Re: [DIYbio] Methodology help needed - how to measure nail light absorbance

Actually, what I was describing was engineering, not science.

Multispectral analysis is how satellites determine what crops are growing where, and where

droughts are occurring, where marijuana farms are, etc. Applying it to "crops" of fungi growing

under a fingernail is simply engineering.

The current technology for detecting nail fungus uses the human eyeball.

Unfortunately, this requires training, and has a false positive rate that means invasive further

testing is done, with the accompanying pain and expense.

A simple, cheap device that can detect certain fungi in seconds would be useful. Similar devices

are already in use to detect fungal growths on strawberries and blueberries in automated

processing plants. The technique is also used to monitor oxygen levels in the blood non-invasively.

There is no way you are going to take a sample from the fingernail, amplify it using PCR, and

then detect fungal genes in a couple seconds with a cheap handheld device. And it is unlikely that

one of us will build that device in our basement. But it is fairly easy to get the results using

multispectral analysis and a $1 microprocessor. Any technique that uses the human eye as the

detector is open to automation using multispectral analysis and machine vision.

Detecting genes in a sample requires knowing which genes to look for, and there are many

commensal fungi that share 99% of their genome with pathogenic fungi, so you would have to

be fairly selective. But the visual methods rule out the commensal varieties simply because

the pathogenic ones will be responsible for almost all of the signal.

As for "All science is goal oriented", I think that is nonsense. Darwin did not board the Beagle

with the goal of coming up with the idea of evolution by natural selection. There are any number

of similar exceptions, from the discovery of penicillin to the discovery of dark energy.

-----

Get a free science project every week! "http://scitoys.com/newsletter.html"

On Thu, Nov 22, 2012 at 1:48 PM, Josiah Zayner <josiah.zayner@gmail.com> wrote:

There is not plenty of precedent. I would say sure, 100 years ago there was precedent but not now. Sure, sometimes "brute force" methods are required because not enough is known but I don't know any professional scientist working today who does experiments just "because". Sure, people want to find answers to questions but why try and find the answer to a question through research when it can be found through a few hours of reading papers? I would understand if there was no papers on spectrometry of cells but spectrometry has been around sooo long a person should be able to find something. You have to know if it is feasible first or you have no idea what to look for. How do you know if your result is just not an artifact? I challenge you to find a Nobel prize in the past 30 years that was acquired out of serendipity and not a clear goal. 

How do I reprogram cells to become pluripotent? Well first I need to understand what makes cells pluripotent, Oct4, Sox2, Nanog,C-Myc, Klf4, Lin28. You think this question would have been discovered or won a Nobel prize if someone just decided to try and add stuff to cells to see if it worked? 

All science is goal oriented. Understanding the function of obscure protein X is goal oriented. There are in fact standard methods for this. The goal was to uncover some new knowledge about protein X. It is an expressed protein so it "must" have a function.

Just because the topic of the thread is spectrophotometry I will again use it as an example. I can try different configurations of LEDs and different data analysis techniques taking derivatives and trying value decomposition but in the end there are an infinite number of possible configuration and analysis methods. One would then also have to test the device on a huge population of nails to prove that it actually works. How correct would a device like this have to be to be usable? 90%? 50%? 

Let us be logical, being logical is the goal of any good Scientist or Vulcan. There is plenty of literature and data on the composition of fungal cells, what do they contain different than other cells if anything? Does this thing absorb? Saying, "I have no clue but I am going to try this anyway." is being ignorant. Research and understanding is what builds science, not ignorance.

On Thu, Nov 22, 2012 at 3:14 PM, Cathal Garvey <cathalgarvey@gmail.com> wrote:

> Why do you plan on doing this?

> That's what granting agencies ask, that is what everyone asks.

These are the kinds of concerns that one has to consider when operating
in a grant-funded environment. For someone just doing it to satisfy
their curiosity, there should be no need to explain *why*, only *how*.

> What I know is that doing experiments just "because" is not a good way to
> advance science that is not how science is advanced. Science is
advanced by
> choosing a problem that needs answering and can be answered.

I disagree. There is plenty of precedent in groundbreaking science where
someone was just scratching an itch and discovered something amazing.
Leaving even that aside, most of the science that allows real
advancement isn't goal-oriented, it's just dedicated to uncovering more
knowledge. I know I've benefited immensely from many, many papers
published from unassuming labs studying niche-y stuff like the precise
workings of irrelevant protein X in obscure species Y.

Further, there may be existing, reliable methods to do what he's
thinking of doing better. That shouldn't preclude investigating a new
method of doing it; who knows? Perhaps he'll discover that he can
reliably and non-invasively identify infections by spectrographic data,
which could easily be packaged into a rapid field test for areas where
PCR etc. are inconvenient. How many genuses of nail-infective fungi are
there in common circulation? Do they differ in absorption enough to ID
them from one another, and from a healthy nail?

I think it's worth trying out any new idea, no matter how outlandish or
redundant. At the very least, it'll scratch the itch and let you move
onto another question. At best, it generates a new way of doing, or knowing.

On 22/11/12 20:46, Josiah Zayner wrote:
> I was not telling anyone that their idea wouldn't work.
> What I know is that doing experiments just "because" is not a good way to
> advance science that is not how science is advanced. Science is advanced by
> choosing a problem that needs answering and can be answered. I can try and
> detect the existence of God using LEDs because no one can tell me it won't
> work. Or I can think about what I am actually trying to do and come up with
> a reasonable hypothesis so I don't waste my time. 90% of good science is
> thinking and developing a good question and a good way to answer it.
>
> I am a Ph.D. student and if I whenever I goto my boss with any idea he asks
> me two questions as every good scientist should:
> How specifically do you plan on doing this?
> Why do you plan on doing this?
>
> If someone wants to build a spectrophotometric nail fungus detector to
> learn something, I am all about it. If one is trying to build
> a spectrophotometric nail fungus detector to help detect nail fungus when
> there are already plenty of good ways to do that already I am slightly
> skeptical of the scientific benefit, which is why I posed some questions. I
> never said it was not possible. I was just asking what specifically people
> planned on looking for. This is what any good scientist would ask.
>
> That's what granting agencies ask, that is what everyone asks. Sure perhaps
> someone could stumble across something innovative but that is not a
> scientists goal. That is gambling and if you are going to gamble why do it
> with something like DIYBio when you could do it with room temperature
> superconductors and perhaps change the world.
>
> Very few clincal PCR assays? I think you meant very many.
>
> https://www.google.com/search?q=clinical+pcr+assays
>
> It is used to isolate and detect basically every type of infection. Can be
> used for detecting cancers and genetic diseases. In fact new born babies
> are screened for at least 21 disorders by LAW in the US within 48 hours of
> birth.
>
> On Thu, Nov 22, 2012 at 2:09 PM, Jeswin <phillyj101@gmail.com> wrote:
>
>> On Thu, Nov 22, 2012 at 2:49 PM, Josiah Zayner <josiah.zayner@gmail.com>
>> wrote:
>>> one would want to know can be discovered. There is idosyncratically no
>> way
>>> to do this with light scatter.
>>>
>> You know, if you tell any grad student, inventor, etc that his idea
>> won't work without letting them figure out if it will or not, no one
>> will advance science. Maybe it won't work. Maybe he will find a way to
>> make it work. Let him figure it out.
>>
>> And I agree with his point. There are very few clinical PCR assays.
>>
>> --
>> -- You received this message because you are subscribed to the Google
>> Groups DIYbio group. To post to this group, send email to
>> diybio@googlegroups.com. To unsubscribe from this group, send email to
>> diybio+unsubscribe@googlegroups.com. For more options, visit this group
>> at https://groups.google.com/d/forum/diybio?hl=en
>> Learn more at www.diybio.org
>> ---
>> You received this message because you are subscribed to the Google Groups
>> "DIYbio" group.
>> To post to this group, send email to diybio@googlegroups.com.
>> To unsubscribe from this group, send email to
>> diybio+unsubscribe@googlegroups.com.
>> Visit this group at http://groups.google.com/group/diybio?hl=en.
>> For more options, visit https://groups.google.com/groups/opt_out.
>>
>>
>>
>

--
www.indiebiotech.com
twitter.com/onetruecathal
joindiaspora.com/u/cathalgarvey
PGP Public Key: http://bit.ly/CathalGKey

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diybio@googlegroups.com.
To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diybio@googlegroups.com.
To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.
 
 

--
-- You received this message because you are subscribed to the Google Groups DIYbio group. To post to this group, send email to diybio@googlegroups.com. To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com. For more options, visit this group at https://groups.google.com/d/forum/diybio?hl=en
Learn more at www.diybio.org
---
You received this message because you are subscribed to the Google Groups "DIYbio" group.
To post to this group, send email to diybio@googlegroups.com.
To unsubscribe from this group, send email to diybio+unsubscribe@googlegroups.com.
Visit this group at http://groups.google.com/group/diybio?hl=en.
For more options, visit https://groups.google.com/groups/opt_out.