bacteria do not, but all eukaryotes do (and strongly conserved). Science amazes me even after all the years I have studied it I never fail to be amazed by the incredible complexity of cellular processes and regulation, and to me it just points to incredible design (by a Designer). JD Dr JDD
A. we don’t know evolution can even evolve a singly constrained system like DNA coding for functional proteins, much less poly constrained — so that is just argument from assertion
But that wasn't what you asked. You asked this:
2. How can natural selection or neutral evolution evolve poly constrained DNA or any poly constrained systems in general?
You didn't ask about the DNA system, you asked about the DNA - and now you've moved the goalposts. We know polyconstrained DNA can evolve because we can see polyconstrained DNA evolving.
B. neutral evolution will scramble polyconstrained DNA and natural selection can’t find it because local fitness peaks will prevent it from finding polyconstrained solutions, the Cornell papers explored the problems.
Would you be referring to the paper by one Jorge Fernandez which 'demonstrated' the unlikelihood of new polyconstrained sequences evolving by including an arbitrary thousand-fold bias in favour of the original? Roy Roy
Roy for transcription you still need DNA polymerase. Can RNA function as that too? Joe
I asked:
3. How did the first organism regulate protein expression and cellular development without regulatory elements or developmental mechanisms?
and Roy responded
they didn’t
So they’d be more dead than a dead dog. Like taking a bunch of parts without any means of assembly, not to mention the parts are not in the right proportions, possibly missing parts as well at a critical time. Essentially a junkyard….
Where are the HARD questions?
I was assuming they were hard because the answer required that the result was a living organism, apparently that implicit requirement was lost upon you.
You were also assuming that the first organism included both proteins and differentiated cells, neither of which assumptions is justified. Apparently your implicit requirement was lost on you, or you might have understood that I was pointing out that the first organism didn't regulate protein expression because if it had no proteins it wouldn't need to. Your question is topologically equivalent to asking how elephants travel to the moon without spaceships, and is equally trivial to answer. Roy Roy
Your response was awfully dismissive, and for the reader’s benefit, I’ll point out why the above dismissive response creates more problems than it solves. What codons does that supposed tRNA bind to if there is no mRNA strand to provide codons?
Who said anything about there being no mRNA strand? I certainly didn't.
A codon that is part of an mRNA sequence that came from where?
From transcription of DNA (or RNA if proteins preceded DNA rather than vice versa) by a ribozyme rather than an enzyme. Were you not aware that RNA molecules can catalyse biochemical reaction? Or that the main reasoning behind the RNA-world hypothesis is that RNA can potentially fill all the roles in the 'protein' production process, since it can act as a template, a catalyst, and a product? That alone renders most of your questions moot.
Speculations abound, but has anybody poured a random mix of amino acids, tRNAs and expect to get a sufficient protein generating machine in place?
No, nor will they since the appropriate timescales and volumes are unachievable.
The closest thing we have are things like a recently dead dog, and you yourself said dead dogs stay dead dogs.
I said no such thing. Roy Roy
Ah, sweet memories. I have a great story about censorship by my communications 501 professor related to this, but for another time. Two actual questions I asked which crushed my professors' spirits: 1.) Given that we can slow light in filter and that deceleration is simply negative acceleration, that the initial expansion of the universe required different speed for light, and that highly massive bodies bend and disperse light, do you HONESTLY believe that photons are objectively massless and that light speed is universally constant? (Asked of Astrophysics III prof - the obvious answer is no, which confounds all estimated distances, ages and chemical makeup of most of cosmology and distant astronomy) 2.) Doesn't it bother you at all that historical "science" cannot be deduced from any evidence without a precommitted conclusion? (Asked of Anthropology 501 prof, after his lecture on common descent, after I handed him a Smithsonian magazine article showcasing fossils which were just shy of preCambrian rabbits) The follow up to this question could be, "why doesn't the talkOrigins website even mention the work of Jerry Macdonald?" jw777
hi scordova. here is 3 questions: 1)how the trochlea in the eye evolve step wise? http://kgov.com/PZ-Myers-trochlea-challenge 2)how an organic- self replicat motor(flagellum)its not evidence for design?the evolution answer is becuse it is have a self replicat system. but from logical prespective- its not logic at all. a self replicat watch for example is more complex and unique then regular watch. so a self replicat watch is even more design then non one. 3)how the Bombarder Beetle evolve its unique system step wise? http://www.explorationfilmsblog.com/post/35721293028/one-of-the-strongest-creatures-on-earth mk
More questions: 1- Is there a way to model unguided/ blind watchmaker evolution? If yes please do so 2- Does unguided/ blind watchmaker evoluion have any predictions borne from its proposed mecahnsims? If yes what are they 3- Does unguided/ blind watchmaker evolution have any testable hypotheses? If yes what are they Every professor asked these questions will fold and be forced to admit evolutionism is just dogma and not science. Joe
Questions to ask should include measurements as in how many mutations does it take to get an upright biped from a quadruped? Or how many mutations would it take to produce a flagella? No measurements, no math, no science Joe
Sal said there were some good answers to Wells' questions and links to someone who posted evidence-free responses. Where are the good responses to Wells' questions? Wells' question on the OoL is relevant because how life started directly impacts how it evolved. OoL= design then it is evolution by design. It is only if blind processes produced life would we infer evolution = the blind watchmaker. Sal's link didn't understand that- well most, if not all, evos are too stupid to grasp that. Joe
Roy:
1. Slowly. The ribosomes merely augment the protein formation process, they aren’t strictly necessary for it. Proteins could be formed by tRNA molecules binding to codons as they are now, it’d just be less reliable.
Too slow for any organism- if functional proteins could actually form that way. Joe
Where did all the water on earth come from? I posted a more in depth version of this question here: https://uncommondescent.com/intelligent-design/enceladus-et-life-researchers-talk-to-ool-researchers/ Never mind. It's short so I'll copy it. Tjguy Apr 08 - 3:40 am How would the Standard Model explain where this water deep underground came from? The problem is exacerbated when it comes to earth! If the Big Bang is the proper explanation for the origin of our solar system, where did all the water come from? http://www.icr.org/article/8036/ http://crev.info/2014/04/water-theories-dry-up/ These two articles speak of recent evidence for a deep deep ocean larger than the surface ocean! How in the world can cosmology explain this?! Can this water on Enceladus and in the depths of the earth(&/or the oceans too) be explained without resorting to a ‘God of the gaps’ argument? tjguy
3. How did the first organism regulate protein expression and cellular development without regulatory elements or developmental mechanisms?
Seriously? Wells thinks the first organisms were multicellular? It’s hard to take this list seriously.
That list was mine, not Wells. Thanks any way for responding as you're helping me review and edit my questions. Bacteria need gene regulation. The phrase "development" does usually pertain to multicellular organisms, however, there are unicellular organisms that are studied as examples of development: http://www.devbio.biology.gatech.edu/?page_id=30 That said, what is the proper word for the control and construction of a cell's architecture if not the word "development"? How about specification or construction? scordova
edit #9 for clarity: Protein synthesis is the process of translating recorded information into specific physical effects during the production of proteins within the cell. Upright BiPed
Art wrote:
Cite an experiment or field observation where a substantially new protein was evolved in real time or is expected to evolve in real time over the next few generations. Been there, done that.
Dr. Hunter's response to Art's claim De Novo Genes Art, if you want to post at the CreationEvolutionUniversity forum, there is no moderation queue there. You can speak freely there for the most part just as you did at ISCID. Just let me know if you want an account. scordova
Apologies to Art Hunt. I didn't look at the comment queue early enough. For the reader's benefit, Art is a science professor, so you can see for yourself the answers! Thanks for weighing in Art. scordova
I asked:
2. How can natural selection or neutral evolution evolve poly constrained DNA or any poly constrained systems in general?
Roy's response:
2. The same way they do when singly constrained. Since almost all evolution involves trades and balances, just about everything is polyconstrained anyway.
A. we don't know evolution can even evolve a singly constrained system like DNA coding for functional proteins, much less poly constrained -- so that is just argument from assertion B. neutral evolution will scramble polyconstrained DNA and natural selection can't find it because local fitness peaks will prevent it from finding polyconstrained solutions, the Cornell papers explored the problems. scordova
Where are the HARD questions?
Protein synthesis is the process of translating recorded information into specific physical effects. How can you translate a medium of information (like DNA/RNA) into a physical effect without an irreducibly complex system of representations and protocols? Both are required in order to bridge the necessary physical discontinuity between the arrangement of the representations and their physical effects, while simultaneously preserving the necessary discontinuity. It's the primeval irreducibly complex system on earth, and is not the product of Darwinian evolution. It cannot be altered from these necessary material conditions without the loss of function. The loss of function in this instance is the real-world capacity to organize the cell. Definitions: representation: an arrangement of matter that evokes an effect within a system, where the arrangement is physicochemically arbitrary to the effect it evokes. protocol: an arrangement of matter that physically establishes the otherwise non-existent relationship between the arrangement of a representation and its effect. Your turn. Upright BiPed
Cite an experiment or field observation where a substantially new protein was evolved in real time or is expected to evolve in real time over the next few generations. Been there, done that. Arthur Hunt
3. How did the first organism regulate protein expression and cellular development without regulatory elements or developmental mechanisms? Seriously? Wells thinks the first organisms were multicellular? It's hard to take this list seriously. Arthur Hunt
I asked:
3. How did the first organism regulate protein expression and cellular development without regulatory elements or developmental mechanisms?
and Roy responded
they didn't
So they'd be more dead than a dead dog. Like taking a bunch of parts without any means of assembly, not to mention the parts are not in the right proportions, possibly missing parts as well at a critical time. Essentially a junkyard....
Where are the HARD questions?
I was assuming they were hard because the answer required that the result was a living organism, apparently that implicit requirement was lost upon you. :-) scordova
1. Slowly. The ribosomes merely augment the protein formation process, they aren’t strictly necessary for it. Proteins could be formed by tRNA molecules binding to codons as they are now,
Your response was awfully dismissive, and for the reader's benefit, I'll point out why the above dismissive response creates more problems than it solves. What codons does that supposed tRNA bind to if there is no mRNA strand to provide codons? A codon that is part of an mRNA sequence that came from where? The mRNA sequence usually comes from the work of an RNA polymerase (a protein) reading a DNA strand (a DNA strand by the way has to come from somewhere), and a DNA polymerase needs to be formed by what mechanism before ribosomes evolve? And DNA needs proteins like DNA polymerase to make them, and those proteins (like DNA polymerase) came from where without ribosomes and DNA? Where does the tRNA come from in a non-RNA world? How will a aminoacyl-tRNA be formed without a aminoacyl-tRNA synthetases (which are themselves proteins)? How will aminoacyl-tRNA floating around break the bonds between the amino acid and tRNA and then polymerize the amino acid into an folded functional protein without a ribosome? Where will the sequencing for aminoacyl-tRNAs synthetases come from without DNA that provides a template for the mRNA, and even if the DNA is present, then they can't come about without a ribosome? If you assume a random mRNA, this will make a random amino acid polymer, and a random amino-acid polymer does not a protein make. Speculations abound, but has anybody poured a random mix of amino acids, tRNAs and expect to get a sufficient protein generating machine in place? The closest thing we have are things like a recently dead dog, and you yourself said dead dogs stay dead dogs. scordova
Interesting to read the two long replies above.From two very different perspectives...! Am not a scientist, but I've long wondered how, when I hear about the Genome project,anyone can tell me with a straight face...that the super detailed DNA just sorta "happened". vikingmom
Roy asks about the hard questions, while not exactly answering the OP with anything really substantial. Here are a few more, with added commentary. FACTS AND QUESTIONS ? Fact: All scientific research indicates that life cannot spring from nonliving matter. Question: What is the scientific basis for saying that the first cell sprang from nonliving chemicals? ? Fact: Researchers have recreated in the laboratory the environmental conditions that they believe existed early in the earth’s history. In these experiments, a few scientists have manufactured some of the molecules found in living things. Question: If the chemicals in the experiment represent the earth’s early environment and the molecules produced represent the building blocks of life, whom or what does the scientist who performed the experiment represent? Does he or she represent blind chance or an intelligent entity? ? Fact: Protein and RNA molecules must work together for a cell to survive. Scientists admit that it is highly unlikely that RNA formed by chance. The odds against even one protein forming by chance are astronomical. It is exceedingly improbable that RNA and proteins should form by chance in the same place at the same time and be able to work together. Question: What takes greater faith—to believe that the millions of intricately coordinated parts of a cell arose by chance or to believe that the cell is the product of an intelligent mind? RNA is required to make proteins, yet proteins are involved in the production of RNA. How could either one arise by chance, let alone both? Roy also mentions that evolution involves some trade-offs (such as something being advantageous but not essential). Human manufacturers often have to sacrifice quality to produce an item at a fast pace. How is it possible, then, that cells can reproduce so fast and so accurately if they are the product of undirected accidents? Here are a few more: ? Fact: DNA is packaged within the chromosomes in a manner so efficient that it has been called a “feat of engineering.” Question: How could such order and organization arise by undirected chance events? ? Fact: DNA’s capacity to store information still has no equal in today’s computer age. Question: If human computer technicians cannot achieve such results, how could mindless matter do so on its own? ? Fact: DNA contains all the instructions needed to build a unique human body and maintain it throughout life. Question: How could such writing come about without a writer, such programming without a programmer? ? Fact: For DNA to work, it has to be copied, read, and proofread by a swarm of complex molecular machines called enzymes, which must work together with precision and split-second timing. Question: Do you believe that highly complex, highly reliable machinery can come about by chance? Without solid proof, would not such a belief amount to blind faith? Barb
1. Slowly. The ribosomes merely augment the protein formation process, they aren't strictly necessary for it. Proteins could be formed by tRNA molecules binding to codons as they are now, it'd just be less reliable. Don't forget that (i) many descriptions of the protein formation add the ribosome as an afterthought, since the process can be effectively described without mentioning it, and (ii) the current set-up has been evolving for a very long time with ribosomes present so could easily have become dependent on it, much like some-one who always walks with a stick may lose muscle power in their leg. 2. The same way they do when singly constrained. Since almost all evolution involves trades and balances, just about everything is polyconstrained anyway. 3. They didn't. 4. They didn't, it wasn't essential when it first evolved, when it first evolved it was advantageous but not essential. 5. One possibility is that RNA originally acted as a template for DNA rather than the other way around. I doubt we'll ever know exactly what did happen as opposed to what could happen. 6. Amino-acid homochirality would be dependent on exactly how protein formation first evolved. And who says the expectation is 50/50? Measurements of amino-acids in meteorites and on clay substrates show that it isn't. 7. Dead dogs don't become live dogs. This is an argument against Christianity; it has absolutely nothing to do with evolution. 8. See #1 9. (i) Less. (ii) That's gibberish. (iii) Very few. 10. ApoA 1 Milano. But who says new proteins have to be substantially new rather than variants on existing ones? Evolutionary biology certainly doesn't. Nevertheless, it's not hard to see how a totally new protein might evolve, given the ability of point mutations to create new starting loci for transcription, and the number of resulting orfan genes found. 11. Lactose tolerance, Apoa 1 milano, and maybe alcohol resistance too. The alternates to thalassaemia and sickle-cell traits might become fixed eventually if malaria is wiped out, though it'd be a slow process since they're both dominant genes. Timescale - billions of years if the population size is maintained, and possibly never if we manage interstellar colonies. Are these questions supposed to be hard? 12. It can't, it doesn't, and nobody ever said it did. Selection is always muddied by differing alleles elsewhere, to the extent that mildly deleterious traits can piggy-back by being associated with strongly beneficial ones. Random chance gets in the way too. 11. Generally, yes. No. No - C14 may result from nearby natural radioactivity, such as Uranium decay. Yet another loaded question. Also, proofread. 12. Yes, what about them, yes. This does not mean all the strata formed in a single year. These are not hard questions at all, and I wouldn't expect anyone with a background in evolutionary biology to even have to think hard about answering them, let alone get concerned that they couldn't. They're more likely to diminish one's opinion of the asker than of evolutionary biology. 13. I'll consider it if it happens. Until then, it's no more a problem for science than asking "What if Moses returns and she's female and tells the world that the Bible was written by a drunken con-artist with diarrhoea?" is a problem for religion. 14. I don't know (but I suspect Google does) but it doesn't matter since the measurement methods overlap in range and so each corroborates the next. The same as for supernovae of stars within galaxies. No, because probabilities don't sum that way. Where are the HARD questions? Roy Roy
Good questions. Thanks. Dionisio

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